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Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Origin of life » Translation through ribosomes, amazing nano machines

Translation through ribosomes, amazing nano machines

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Ribosomes amazing nano machines

https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines

1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder, does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.


The ribosome is a crucial player in the context of basic cellular processes since it serves to interpret the genetic code brought by the messenger RNA and build up the chain of amino acids delivered by transfer RNA, which in turn folds into fully functional proteins, an extremely complex process called translation. 9

The Ribosome is one of the greatest wonders of molecular nanotechnology ever devised by our amazing unfathomable creator.

David S. Goodsell Atomic Evidence Seeing the Molecular Basis of Life page 7
Researchers have been working for decades on this elusive subject, assembling information from many sources to build the detailed understanding we have today.Crystallography has revealed the inner secrets of the ribosome in glorious detail. For many years, researchers studied the individual proteins by crystallography, slowly building up a picture of the whole molecule. Th en, in 2000, three labs presented atomic structures of the intact ribosomal subunits. One major insight from these structures was the discovery that the ribosome is a ribozyme, with one particular nucleotide in the RNA catalyzing the proteinbuilding reaction. The structures also revealed how the small subunit positions the messenger RNA, the details of the tunnel where the newly synthesized protein exits from the construction site, and a host of other interesting details.

Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name!

My comment: Fortunately, people that recognize the magnificence of the creator of the Ribosome, build him churches and temples all over the globe, and give HIM glory.

The smallest known cytoplasmic ribosome is found in prokaryotic cells; these ribosomes are about 2.5 MDa and contain more than 4000 nucleotides of RNA and greater than 50 proteins. 10

Translation is one of the most complex biological processes, involving diverse protein factors and enzymes as well as messenger and transfer RNAs. The sequence of the PTC is possibly the most relevant stretch of nucleic acid to be studied if one aims to understand the origin of life. Nowadays, it is a consensus that the ribosome should be understood as a prebiotic machine that predated the origin of cells. The contingent appearance of this ribozyme capable of binding amino acids together was crucial to both the initial emergence and further development of the phenomenon of life7

The ribosome is a ‘‘living fossil‘‘, a particle so central to all cellular processes that it has essentially become frozen in time, preserving many ancestral features in its molecular structure. 8

The origin of the ribosomal protein synthesis network is considered to be the singular defining event in the origin of cells and the Tree of Life 4

The ribosome is a multi-part machine responsible for translating the genetic instructions during the assembly of proteins. According to Craig Venter, a widely respected biologist, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. Bacterial cells may contain up to 100,000 ribosomes, and human cells may contain millions. Biologist Ada Yonath, who won the Nobel Prize for her work on ribosomes, observes that they are “ingeniously designed for their functions.”

The translation of the nucleotide sequence of an mRNA molecule into protein takes place in the cytosol on a large ribonucleoprotein assembly called a ribosome. Each amino acid used for protein synthesis is first attached to a tRNA molecule that recognizes, by complementary base-pair interactions, a particular set of three nucleotides (codons) in the mRNA. As an mRNA is threaded through a ribosome, its sequence of nucleotides is then read from one end to the other in sets of three according to the genetic code. To initiate translation, a small ribosomal subunit binds to the mRNA molecule at a start codon (AUG) that is recognized by a unique initiator tRNA molecule. A
large ribosomal subunit then binds to complete the ribosome and begin protein synthesis. During this phase, aminoacyl-tRNAs—each bearing a specific amino acid—bind sequentially to the appropriate codons in mRNA through complementary base-pairing between tRNA anticodons and mRNA codons. Each amino acid is added to the C-terminal end of the growing polypeptide in four sequential steps: aminoacyl-tRNA binding, followed by peptide bond formation, followed by two ribosome translocation steps. Elongation factors use GTP hydrolysis both to drive these reactions forward and to improve the accuracy of amino acid selection. The mRNA molecule progresses codon by codon through the ribosome in the 5ʹ-to-3ʹ direction until it reaches one of three stop codons. A release factor then binds to the ribosome, terminating translation and releasing the completed polypeptide. Eukaryotic and bacterial ribosomes are closely related, despite differences in the number and size of their rRNA and protein components. The rRNA has the dominant role in translation, determining the overall structure of the ribosome, forming the binding sites for the tRNAs, matching the tRNAs to codons in the mRNA, and creating the active site of the peptidyl transferase enzyme that links amino acids together during translation.


* Each cell contains around 10 million ribosomes, i.e. 7000 ribosomes are produced in the nucleolus each minute.
* Each ribosome contains around 80 proteins, i.e. more than 0.5 million ribosomal proteins are synthesized in the cytoplasm per minute.
* The nuclear membrane contains approximately 5000 pores. Thus, more than 100 ribosomal proteins are imported from the cytoplasm to the nucleus per pore and minute. At the same time 3 ribosomal subunits are exported from the nucleus to the cytoplasm per pore and minute.

The evidence from the ribosome
a. “Spontaneous formation of the unlocked state of the ribosome is a multi-step process.”
b. The L1 stalks of the ribosome bend, rotate and uncouple – undergoing at least four distinct stalk positions while each tRNA ratchets through the assembly tunnel.  At one stage, for instance, “the L1 stalk domain closes and the 30S subunit undergoes a counterclockwise, ratchet-like rotation” with respect to another domain of the factory.  This is not simple.  “Subunit ratcheting is a complex set of motions that entails the remodeling of numerous bridging contacts found at the subunit interface that are involved in substrate positioning.”
c.The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler (insisting) the ribosome is about high-fidelity protein synthesis. (Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics: The Ribosome: Perfectionist Protein-maker Trashes Errors, 2009)
4. Interactions between molecules are not simply matters of matching electrons with protons.  Instead, large structural molecules form machines with moving parts.  These parts experience the same kinds of forces and motions that we experience at the macro level: stretching, bending, leverage, spring tension, ratcheting, rotation and translocation.  The same units of force and energy are appropriate for both – except at vastly different levels.
5. Every day,  Every day, essays about molecular machines are giving more and more biomolecular details, many without mentioning evolution and giving details about the process of how these machines evolved. Ribosomes, however, are life essential, and a prerequisite to make the proteins which replicate DNA, hence, it had to emerge prior evolution could start. So its emergence cannot be explained by evolution.  
6. These complexities are best explained by the work of an intelligent agency.
7. Hence, most probably, God exists.

Comparative genomic reconstructions of the gene repertoire of LUCA(S) point to a complex translation system that includes at least 18 of the 20 aminoacyl-tRNA synthetases (aaRS), several translation factors, at least 40 ribosomal proteins, and several enzymes involved in rRNA and tRNA modification. It appears that the core of the translation system was already fully shaped in LUCA(S) (Anantharaman, et al., 2002).

The RNA Message Is Decoded in Ribosomes
The synthesis of proteins is guided by information carried by mRNA molecules. To maintain the correct reading frame and to ensure accuracy (about 1 mistake every 10,000 amino acids), protein synthesis is performed in the ribosome, a complex catalytic machine made from more than 50 different proteins (the ribosomal proteins) and several RNA molecules, the ribosomal RNAs (rRNAs). A typical eukaryotic cell contains millions of ribosomes in its cytoplasm

Translation through ribosomes,  amazing nano machines Riboso10

The large and small ribosome subunits are assembled at the nucleolus, where newly transcribed and modified rRNAs associate with the ribosomal proteins that have been transported into the nucleus after their synthesis in the cytoplasm. These two ribosomal subunits are then exported to the cytoplasm, where they join together to synthesize proteins. Eukaryotic and bacterial ribosomes have similar structures and functions, being composed of one large and one small subunit that fit together to form a complete ribosome with a mass of several million daltons

Translation through ribosomes,  amazing nano machines A_comp10
The small subunit provides the framework on which the tRNAs are accurately matched to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain (see Figure above). When not actively synthesizing proteins, the two subunits of the ribosome are separate. They join together on an mRNA molecule, usually near its 5ʹ end, to initiate the synthesis of a protein. The mRNA is then pulled through the ribosome, three nucleotides at a time. As its codons enter the core of the ribosome, the mRNA nucleotide sequence is translated into an amino acid sequence using the tRNAs as adaptors to add each amino acid in the correct sequence to the growing end of the polypeptide chain. When a stop codon is encountered, the ribosome releases the finished protein, and its two subunits separate again. These subunits can then be used to start the synthesis of another protein on another mRNA molecule. Ribosomes operate with remarkable efficiency: in one second, a eukaryotic ribosome adds 2 amino acids to a polypeptide chain; the ribosomes of bacterial cells operate even faster, at a rate of about 20 amino acids per second. To choreograph the many coordinated movements required for efficient translation, a ribosome contains four binding sites for RNA molecules: one is for the mRNA and three (called the A site, the P site, and the E site) are for tRNAs

Translation through ribosomes,  amazing nano machines Riboso20
The RNA-binding sites in the ribosome. 
Each ribosome has one binding site for mRNA and three binding sites for tRNA: the A, P, and E sites (short for aminoacyl-tRNA, peptidyl-tRNA, and exit, respectively). 
(A) A bacterial ribosome viewed with the small subunit in the front (dark green) and the large subunit in the back (light green). Both the rRNAs and the ribosomal proteins are illustrated. tRNAs are shown bound in the E site (red), the P site (orange), and the A site (yellow). Although all three tRNA sites are shown occupied here, during the process of protein synthesis not more than two of these sites are thought to contain tRNA molecules at any one time. 
(B) Large and small ribosomal subunits arranged as though the ribosome in (A) were opened like a book. 
(C) The ribosome in (A) rotated through 90° and viewed with the large subunit on top and small subunit on the bottom. (D) Schematic representation of a ribosome [in the same orientation as (C)], which will be used
in subsequent figures.

A tRNA molecule is held tightly at the A and P sites only if its anticodon forms base pairs with a complementary codon (allowing for wobble) on the mRNA molecule that is threaded through the ribosome. 

Translation through ribosomes,  amazing nano machines Riboso21
The path of mRNA (blue) through the small ribosomal subunit

The A andP sites are close enough together for their two tRNA molecules to be forced to form base pairs with adjacent codons on the mRNA molecule. This feature of the ribosome maintains the correct reading frame on the mRNA.


Comment: that means, in order to maintain the correct reading frame on the mRNA, the configuration of the A and P sites to be close enough together IS VITAL. How could this configuration have emerged randomly? Trial and error ? This tiny fact means, there is no tolerance here. It is an all or nothing business. The configuration HAS TO BE RIGHT just from the beginning. A down up development to get the right distance will be always non-functional. Another important evidence that demonstrates that evolutionary means are not adequate to explain the feat in question.   


Once protein synthesis has been initiated, each new amino acid is added to the elongating chain in a cycle of reactions containing four major steps: 

tRNA binding (step 1), 
peptide bond formation (step 2), 
large subunit translocation (step 3), 
and small subunit translocation (step 4). 

As a result of the two translocation steps, the entire ribosome moves three nucleotides along the mRNA and is positioned to start the next cycle.

Comment: this is a process that only works in a fully developed arrangement and sequence. If ANY of the four steps is missing, no deal. The machinelike  polymerization process will not work.  

Translation through ribosomes,  amazing nano machines Elonga10
Translating an mRNA molecule. 
Each amino acid added to the growing end of a polypeptide chain is selected by complementary basepairing between the anticodon on its attached tRNA molecule and the next codon on the mRNA chain. Because only one of the many types of tRNA molecules in a cell can base-pair with each codon, the codon determines the specific amino acid to be added to the growing polypeptide chain. The four-step cycle shown is repeated over and over during the synthesis of a protein. In step 1, an aminoacyl-tRNA molecule binds to a vacant A site on the ribosome. In step 2, a new peptide bond is formed. In step 3, the large subunit translocates relative to the small subunit, leaving the two tRNAs in hybrid sites: P on the large subunit and A on the small, for one; E on the large subunit and P on the small, for the other. In step 4, the small subunit translocates carrying its mRNA a distance of three nucleotides through the ribosome. This “resets” the ribosome with a fully empty A site, ready for the next aminoacyl-tRNA molecule to bind. As indicated, the mRNA is translated in the 5ʹ-to-3ʹ direction, and the N-terminal end of a protein is made first, with each cycle adding one amino acid to the C-terminus of the polypeptide chain

Comment:  proof reading is required for getting an error rate which keeps the mutation rates sufficiently low.  Elongation factors EF-Tu and EF-G are part of the toolkit providing that error reduction. This is clear evidence of a designed process. Without the mechanisms to provide that error reduction, there would be no life. 

The image above illustrates this four-step process, beginning at a point at which three amino acids have already been linked together and there is a tRNA molecule in the P site on the ribosome, covalently joined to the C-terminal end of the short polypeptide. In step 1, a tRNA carrying the next amino acid in the chain binds to the ribosomal A site by forming base pairs with the mRNA codon positioned there, so that the P site and the A site contain adjacent bound tRNAs. In step 2, the carboxyl end of the polypeptide chain is released from the tRNA at the P site (by breakage of the high-energy bond between the tRNA and its amino acid) and joined to the free amino group of the amino acid linked to the tRNA at the A site, forming a new peptide bond. This central reaction of protein synthesis is catalyzed by a peptidyl transferase contained in the large ribosomal subunit. In step 3, the large subunit moves relative to the mRNA held by the small subunit, thereby shifting the acceptor stems of the two tRNAs to the E and P sites of the large subunit. In step 4, another series of conformational changes moves the small subunit and its bound mRNA exactly three nucleotides, ejecting the spent tRNA from the E site and resetting the ribosome so it is ready to receive the next aminoacyl-tRNA. Step 1 is then repeated with a new incoming aminoacyl-tRNA, and so on. This four-step cycle is repeated each time an amino acid is added to the polypeptide chain, as the chain grows from its amino to its carboxyl end.

Elongation Factors Drive Translation Forward and Improve Its Accuracy
The basic cycle of polypeptide elongation shown in outline in Figure above has an additional feature that makes translation especially efficient and accurate. Two elongation factors enter and leave the ribosome during each cycle, each hydrolyzing GTP to GDP and undergoing conformational changes in the process. These factors are called EF-Tu and EF-G in bacteria, and EF1 and EF2 in eukaryotes. Under some conditions in vitro, ribosomes can be forced to synthesize proteins without the aid of these elongation factors and GTP hydrolysis, but this synthesis is very slow, inefficient, and inaccurate. Coupling the GTP hydrolysis-driven changes in the elongation factors to transitions between different states of the ribosome speeds up protein synthesis enormously. The cycles of elongation factor association, GTP hydrolysis, and dissociation also ensure that all such changes occur in the “forward” direction, helping translation to proceed efficiently

Translation through ribosomes,  amazing nano machines Detail12
Detailed view of the translation cycle. 
Shown are the roles of the two elongation factors EF-Tu and EF-G, which drive translation in the forward directionEF-Tu provides opportunities for proofreading of the codon– anticodon match. In this way, incorrectly paired tRNAs are selectively rejected, and the accuracy of translation is improved. The binding of a molecule of EF-G to the ribosome and the subsequent hydrolysis of GTP lead to a rearrangement of the ribosome structure, moving the mRNA being decoded exactly three nucleotides through it

In addition to moving translation forward, EF-Tu increases its accuracy.  EF-Tu can simultaneously bind GTP and aminoacyl-tRNAs, and it is in this form that the initial codon–anticodon interaction occurs in the A site of the ribosome. Because of the free-energy change associated with base-pair formation, a correct codon–anticodon match will bind more tightly than an incorrect interaction. However, this difference in affinity is relatively modest and cannot by itself account for the high accuracy of translation. To increase the accuracy of this binding reaction, the ribosome and EF-Tu work together in the following ways. First, the 16s rRNA in the small subunit of the ribosome assesses the “correctness” of the codon–anticodon match by folding around it and probing its molecular details

Translation through ribosomes,  amazing nano machines Recogn10
Recognition of correct codon–anticodon matches by the small-subunit rRNA of the ribosome. 
Shown here is the interaction between a nucleotide of the small-subunit rRNA and the first nucleotide pair of a correctly paired codon–anticodon. Similar interactions form between other nucleotides of the rRNA and the second and third positions of codon– anticodon pair. The small-subunit rRNA can form this network of hydrogen bonds only when an anticodon is correctly matched to a codon. As explained in the text, this codon–anticodon monitoring by the small-subunit rRNA increases the accuracy of protein synthesis.


Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
https://sci-hub.st/https://science.sciencemag.org/content/292/5518/897

The ribosome recognizes the geometry of codonanticodon base pairing in a way that would discriminate against near-cognate tRNAs. The minor groove of the first and second base pairs between the codon and anticodon is closely monitored by a set of interactions that are induced by the binding of cognate tRNA. These interactions would be disrupted by mismatches, so that the induced structural changes would no longer be energetically favorable. The third or “wobble” position has less stringent constraints, and therefore can allow a broader range of base-pairing geometries, consistent with the requirements of the genetic code. The binding of paromomycin partially induces the changes that normally are induced by cognate tRNA. 

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form NOVEMBER 27, 2002
https://www.cell.com/fulltext/S0092-8674(02)01086-3
The selection by the ribosome of substrate aminoacyl-transfer RNAs (aa-tRNAs) for incorporation of amino acids into a growing peptide chain depends on base complementarity between the codon on mRNA and the anticodon on tRNA. However, near-cognate tRNAs, which differ from the correct or cognate tRNAs by a single, subtle mismatch in codon-anticodon base-pairing, cannot be accurately discriminated against on the basis of differences in the free energy of base-pairing alone.  The ribosome recognizes base-pairing geometry during decoding, thus raising the intrinsic selectivity of each step to the levels required. The structure of the 30S subunit with A site codon and cognate tRNA anticodon stem loop (ASL) subsequently revealed conformational changes in the 30S, in which A1492, A1493, and G530 interact intimately with the minor groove of the first two codon-anticodon base pairs For any given codon in the A site, the ribosome must be able to distinguish cognate tRNA from all others, in a sequence-independent manner.

Both the 30S subunit and polymerases undergo a rearrangement from an open to a closed form, which interacts intimately with the minor groove of Watson-Crick substrate base pairs. Thus, a common mechanistic principle ensures accurate complementary base-pairing during replication, transcription, and translation of the genetic information.

Before an amino acid is added to a growing polypeptide chain, the ribosome folds around the codon–anticodon interaction, and only when the match is correct is this folding completed and the reaction allowed to proceed. Thus, the codon–anticodon interaction is thereby checked twice—once by the initial complementary base-pairing and a second time by the folding of the ribosome, which depends on the correctness of the match. This same principle of induced fit is seen in transcription by RNA polymerase; here, an incoming nucleoside triphosphate initially forms a base pair with the template; at this point the enzyme folds around the base pair (thereby assessing its correctness) and, in doing so, creates the active site of the enzyme. The enzyme then covalently adds the nucleotide to the growing chain. Because their geometry is “wrong,” incorrect base pairs block this induced fit, and they are therefore likely to dissociate before being incorporated into the growing chain. A second principle used to increase the specificity of complementary base-pairing is called kinetic proofreading. We have seen that after the initial codon‒anticodon pairing and conformational change of the ribosome, GTP is hydrolyzed. This creates an irreversible step and starts the clock on a time delay during which the aminoacyl-tRNA moves into the proper position for catalysis. During this delay, those incorrect codon–anticodon pairs that have somehow slipped through the induced-fit scrutiny have a higher likelihood of dissociating than correct pairs. There are two reasons for this: (1) the interaction of the wrong tRNA with the codon is weaker, and (2) the delay is longer for incorrect than correct matches. kinetic proofreading thus increases the specificity of complementary base-pairing above what is possible from simple thermodynamic associations alone. The increase in specificity produced by kinetic proofreading comes at an energetic cost in the form of ATP or GTP hydrolysis. Kinetic proofreading is believed to operate in many biological processes, but its role is understood particularly well for translation.

Accuracy in Translation Requires an Expenditure of Free Energy
Translation by the ribosome is a compromise between the opposing constraints of accuracy and speed. We have seen, for example, that the accuracy of translation (1 mistake per 104 amino acids joined) requires time delays each time a new amino acid is added to a growing polypeptide chain, producing an overall speed of translation of 20 amino acids incorporated per second in bacteria. Mutant bacteria with a specific alteration in the small ribosomal subunit have longer delays and translate mRNA into protein with an accuracy considerably higher than this; however, protein synthesis is so slow in these mutants that the bacteria are barely able to survive.

Question: How could the right speed have been obtained with trial and error, if slow mutants do not survive? Had the speed not to be right right from the beginning?

We have also seen that attaining the observed accuracy of protein synthesis requires the expenditure of a great deal of free energy; this is expected, since, there is a price to be paid for any increase in order in the cell. In most cells, protein synthesis consumes more energy than any other biosynthetic process. At least four high-energy phosphate bonds are split to make each new peptide bond: two are consumed in charging a tRNA molecule with an amino acid, and two more drive steps in the cycle of reactions occurring on the ribosome during protein synthesis itself. In addition, extra energy is consumed each time that an incorrect amino acid linkage is hydrolyzed by a tRNA synthetase  and each time that an incorrect tRNA enters the ribosome, triggers GTP hydrolysis, and is rejected. To be effective, any proofreading mechanism must also allow an appreciable fraction of correct interactions to be removed; for this reason, proofreading is even more costly in energy than it might at first seem.

My comment: So we see the same proofreading principles applied in totally distinct protein complexes. Furthermore, proof reading requires energy.  This is, therefore, clear evidence of design. 

The Ribosome Is a Ribozyme
The ribosome is a large complex composed of two-thirds RNA and one-third protein. The determination, in 2000, of the entire three-dimensional conformation of its large and small subunits is a major triumph of modern structural biology. The findings confirm earlier evidence that rRNAs—and not proteins—are responsible for the ribosome’s overall structure, its ability to position tRNAs on the mRNA, and its catalytic activity in forming covalent peptide bonds. The ribosomal RNAs are folded into highly compact, precise three-dimensional structures that form the compact core of the ribosome and determine its overall shape

Translation through ribosomes,  amazing nano machines Ribozy10
Structure of the rRNAs in the large subunit of a bacterial ribosome, as determined by x-ray crystallography.
(A) Three-dimensional conformations of the large-subunit rRNAs (5S and 23S) as they appear in the ribosome. One of the protein subunits of the ribosome (L1) is also shown as a reference point, since it forms a characteristic protrusion on the ribosome.
(B) Schematic diagram of the secondary structure of the 23S rRNA, showing the extensive network of base-pairing. The structure has been divided into six “domains” whose colors correspond to those in (A). The secondarystructure diagram is highly schematized to represent as much of the structure as possible in two dimensions. To do this, several discontinuities in the RNA chain have been introduced, although in reality the 23S rRNA is a single RNA molecule. For example, the base of Domain III is continuous with the base of Domain IV even though a gap appears in the diagram.

In marked contrast to the central positions of the rRNAs, the ribosomal proteins are generally located on the surface and fill in the gaps and crevices of the folded RNA

Translation through ribosomes,  amazing nano machines Locati10
Location of the protein components of the bacterial large ribosomal subunit.
The rRNAs (5S and 23S) are shown in blue and the proteins of the large subunit in green. This view is toward the outside of the ribosome; the interface with the small subunit is on the opposite face.

Some of these proteins send out extended regions of polypeptide chain that penetrate short distances into holes in the RNA core

Translation through ribosomes,  amazing nano machines L15_pr10
L15 protein in the large subunit of the bacterial ribosome. 
The globular domain of the protein lies on the surface of the ribosome and an extended region penetrates deeply into the RNA core of the ribosome. The L15 protein is shown in green and a portion of the ribosomal RNA core is shown in blue.

The main role of the ribosomal proteins seems to be to stabilize the RNA core, while permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis. 

My comment: There is clear teleological meaning here. Why would random events produce these proteins with a distant gole ( to stabilize the RNA core ) , if they are only becoming functional, once the ribosome multiprotein macromolecule holocomplex is fully assembled and working in an integrated fashion? 

The proteins also aid in the initial assembly of the rRNAs that make up the core of the ribosome.

My comment: Foreknowledge is required to know that tRNA's are required in the process of translation, and helping in the biosynthesis of those. From a naturalistic/evolutionary standpoint, it would make no sense whatsoever to predict that ribosome proteins would be helping in assembling other proteins. 

Not only are the A, P, and E binding sites for tRNAs formed primarily by ribosomal RNAs, but the catalytic site for peptide bond formation is also formed by RNA, as the nearest amino acid is located more than 1.8 nm away. This discovery came as a surprise to biologists because, unlike proteins, RNA does not contain easily ionizable functional groups that can be used to catalyze sophisticated reactions like peptide bond formation. Moreover, metal ions, which are often used by RNA molecules to catalyze chemical reactions, were not observed at the active site of the ribosome. Instead, it is believed that the 23S rRNA forms a highly structured pocket that, through a network of hydrogen bonds, precisely orients the two reactants (the growing peptide chain and an aminoacyl-tRNA) and thereby greatly accelerates their covalent joining. An additional surprise came from the discovery that the tRNA in the P site contributes an important OH group to the active site and participates directly in the catalysis. This mechanism may ensure that catalysis occurs only when the P site tRNA is properly positioned in the ribosome. RNA molecules that possess catalytic activity are known as ribozymes. We saw earlier in this chapter that some ribozymes function in self-splicing reactions.


 
Translation through ribosomes,  amazing nano machines Ribosome-1

Translation through ribosomes,  amazing nano machines 70s_atrna_nolabels-1024x843

Two massive polymolecular units that combine to make the ribosome are needed for translation. The small unit is on the left and the large unit is on the right. Combined they represent 4 large RNA molecules with 70 proteins attached to the frame. The unit is a masterpiece of precision engineering… not a random association of stuff. 6

Translation through ribosomes,  amazing nano machines Ribosome
Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
https://sci-hub.st/https://science.sciencemag.org/content/292/5518/897


The ribosome recognizes the geometry of codon anticodon base pairing in a way that would discriminate against near-cognate tRNAs. The minor groove of the first and second base pairs between the codon and anticodon is closely monitored by a set of interactions that are induced by the binding of cognate tRNA. These interactions would be disrupted by mismatches, so that the induced structural changes would no longer be energetically favorable. The third or “wobble” position has less stringent constraints, and therefore can allow a broader range of base-pairing geometries, consistent with the requirements of the genetic code. 

My comment: Monitoring and taking action when something is wrong requires "knowledge" of the correct state, "knowledge" of the wrong state, and know how to correct the wrong state. Knowledge, monitoring, error recognition and repair are actions only known to be performed by intelligence. 

Translation
http://europepmc.org/article/med/19595805#R18
The ribosome “reads” mRNA in a 5’-3’ direction and synthesizes the corresponding protein from its N-terminus. Both ribosomal subunits contain three binding sites for tRNA molecules that are in distinct functional states:

(i) the A site binds the aminoacyl-tRNA, which brings a new amino acid that is to be incorporated into the growing polypeptide,
(ii) the P site binds the peptidyl-tRNA (as well as the initiator fMet-tRNAfmet), and
(iii) the E site binds the deacylated tRNA that is to be soon dissociated from the ribosome.

The 30S subunit binds mRNA and it ensures the fidelity of translation through close monitoring of the anticodon-codon interactions. The 50S subunit, on the other hand, binds the acceptor ends of substrate tRNAs and it catalyzes the peptide bond formation in which an α-amino group of the aminoacyl-tRNA attacks the carbonyl carbon of the peptidyl-tRNA. From a chemical standpoint the reaction is an aminolysis of an acyl-ester link formed between the carbonyl carbon of the peptidyl moiety and the O3’ atom of the P-site A76. Upon peptide bond synthesis, the lengthened peptidyl-tRNA is bound to the A site, whereas the deacylated tRNA is in the P site. Peptide elongation is further promoted by the GTP-dependent protein elongation factors EF-G and EF-Tu. EF-G promotes translocation of the A-site bound peptidyl-tRNA into the P site and of the P-site bound deacylated tRNA into the E site. Consequently, the ribosome moves down the mRNA filament with an active site that is ready for a new reaction cycle. Then, the elongation factor EF-Tu delivers the aminoacyl-tRNA to the A site. The proper codon-anticodon interactions stimulate the GTP-ase activity of EF-Tu, leading to its dissociation from the complex. The acceptor end of the A-site aminoacyl-tRNA reorients and positions an incoming amino acid for the reaction with the peptidyl moiety attached to the P-site peptidyl-tRNA in a process known as accommodation. The rate of accommodation is significantly slower than the rate of peptide bond formation and is measured to be ~10s−1. This rate is, however, much higher when small analogs are used and is estimated to be ~50s−1 allowing detailed kinetic studies using this system.

Question: How could this finely tuned and precise orchestration have emerged throug a stepwise evolutionary process, in face of the fact that ALL players have an essential role in the peptyde bond formation and polymer elongation process? 

The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition
https://geneticacomportamento.ufsc.br/files/2013/08/Polacek05-Ribozima-peptidil-transferase.pdf
The distinctive features of the modern ribosome are its mammoth size and enormous structural complexity. The molecular weight of the ribosome exceeds 2.5 million daltons and the particle comprises at least three large rRNA molecules and more than 50 different ribosomal proteins. It is unimaginable that the ribosome, which contains rRNAs of thousands of nucleotides in length, evolved in a single evolutionary step.

There are millions of protein factories in every cell. Surprise, they’re not all the same 2

The plant that built your computer isn't churning out cars and toys as well. But many researchers think cells' crucial protein factories, organelles known as ribosomes, are interchangeable, each one able to make any of the body's proteins. Now, a provocative study suggests that some ribosomes, like modern factories, specialize in manufacturing only certain products. Such tailored ribosomes could provide a cell with another way to control which proteins it generates. They could also help explain the puzzling symptoms of certain diseases, which might arise when particular ribosomes are defective.

Biologists have long debated whether ribosomes specialize, and some remain unconvinced by the new work. But other researchers say they are sold on the finding, which relied on sophisticated analytical techniques. "This is really an important step in redefining how we think about this central player in molecular biology," says Jonathan Dinman, a molecular biologist at the University of Maryland in College Park.

A mammalian cell may harbor as many as 10 million ribosomes, and it can devote up to 60% of its energy to constructing them from RNA and 80 different types of proteins. Although ribosomes are costly, they are essential for translating the genetic code, carried in messenger RNA (mRNA) molecules, into all the proteins the cell needs. "Life evolved around the ribosome," Dinman says.

The standard view has been that a ribosome doesn't play favorites with mRNAs—and therefore can synthesize every protein variety. But for decades, some researchers have reported hints of customized ribosomes. For example, molecular and developmental biologist Maria Barna of Stanford University in Palo Alto, California, and colleagues reported in 2011 that mice with too little of one ribosome protein have short tails, sprout extra ribs, and display other anatomical defects. That pattern of abnormalities suggested that the protein shortage had crippled ribosomes specialized for manufacturing proteins key to embryonic development.

Definitive evidence for such differences has been elusive, however. "It's been a really hard field to make progress in," says structural and systems biologist Jamie Cate of the University of California (UC), Berkeley. For one thing, he says, measuring the concentrations of proteins in naturally occurring ribosomes has been difficult.

In their latest study, published online last week in Molecular Cell, Barna and her team determined the abundances of various ribosome proteins with a method known as selected reaction monitoring, which depends on a type of mass spectrometry, a technique for sorting molecules by their weight. When the researchers analyzed 15 ribosomal proteins in mouse embryonic stem cells, they found that nine of the proteins were equally common in all ribosomes. However, four were absent from 30% to 40% of the organelles, suggesting that those ribosomes were distinctive. Among 76 ribosome proteins the scientists measured with another mass spectrometry-based method, seven varied enough to indicate ribosome specialization.

Barna and colleagues then asked whether they could identify the proteins that the seemingly distinctive ribosomes made. A technique called ribosome profiling enabled them to pinpoint which mRNAs the organelles were reading—and thus determine their end products. The specialized ribosomes often concentrated on proteins that worked together to perform particular tasks. One type of ribosome built several proteins that control growth, for example. A second type churned out all the proteins that allow cells to use vitamin B12, an essential molecule for metabolism. That each ribosome focused on proteins crucial for a certain function took the team by surprise, Barna says. "I don't think any of us would have expected this."

Ribosome specialization could explain the symptoms of several rare diseases, known as ribosomopathies, in which the organelles are defective. In Diamond-Blackfan anemia, for instance, the bone marrow that generates new blood cells is faulty, but patients also often have birth defects such as a small head and misshapen or missing thumbs. These seemingly unconnected abnormalities might have a single cause, the researchers suggest, if the cells that spawn these different parts of the body during embryonic development carry the same specialized ribosomes.

Normal cells might be able to dial protein production up or down by adjusting the numbers of these specialized factories, providing "a new layer of control of gene expression," Barna says. Why cells need another mechanism for controlling gene activity isn't clear, says Cate, but it could help keep cells stable if their environment changes.

Crystal Structure Of The 30s Ribosomal Subunit From Thermus Thermophilus In Complex With The Translation Initiation Factor If3 (C-Terminal Domain)
https://www.ncbi.nlm.nih.gov/Structure/pdb/1I96





https://www.youtube.com/watch?v=Z2XOhgRJVb4&t=311s


https://www.youtube.com/watch?v=5_64XkJeSLU


https://www.youtube.com/watch?v=C4QiMqBSDe4


animation:
http://telstar.ote.cmu.edu/biology/animation/ProteinSynthesis/proteinsynthesis.html

1. from the book: The Logic of Chance: The Nature and Origin of Biological Evolution , page 228, By Eugene V. Koonin
2. http://www.sciencemag.org/news/2017/06/there-are-millions-protein-factories-every-cell-surprise-they-re-not-all-same
3. http://www.nobelprize.org/educational/medicine/dna/a/translation/ribosome_ass.html
4. https://www.sciencedirect.com/science/article/pii/S0040580918300789
5. https://sci-hub.tw/https://www.nature.com/articles/nrm2352
6. https://blueprintsforliving.com/cellular-ribosomes-the-origin-of-life/
7. https://jcs.biologists.org/content/117/17/3725
8. https://pubmed.ncbi.nlm.nih.gov/28454764/
9. https://sci-hub.st/https://www.sciencedirect.com/science/article/pii/B9780081022689000057
10. https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.10221[/b][/b]



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In eukaryotes, translation initiation results in the recruitment of the 40S ribosomal subunit (SSU), initiation factors and the initiator Met-tRNAi Met to the start codon, followed by joining of the 60S ribosomal subunit to form the 80S ribosome.


Translation through ribosomes,  amazing nano machines Experi10
Experimental views of a bacterial ribosome.
The upper image shows a 3D reconstruction from electron microscopy, with the small subunit in green and the large subunit in blue . The lower image is an atomic structure from x-ray crystallography and an NMR structure of a fl exible protein stalk that is not observed in the crystal structure

More Non-Random DNA Wonders
https://web.archive.org/web/20130406102730/http://iaincarstairs.wordpress.com/2011/12/26/more-non-random-dna-wonders/

Translation through ribosomes,  amazing nano machines Riboso10 keggs pathway

Translation through ribosomes,  amazing nano machines Riboso10

Translation through ribosomes,  amazing nano machines Riboso10

An overview of ribosomal structure and mRNA translation.
mRNA translation is initiated with the binding of tRNA to the P site . An incoming tRNA is delivered to the A site in complex with elongation factor (EF)-Tu–GTP. Correct codon–anticodon pairing activates the GTPase centre of the ribosome, which causes hydrolysis of GTP and release of the amino acyl end of the tRNA from EF-Tu. Binding of tRNA also induces conformational changes in ribosomal (r)RNA that optimally orientates the peptidyl-tRNA and aminoacyl-tRNA for the peptidyl-transferase reaction to occur, which involves the transfer of the peptide chain onto the A-site tRNA. The ribosome must then shift in the 3′ mRNA direction so that it can decode the next mRNA codon. Translocation of the tRNAs and mRNA is facilitated by binding of the GTPase EF-G, which causes the deacylated tRNA at the P site to move to the E site and the peptidyl-tRNA at the A site to move to the P site upon GTP hydrolysis. The ribosome is then ready for the next round of elongation. The deacylated tRNA in the E site is released on binding of the next aminoacyl-tRNA to the A site. Elongation ends when a stop codon is reached, which initiates the termination reaction that releases the polypeptide 5

Translation through ribosomes,  amazing nano machines Nihms131608f1
A schematic diagram of the elongation phase of the ribosome-catalyzed translation.
A peptidyl-tRNA is bound to the P site and the deacylated tRNA is in the ribosomal E site. The elongation factor EF-Tu complexed with GTP (orange) delivers an aminoacyl-tRNA to the A site. The deacylated tRNA dissociates from the E site on binding of the aminoacyl-tRNA to the A site. Upon codon recognition the GTP-ase activity of EF-Tu is stimulated and this causes a conformational change in EF-Tu upon which the factor dissociates from the ribosome. If the appropriate codon-anticodon interaction is established the CCA-end of the A-site aminoacyl-tRNA undergoes conformational change in a process known as accommodation, whereas the non-cognate tRNA is rejected at this point. After accommodation a free α-amino group of the aminoacyl-tRNA is oriented properly for the nucleophilic attack onto the acyl-ester link of the peptidyl-tRNA in the P site. The peptidyl transfer reaction occurs rapidly yielding a lengthened peptidyl-tRNA bound to the A site and the deacylated tRNA in the P site. The translocation of the reaction products and mRNA is promoted by the elongation factor EF-G in a GTP-dependent manner. The peptidyl-tRNA moves from the A site into the P site, whereas the deacylated tRNA moves from the P site into the E site. Also, the ribosome has now shifted in the 3’ direction of the mRNA and a new codon occupies the A site on the 30S subunit. After dissociation of the EF-G:GDP complex from the ribosome a new round of peptide synthesis ensues. Once the ribosome encounters the translational stop codon the termination phase of protein synthesis is initiated (not shown).

Translation through ribosomes,  amazing nano machines An_ove10
An overview of termination of translation. 
A stop codon in the mRNA A site (red hexagon) recruits either release factor-1 (RF1) or RF2 to mediate the hydrolysis and release of the peptide from the tRNA in the P site. This functions as a signal to recruit RF3–GDP, which induces the release of RF1/2. Exchange of GDP for GTP on RF3 and subsequent hydrolysis is thought to release RF3. The ribosome is left with mRNA and a deacylated tRNA in the P site. This complex is disassembled by the binding of ribosomal release factor (RRF) and the EF-G elongation factor62. GTP hydrolysis causes the dissociation of the 50S ribosomal subunit, and initiation factor-3 (IF3) is required to dissociate the deacylated tRNA from the P site.

Translation through ribosomes,  amazing nano machines Riboso28
Ribosomes in action.
Three atomic structures capture ribosomes ( blue and green ) in the process of building a protein chain. Elongation factor Tu ( magenta ) delivers a new transfer RNA ( yellow ), pairing its anticodon with the messenger RNA ( red ) codon. The ribosome then catalyzes the formation of the peptide bond; the structure at the center includes two transfer RNA molecules with amino acids attached ( bright green ) and positioned in the catalytic
site. Finally, elongation factor G ( magenta ) shifts everything by one codon (toward the right in this illustration), opening a space for the next transfer RNA

Trans-Translation

The final step of the central dogma is the most complex, where the information in RNA is translated to build proteins. A constellation of proteins and specialized RNA molecules are needed to prepare and deliver the amino acids needed for each step, and researchers have studied them one by one, filling out all the pieces to this biomolecular puzzle.  Ribosomes occasionally get stalled when faulty messenger RNA molecules are read, for
instance, for a messenger RNA that has broken and is thus is missing its stop codon. A special mechanism is used to rescue these stalled ribosomes when they get stuck at the end of the truncated chain. A strangely shaped RNA molecule mimics both a transfer RNA and a messenger RNA, restarting the process and cleaning up the mess.

Translation through ribosomes,  amazing nano machines Transf10
Transfer-messenger RNA.
Transfer-messenger RNA (top ) includes a portion that mimics a transfer RNA ( red ) and a portion that mimics a messenger RNA ( magenta ), complete with a stop codon. It binds to stalled ribosomes ( bottom ), resuming synthesis using its own short message. Amazingly, this message encodes a small tag that is added to the end of the truncated protein, signaling to the cell that the protein is faulty and needs to be destroyed

My comment:  This is awesome. Wow!! How could random non-guided, non-intelligent mechanisms have foresight, and the knowledge of this problem of truncated messenger RNA's that do not have a stop codon, and a sophisticated mechanism to deal with it? This is a masterfully crafted salvage mechanism in order to prevent the cell to produce toxic polymer strands that would accumulate, and in the end, destroy the cell. This is an engineering marvel of extraordinary sophistication.

Transfer-messenger RNA (abbreviated tmRNA ) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with 

Small Protein B (SmpB), 
Elongation Factor Tu (EF-Tu), and 
ribosomal protein S1. 

In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA

Mispairing of bases also plays an essential role during the synthesis of proteins. The 20 amino acids in proteins are encoded by triplet codons in DNA, along with a few codons used to specify the end of a protein. Doing the math, we see that there are 64 possible codons, so there is some degeneracy to the code, and several different codons are used to specify the same amino acid. However, if we look inside the nucleus, we find that there are only 20 or so types of transfer RNA that match up the appropriate amino acids with its codon. This requires some mismatching of the transfer RNA anticodon with all of these different codons. This is accomplished
by allowing some “wobble” in the third position of the codon, so that different pairings are allowed. When the structures of ribosomes were solved, it was found that the first two bases in the codon are tightly controlled by the ribosome, ensuring only the proper pairing, but the third position is looser, allowing some wobble

Catalytic mechanism
The ribosome catalyzes an aminolysis of an acyl-ester bond in the P site. The reaction begins with a nucleophilic attack of the α-amino group of the aminoacyl-tRNA bound in the A site onto the carbonyl carbon of the peptidyl-tRNA positioned in the P site and it proceeds through a tetrahedral oxyanion intermediate. The intermediate collapses into the lengthened peptidyl-tRNA in the A site and the deacylated tRNA in the P site. The ribosome brings ~10^7, or 10,000,000 ( 10 million )-fold increase in the reaction rate compared to an uncatalyzed reaction in solution

the ribosome utilizes a combination of the entropic, general acidbase and electrostatic shielding mechanisms to promote peptide bond formation. The two binding interfaces in the PTC, the A loop and the P loop, specifically recognize the acceptor ends of the aminoacyl- and the peptidyl-tRNA, respectively. The binding of the A-site substrate induces conformational change in the PTC, which allows reactive groups to be oriented properly for the peptidyl-transfer reaction (entropic component). Peptide bond formation is further promoted by a substrate-assisted mechanism in which the O2’ hydroxyl group of the P-site A76 plays a crucial role in the proton shuttling (general acid-base component), whereas a water molecule coordinated by the ribosomal bases stabilizes the oxyanion of the tetrahedral intermediate (electrostatic shielding component).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783306/

Peptide Bond Formation Mechanism Catalyzed by Ribosome
Peptide bond formation during protein polypeptide synthesis in the ribosome is one of the most important chemical reactions in life.  Peptide bond formation is of particular importance, being the heart of protein synthesis. 1 The process is so intriguingly complex, that a science paper in 2015 had still to admit that: The detailed mechanism of peptidyl transfer, as well as the atoms and functional groups involved in this process are still in limbo.
Another science paper confessed: The mechanism of this process and the origin of the catalytic power of this ancient enzyme are still an unsolved puzzle. As we know now, the process requires a precise and exquisitely engineered molecular arrangement, where one ribose molecule has the pivotal role as proton shuttle. 

Interactions between active site residues and the 2′-OH are pivotal in orienting substrates in the active site for optimal catalysis. A second 2′-OH group  was identified to be crucial for peptide bond formation, namely that of A2451. The 2′- OH of A2451 was shown to be of potential functional importance. 9

The ribosome promotes the reaction of the amino acid condensation by properly orienting the reaction substrates.

Translation through ribosomes,  amazing nano machines Riboso32
Representation of 4-, 6- and 8-membered ring TS structures (A), ribosome structure (B) and schematic representation of the A and P site of Ribosome (C). Atoms included in the QM region are in shaded region. 2

A key role is given to the 2’ hydroxyl of the P site substrate, A76, by serving as a proton shuttle. It would act as a general base that would abstract the proton from the α-amino group and would donate a proton to the deacylated 3’ hydroxyl.

The full mechanism can be decomposed in three stages. These three stages take place in a single concerted step and they slightly overlap during the evolution of the system along the reaction path. The ribosome promotes an entropy trap, in the sense that it enhances the rate of the peptide bond formation positioning the substrates and/or excluding waters from the active site.

Key in the reaction is the presence of a proton shuttling group The observed 100-fold reduction in the reaction rate by mutation of P-site A76 20-OH group, however small, can be the indication of this group's activity during peptidyl transfer reaction.

Atomic mutagenesis suggests that nucleobases do not carry functional groups directly involved in peptide bond formation. Instead,A single ribose 20-hydroxyl group at A2451 was identified tobe of pivotal importance. 3

Translation through ribosomes,  amazing nano machines P-site10
Ribosomal Protein Synthesis
Amide bond formation is the fundamental chemical reaction catalyzed by the PTC of the ribosome. The PTC possesses ribozyme activity: Attack of the a-amino group of the amino acid-charged A-site tRNA (orange) at the ester carbonyl carbon of the methionyl- or peptidyl-tRNA in the P site (blue) is supported to yield the amide linkage. The present study reveals details of this mechanism.

By using an atomic mutagenesis approach to investigate all the 23S rRNA residues that compose the inner core of the peptidyl transferase center, we identified a single functional group with crucial importance for peptide bond catalysis— namely, the ribose 20'-OH at A2451. This ribose 20 group needs to maintain hydrogen donor characteristics in order to promote effective amide bond formation. By combining these novel findings with biochemical and structural data that have accumulated over the last 2 decades highlighting the importance of the P-tRNA ribose 20'-OH at A76. The A2451 20 -hydroxyl directly assists in positioning the P-site tRNA-A76 ribose via hydrogen bond formation. This can promote an effective A76 ribose C20 -endo conformation to support amide synthesis via a proton shuttle mechanism. This synergistic approach appreciates the concept of ‘‘substrate-assisted catalysis’’ , and combines with it the strict functional requirement of the ribose 20 group at A2451 of 23S rRNA to possess hydrogen donor capability. 3

The A2451 2′-OH is central for establishing a proton wire 5.  In the proposed model the A2451 2′-OH is part of an array of H-donors/acceptors that subtracts a proton from the nucleophilic α-amine, and thereby facilitating the nucleophilic attack of the α-amine of the A-site aminoacyl-tRNA onto the ester carbonyl carbon of the P-site peptidyl-tRNA. As the intermediate breaks down to form a new peptide bond, the proton wire then relays a proton back to saturate the 3′-O− of the P-site tRNA leaving group. Evidently, the positioning of all substrates, transition states, and ribosomal residues contributing to the concerted redistribution of charges must be tightly controlled to achieve efficient transpeptidation compatible with the observed in vivo rates of amino acid polymerization of about 20 s–1.

This 2'-OH renders almost full catalytic power. These data highlight the unique functional role of the A2451 2'-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site.

My comment: A precise, minutely orchestrated arrangement of just two main players,  the interaction of ribose 2'-OH at position A2451 , and the 2’ hydroxyl of the P site substrate A76  are pivotal in orienting substrates in the active site for optimal catalysis, and play a key role in polypeptide bond formation. The ribosome promotes the reaction of the amino acid condensation by properly orienting the reaction substrates. Key in the reaction is the presence of a proton shuttling group.  The observed 100-fold reduction in the reaction rate by mutation of P-site A76 20-OH group  is indication of this group's activity during the peptidyl transfer reaction.

The positioning of all substrates, transition states, and ribosomal residues contributing to the concerted redistribution of charges must be tightly controlled to achieve efficient transpeptidation. This 2'-OH renders almost full catalytic power. These data highlight the unique functional role of the A2451 2'-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site.

Interactions between active site residues and the 2′-OH of A76 of the peptidyl-tRNA are pivotal in orienting substrates in this active site for optimal catalysis.

The 23S ribosomal RNA is 2904 nucleotides long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome. In general, rRNA has an essential function of peptidyl transferase, the stimulating core of the ribosome plays role in the peptide bond configuration. Both peptidyl-tRNA and aminoacyl-tRNA are important for synthesizing protein and transpeptidation response. However, 23S rRNA positions which are G2252, A2451, U2506, and U2585 have a significant function for tRNA binding in P site of the large ribosomal subunit.

In the upper part of the tunnel, results suggest that A2062 and A2451 can communicate in both directions for translation stalling, mostly through dynamically coupled C2063, C2064, and A2450.

My comment:  This is truly awe-inspiring. The functional group A2451, which is not only of crucial importance as described above for peptyde bond catalysis, but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here", 

The large subunit 50S catalyzes peptide bond synthesis at the highly conserved catalytic cavity peptidyl transferase center (PTC), where nucleotides G2251, G2252, A2451, C2452, U2506, U2585, A2602 play critical roles in the translation process. 

Translation through ribosomes,  amazing nano machines P-site12
Large subunit 50S, including P-tRNA (gray), polyAla chain (turquoise) and ribosomal proteins protruding to the ribosomal tunnel, namely uL4 (pink), uL22 (brown), uL23 (red) are shown. Nucleotides A2451 (PTC), A2062, U2585–U2586 (ribosomal tunnel), and residues Gly91 (tip of uL22 loop), Glu18 (trigger factor binding site on uL23), Gln72 (tip of uL23 loop), which are investigated in this study are also indicated. In all figures, PyMol (DeLano Scientific LLC., 2002) is used for the molecular visualization.

The ribosomal tunnel is not a passive passageway but is actively taking a role in translation regulation. The dynamics of the large subunit, the ribosomal tunnel geometry together with its electrostatic potential seems to play an important role on complexity and production rate of small folded proteins .  During its passage through the ribosomal tunnel, compacted chain interacts with the ribosomal tunnel elements and affects the recruitment of chaperones to the exit of the tunnel in bacteria. This suggests conformational crosstalk not only within the tunnel but also outside the tunnel at the solvent side.  This is literally a network of nucleotides and residues on the ribosomal tunnel taking a role in constant communication of the distant functional regions.

My comment:  What we see here, is a vivid and active masterfully performing information exchange taking place. The entire translation process is a carefully monitored, controlled, and regulated process where where information and signals are constantly being exchanged in order to guarantee a faithful and error minimized process of protein production. The key components that play in regulating the translation process are dispersed along the exit pathway.
 
1. https://sci-hub.st/https://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra02767e#!divAbstract
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582011/
3. https://core.ac.uk/download/pdf/81150349.pdf
4. https://en.wikipedia.org/wiki/23S_ribosomal_RNA
5. https://academic.oup.com/nar/article/46/4/1945/4788351
6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116277/
7. https://www.frontiersin.org/articles/10.3389/fmolb.2020.586075/full
8. https://www.x-mol.com/paper/3338695?adv
9. https://sci-hub.st/https://pubs.acs.org/doi/full/10.1021/ja209558d



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Internal Ribosome Entry Sites Provide Opportunities for Translational Control

Although approximately 90% of eukaryotic mRNAs are translated beginning with the first AUG downstream from the 5ʹ cap, certain AUGs can be skipped over during the scanning process. Cells can initiate translation at positions distant from the 5ʹ end of the mRNA, using a specialized type of RNA sequence called an internal ribosome entry site (IRES). In some cases, two distinct protein-coding sequences are carried in tandem on the same eukaryotic mRNA; translation of the first occurs by the usual scanning mechanism, and translation of the second occurs through an IRES. IRESs are typically several hundred nucleotides in length and fold into specific structures that bind many, but not all, of the same proteins that are used to initiate normal 5ʹ cap-dependent translation. 

Translation through ribosomes,  amazing nano machines Two_me10
Two mechanisms of translation initiation.
(A) The normal, capdependent mechanism requires a set of initiation factors whose assembly on the mRNA is stimulated by the presence of a 5ʹ cap and a poly-A tail .
(B) The IRES-dependent mechanism, seen mainly in viruses, requires only a subset of the normal translation initiating factors, and these assemble directly on the folded IRES

In fact, different IRESs require different subsets of initiation factors. However, all of them bypass the need for a 5ʹ cap structure and the translation initiation factor that recognizes it, eIF4E.



Nobel Prize Winner Cites the "Ingeniously Designed" Architecture of the Ribosome

In 2009, Israeli structural biologist Ada Yonath shared the Nobel Prize in Chemistry for her work on the structure and function of the ribosome. More recently, she had this to say about the "ingeniously designed" architecture of the ribosome:

Ribosomes, the key players in the translation process, are universal ribozymes performing two main tasks: decoding genetic information and polymerizing amino acids. Hundreds of thousands of ribosomes operate in each living cell due to the constant degradation of proteins through programmed cell death, which is matched by simultaneous production of proteins. For example, quickly replicating cells, e.g. liver cells, may contain a few million ribosomes. Even bacterial cells may contain [up] to 100,000 ribosomes during their log period. Other constituents are the mRNA chains, produced by the transcription of the segments of the DNA that should be translated, which carry the genetic information to the ribosomes, and tRNA molecules bring the cognate amino acids to the ribosome. To increase efficiency, a large number of ribosomes act simultaneously as polymerases, synthesizing proteins by one-at-a-time addition of amino acids to a growing peptide chain, while translocating along the mRNA template, and producing proteins on a continuous basis at an incredible speed, namely up to 20 peptide bonds per second.

Ribosomes are giant assemblies composed of many different proteins
(r-proteins) and long ribosomal RNA (rRNA) chains. Among these, the RNA moieties perform the two ribosomal main functions. The ratio of rRNA to r-proteins (~2:1) is maintained throughout evolution, except in mitochondrial ribosome (mitoribosome) in which ~half of the bacterial rRNA is replaced by r-proteins. Nevertheless, the active regions are almost fully conserved in all species. In all organisms ribosomes are built of two subunits, which associate to form the functionally active ribosomes. In prokaryotes, the small subunit, denoted as 30S, contains an RNA chain (16S) of ~1500 nucleotides and ~20 different proteins. The large subunit (50S in prokaryotes) has two RNA chains (23S and 5S RNA) of about 3000 nucleotides in total, and different >31 proteins. The available three dimensional structures of the bacterial ribosome and their subunits show that in each of the two subunits the ribosomal proteins are entangled within the complex rRNA conformation, thus maintaining a striking dynamic architecture that is ingeniously designed for their functions: precise decoding; substrate mediated peptide-bond formation and efficient polymerase activity.



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http://cshperspectives.net/content/2/9/a003483.full

By the time of LUCA, the ribosome clearly exists in essentially its modern form.Thus, laboratory reconstructions will be needed. However, there would be limited value in resurrecting the complete ribosome of LUCA, because it was in effect a modern ribosome itself.

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5Translation through ribosomes,  amazing nano machines Empty Origin and Evolution of the Ribosome on Wed Apr 09, 2014 4:53 pm

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When opponents of special creation asked about how x arised, they often make a quick web search, come up with the first search result which looks like a " serious " scientific paper, which explains how x evolved, and post it as a answer. When asked to quote the relevant part of the paper, which convinced them evolution were the best answer, commonly they don't answer, because they did not make the effort to analise carefully the proposed evidence. That shows nicely their confirmation bias. They determined already evolution must be true, since it fits their preconceived and wished world view, so all they do, is to try to fit everything they find into their naturalistic world view, without carefully looking if the evidence is compelling. Most scientific papers on evolution are perfect examples of how methodological naturalism works, and obliges specially historical sciences to wear blinkers. Since evolution is the only naturalistic possible explanation for the biodiversity on earth, evolution is supposed to be the answer right from the beginning, rather to start with a agnostic standpoint , and after careful examination, permitting the evidence to lead wherever it is, and propose evolution as the best explanation if that is the outcome that fits best. These pappers start with evolution, end with evolution, and in the middle is a not rarely high concentration of guess work, ad hoc explanations , and fairy tale stories.

Origin and Evolution of the Ribosome

http://cshperspectives.net/content/2/9/a003483.full

Abstract :   likely, it is argued, were likely, likely order, may have, Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed

The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely the guesswork begins    Very Happy  lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

and as final not of the paper :
In the end, no matter how complete a picture is developed of ribosomal development over time it will be hypothetical. The ultimate issue will be to prove at least the major parts of it. Thus, laboratory reconstructions will be needed. However, there would be limited value in resurrecting the complete ribosome of LUCA, because it was in effect a modern ribosome itself.



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6Translation through ribosomes,  amazing nano machines Empty The Miracle of Ribosome Assembly Evolution on Sat Apr 12, 2014 7:06 pm

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http://darwins-god.blogspot.com.br/2010/12/miracle-of-ribosome-assembly-evolution.html

New research is uncovering the details of how the cell’s protein factory—the ribosome—is constructed. The ribosome translates messenger RNA molecules—edited copies of DNA protein-coding genes—into a string of amino acids, according to the genetic code. The ribosome has two major components (one smaller and one larger), each made up of both RNA and protein molecules, and is constructed via a complex sequence of events.

The RNA components of the ribosome are copies of DNA genes. These ribosomal RNA molecules—known as rRNAs—are initially in a raw copy of DNA which eventually is edited. For instance, one of these copies of DNA may contain many rRNAs, separated by spacer segments. The spacer segments need to be removed, leaving the individual rRNAs ready for assembly.

One of the findings of the new research is that in the early stages of assembly, one of the DNA copies folds up such that a spacer segment binds to one of the rRNAs. In particular, the spacer binds to the special segment of the rRNA that reads the messenger RNA molecules, in the final, assembled ribosome. When the spacer is removed, the rRNA switches to its correct shape, for function in the ribosome. One implication of this finding is that ribosome construction can be regulated by this switch. Remove the spacer and ribosome construction proceeds. Leave the spacer, and ribosome construction halts. As the researchers concluded:

our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.


RNA tends to fold up into a variety of shapes. In this case, as lead researcher Katrin Karbstein suggests, RNA folding properties are part of the design:

Perhaps, nature has found a way to exploit RNA’s Achilles’ heel—its propensity to form alternative structures … Nature might be using this to stall important biological processes and allow for quality control and regulation.

But of course this mechanism brings yet more complexity:

What is interesting is that as the organism becomes more complex, the number of cleavages needed increases. This may make the process more accurate and that may be an evolutionary advantage, but even in bacteria this cutting is not done in a simple way. We still don’t know exactly why that is.


Karbstein suggests that the strictly ordered cutting and pasting steps in ribosome assembly are introduced to produce singularly perfect intermediates. As she explains:

Ribosomes make mistakes rarely, on the order of one in 10,000 amino acid changes. A lot of this accuracy depends on conversations between different parts of the ribosomes, so if the structure of the RNA isn’t correct, these conversations can’t happen. And that means more mistakes, and that’s not good because it can lead to any number of disease states.


Ribosomes don’t just happen. They are not easily assembled and the evolution of this choreography calls for several just-so heroics. Yes, this fine-tuned set of mechanisms makes for fantastic regulation of the cellular protein making factory, but it means that evolution must have gone through a stage where life didn’t work. For the spacer segment that binds to the rRNA is a show-stopper. It would be selected against instantly.

The only way to resolve this problem is to have the spacer removal mechanism already in place, before the spacer sequence itself evolved. As usual, evolutionists would need to rely on the needed mechanism just happening to serve some other useful purpose, and when the spacer sequence happened to arise for no reason, the removal mechanism found new work for itself. In other words, mutations arose that caused the DNA copy to fold, rendering ribosome synthesis—and life itself—impossible. But as luck would have it, there just happened to be the right molecular machine lying around that removed the problematic segment at just the right time and place. Not only was the fatal flaw obviated, but a brilliant new means of regulation invented. Amazing. Over time, further mutations happened to refine its actions and today we have the fine-tuned ribosome assembly process.

There you have it—evolution’s just-add-water version of science. For the umpteenth time evolution becomes a charade. Behind the scenes, in deep-time where no one can see it working, evolution once again performs miracle after miracle.


An RNA conformational switch regulates pre-18S rRNA cleavage.


Abstract


To produce mature ribosomal RNAs (rRNAs), polycistronic rRNA transcripts are cleaved in an ordered series of events. We have uncovered the molecular basis for the ordering of two essential cleavage steps at the 3'-end of 18S rRNA. Using in vitro and in vivo structure probing, RNA binding and cleavage experiments, and yeast genetics, we demonstrate that a conserved RNA sequence in the spacer region between the 18S and 5.8S rRNAs base-pairs with the decoding site of 18S rRNA in early assembly intermediates. Nucleolar cleavage at site A(2) excises this sequence element, leading to a conformational switch in pre-18S rRNA, by which the ribosomal decoding site is formed. This conformational switch positions the nuclease Nob1 for cytoplasmic cleavage at the 3'-end of 18S rRNA and is required for the final maturation step of 18S rRNA in vivo and in vitro. More generally, our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.

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7Translation through ribosomes,  amazing nano machines Empty Perfectionist protein-maker trashes errors on Sat Apr 12, 2014 10:11 pm

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But the Ribosome is fascinating, and worth a closer look about its amazing properites and functions :

http://www.hopkinsmedicine.org/news/media/releases/Lost_In_Translation

The Ribosome: Perfectionist Protein-Maker Trashes Error

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist

Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button.

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. "The cell is a wasteful system in that it makes something and then says, forget it, throw it out,"

That looks all ingeniously designed....... :smile: :smile: :thumbup:

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http://www.evolutionnews.org/2012/03/study_questions057501.html

The Ribosome
The ribosome is an intricate, complex protein and RNA structure containing two subunits that fit together like two hands in a cupped clap. The "cup" that the hands make is an empty space through which messenger RNA (mRNA) passes, is read, and translated into an amino acid connected to transfer RNA (tRNA).

The authors of the study propose that the individual sub units of the ribosome evolved separately but each subunit co-evolved with ribosomal RNA (rRNA) and then with the portion of the tRNA molecule that the modern-day subunit interacts with (the particular binding sites). The authors propose that these separate and simpler systems were co-opted very early in primordial history to form the machinery that we see today.

Co-Evolution of Ribosomal Proteins and RNA
The authors provide the following lines of evidence for the co-evolution of ribosomal proteins and RNA:

(1) Traditionally, the PTC active site has been considered the oldest part of the ribosomal protein. The idea behind stems from function, as well as an assumption that the proteins were built up in a step-by-step fashion. If this was the case, the outer components are likely "newer." The authors instead looked at the tertiary structure and employed studies using structural similarities to determine evolutionary age:

   In contrast, here we infer the history of the complete RNP ensemble using phylogenetic methods that employ standard cladistics principles widely used for example in the analysis of morphological characteristics of organisms. Shared-derived features of structure defined by crystallography and comparative sequence analysis are treated as phylogenetic characters and used to build structural phylogenies.

The authors found that due to the age difference in portions of the ribosome, there was likely a functional core that pre-dates the PTC active site. This particular study raises some red flags, however, because homology (structural or genetic similarities) is a tricky thing. Usually evolutionary biologists apply homology to organisms.

(2) The authors' studies indicate that the ribosome subunits may have originally interacted separately until a "major transition" occurred that brought the subunits together. This "major transition" coincided with the evolution of tRNA. These studies dealt with the supposed evolution of the inter-subunit bridge through which the two subunits interact. The authors note that any mutations to this bridge leads to non-functionality.

(3) Tertiary interactions between RNA-RNA and RNA-protein occurred after the first major transition.

   We propose that A-minor and other tertiary interactions evolved to stabilize and maintain the ribosome structure during elongation, leading to increased ribosomal processivity. Scarcity of A-minor interactions before the major transition implies that the early proto-ribosome structure was mostly stabilized by r-proteins or their precursors.

(4) According to authors' studies, tRNA is at the center of ribosomal evolution. There are two major sections of tRNA and each one interacts almost exclusively with a particular subunit of the ribosome. These RNA/subunit partners evolved individually, then came together to form the modern-day complex sometime after the first major transition. The modern-day complex was built around tRNA:

   These remarkable patterns suggest that subunit interactions with a full modern cloverleaf tRNA structure were recruited for translation after the major transition and that the ribosome was built around tRNA or tRNA-like structures...

(5) Phylogenetic studies show that the oldest parts of the ribosome interact with the oldest parts of the ribosomal RNA (rRNA), and the evolution of these two are "linked" in such a way that as one evolves so does the other. The authors state that this is evidence for their co-evolution and believe that this intimate interaction is the reason why ribozyme studies have not progressed:

   We propose complex ribosomal functionality emerged from the cooperative interaction of rRNA and r-proteins (or their precursors), which existed from the earliest stages of ribosome evolution. Thus far, in vitro peptidyl transferase activity catalyzed by protein-free rRNA derived from extant rRNA or ribozymes is not demonstrated. Perhaps, the primordial cooperative property of the RNP complex explains why such attempts have failed.

The same evidence, however, could also show that these structures are irreducibly complex, rather than that they co-evolved.

(6) A second major transition occurred in which ribosome evolution coincides with the emergence of a particular protein complex that "stimulates the GTPase activity of EF-G, a ribosomal factor that catalyzes elongation and is responsible for marked increases in the processivity of the ribosome." In other words, this transition has to do with important specific activities involved in building proteins.

(7) The ribosomal core has components that are similar to ribozyme-like activity and therefore provide evidence for recruiting various parts to form the translation system, or co-option:

   Thus, it is likely that the ribosomal catalytic core had origins in processive substructures common to replication and translation and is a descendant of a primitive templating complex...Since structural components of a proto-ribosome involved in tRNA, mRNA and intersubunit interactions are older than others, these results also support the replicative origin of tRNA.

( 8 ) Certain components, such as translation initiation factors, tRNA binding proteins, DNA binding proteins, and telomere binding proteins have a similar folding arrangement, and therefore likely have a common origin:

   RNA binding and DNA binding proteins therefore have a common evolutionary origin, suggesting ancient r-proteins and homologs were originally part of primitive replication machinery, which diversified and was co-opted for modern translation. This ancient replicative function most likely involved processivity and biosynthetic activities that we believe remain hidden today in ribosome function." (emphasis added)

Unfortunately, while the authors suggest co-option, they do not have a model system on which to base the prior function of these mechanical parts, which makes this highly speculative.

Assessment
Overall, the authors appeal to co-option and co-evolution and justify this using phylogenetic homology studies. They contend as many in the ID camp do that "the de novo appearance of complex functions is highly unlikely. Similarly, it is highly unlikely that a multi-component molecular complex harboring several functional processes needed for modern translation could emerge in a single or only a few events of evolutionary novelty." Their explanation, however, is that a simpler system was performing a different function, and then was recruited into the complex protein translation machine.

The question that follows is what exactly did the recruiting? What provokes recruitment to another system? The authors labeled this time of recruitment the "first major transition" but their explanation of the transition is a little cloudy.

They seem to answer the question of "motivation to recruitment" by appealing to co-evolution. The RNA and ribosome proteins are co-dependent such that as one evolves, the other does too and somehow it reached a point where a "major transition" occurs.

There are many striking features of this study, such as the authors' acknowledgement of the deficiency of ribozymes to account for the "chicken-and-egg" problem with protein synthesis, and their recognition of the improbable evolution of RNA apart from the ribosomal protein in view of the fact that the relevant functions are so intimately intertwined.

While these results show a relationship and even a correlation between tRNA and the ribosome, it is still unclear what exactly promoted recruitment, what attracted the tRNA to the proto-ribosome, or why co-option must be the conclusion. Could this not also be a case of an irreducibly complex machine?

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Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis

Ribosome synthesis in eukaryotes requires a multitude of trans-acting factors. These factors act at many steps as the pre-ribosomal particles travel from the nucleolus to the cytoplasm.

Ribosome biogenesis is a fundamental multistep process that, in eukaryotes, takes place largely within the nucleolus.Late steps in both 40S and 60S ribosomal subunit (r-subunit) synthesis occur in the nucleoplasm and after nuclear export of precursor particles in the cytoplasm . Ribosome synthesis is evolutionarily conserved throughout eukaryotes , and so far most of our understanding of this process has been obtained from studies with Saccharomyces cerevisiae . In the yeast nucleolus, three of the four rRNA(18S, 5.8S and 25S) are transcribed as a single large primary transcript by RNA polymerase I and processed to the first detectable rRNA precursor (pre-rRNA), the so-called 35S pre-rRNA. The fourth rRNA (5S) is independently transcribed as a pre-rRNA (pre-5S) by RNA polymerase III. In the 35S pre-rRNA, the mature rRNA sequences are separated by two internal transcribed spacers (ITS1 and ITS2) and flanked by two external transcribed spacers (5′ ETS and 3′ ETS), which must be precisely and efficiently processed to ensure correct formation of mature rRNAs . Maturation of rRNAs is a well-defined pathway  and involves numerous trans-acting factors that are required for the processing and covalent rRNA modification reactions, such as small nucleolar RNA–protein (snoRNP) complexes, endonucleases and exonucleases, and different base methylases . Concomitantly to rRNA maturation, the pre-rRNAs assemble in an ordered manner with the 79 ribosomal proteins (r-proteins) and a large number of trans-acting factors that are generally referred to as r-subunit assembly factors  (for examples of trans-acting factors see http://www.medecine.unige.ch/~linder/proteins.html). The process of r-subunit assembly is still poorly understood. An outline of this process was provided by sucrose density gradient analyses in the 1970s, which identified 90S, 66S and 43S pre-ribosomal particles . Recent advances employing proteomic approaches have revealed several distinct, successive pre-ribosomal particles and refined the model for the maturation of both 40S and 60S r-subunits [for a review . These proteomic approaches have also led to the identification of novel non-ribosomal proteins, increasing the number of trans-acting factors involved in ribosome biogenesis to over 180. Evidence towards an understanding of the function of many of these trans-acting factors has been obtained by using a complete repertoire of techniques, thus, addressing their temporal association with pre-ribosomal particles and revealing the pre-rRNA processing and nucleocytoplasmic export defects caused by their mutational inactivation or depletion .

http://www.ncbi.nlm.nih.gov/pubmed/21529161
Ribosome assembly needs  the contributions of several  assembly cofactors , including Era, RbfA, RimJ, RimM, RimP, and RsgA, which associate with the 30S subunit, and CsdA, DbpA, Der, and SrmB, which associate with the 50S subunit.



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http://www.reasons.org/articles/proteins-made-by-design-part-1-of-3

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http://rnajournal.cshlp.org/content/10/12/1833.full

recent crystallographic studies have revealed the ribosome to be a structure of unprecedented complexity

Most importantly, they cannot have evolved initially to make functional proteins, in the modern sense, because of the vanishingly small probability that the first attempts at polypeptide synthesis by a primitive translational apparatus could yield a protein with any useful enzymatic activity (Woese 1967).

That is to say, the RNA world could not have anticipated that the evolution of a macromolecular machine with the complexity of the ribosome would in turn eventually lead to the evolution of long polypeptide chains of specific sequence that fold into stable, three-dimensional structures with desirable biological functions. Clearly, until the first active proteins emerged, no selective advantage would exist for evolution of a translational machinery, if its only purpose was to synthesize functional proteins.

Yet, we know it evolved, because here it is ( funny, as if there were no other options, like special creation...... )

More likely, protein synthesis initially arose not to create fully functional enzyme-like proteins, but for some other purpose. ( how do they know ? )

Specification of amino acids by RNA sequences most likely emerged later, requiring coevolution of the ribosome and its tRNAs (Noller 1993; ( further guesswork... nice ! )

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Ribosome Checks for Translation Errors (and a bunch of other stuff)

1

There is a vast network of information flow in a typical cell, and along with that flow there is a vast network of error checking. Damage to DNA sequences is remedied, the transcribing of DNA is checked and corrected, and at the ribosome the translation process is checked and controlled. In fact, recent research has found that the ribosome not only carefully sets up the codon-to-amino-acid translation process for success, but if an error is made the ribosome detects it and takes action after the translation process.

When the ribosome detects a translation error it takes action 10,000 times faster than it normally does. "These are not subtle numbers," explained the lead researcher. As one report explains, "the ribosome exerts far tighter quality control than anyone ever suspected."

How does the ribosome do it? The ribosome--which creates proteins--consists of RNA and protein molecules. If the ribosome is the machine that builds proteins, then from where did the ribosome's proteins come in the first place? Evolutionists believe that initial versions of the ribosome--the proto-ribosome--had only the RNA molecules and the proteins came later.

Perhaps so, but the translation task is not simple, and the ribosome's proteins do not appear simply to be innocent bystanders that evolution, for no particular reason, kludged onto the ribosome. Rather, the proteins are deeply embedded in the ribosome, and appear to be important for both the ribosome's structure construction and conformation. This is probably why RNA-only proto-ribosomes don't seem to work.

But this is not all. Even ignoring the problem of obtaining an RNA-only translation machine, the evolutionary hypothesis raises the question: From where did the protein-coding sequences come which it would translate? In other words, even if a long sequence of RNA residues just happened to assemble and fold and function as a proto-ribosome, why would it be selected for if there were no protein-coding sequences lying around? One could add to this a long list of other requirements, such as a ready made pool of amino acids, and of course something for the newly minted protein to do.

Of course evolutionists can always speculate. For instance, perhaps a functional RNA molecule just happened to also code for a useful protein. How convenient.

Fortunately, in a world where confessions of evolution's heroics are rare, one nobel laureate scientist gave this judicious observation: "How evolution managed to progress from making a random peptide to messenger-directed synthesis, we haven't a clue." And yet evolution is a fact? I think I want my money back.

1) http://darwins-god.blogspot.com.br/2010/01/ribosome-checks-for-translation-errors.html

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A . Earliest Beginnings: RNA World

1. Initial Formation of Peptidyl Transferase Center in RNA World
A. Emergence of RNAs that can aminoacylate RNAs -leads to small charged
RNAs (minihelices)
B. Emergence of RNAs that can catalyze peptide bond formation between minihelices.
2. Beginnings of coherent SOS subunit
Portions of Domain V of 23S rRNA likely present. Addition of more RNA or
essentially random peptides might have decreased hydrolysis reaction and increase
activity by protecting the core reaction.
3. Extension of tRNA to two domains;
Second tRNA domain allows templating, which significantly increases reaction rate.
Characteristic conformational changes associated with translocation are present.
4. Beginnings of coding
It is now possible to store information. This makes it useful to have a genome (RNA)
and hence primitive polymerases might offer a significant selective advantage to
progenotes that have them.
B. Beginnings of Transition to Protein World: Late RNA World
5. Ancestors of core proteins such as L3 and L4 are present.
Emergence of defined sequence peptides means RNA World will soon end.
6. Initial creation of 30S particle
Further protection of the reaction machinery is possible by stabilizing template.
Bridges between subunits were probably initially only RNA. Portions of Domain IV
of 23S rRNA that interact with 30S subunit are likely to be present.
C. Early Protein World: Major Refinements Increase Speed and Accuracy
7. EF-Tu ancestor
Improved control of tRNA access to machinery
8. Addition of 5S rRNA complex
Further development of SOS subunit underway. Many new proteins present such as LS
and LI 8 that are associated with SS rRNA incorporation
9. GTPase Reaction Center Formed
The emerging protein world allows the development of the translocation machinery.
LI 0 now present. At least portions of 23S rRNA Domain II are present.

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Molecular basis for protection of ribosomal protein L4 from cellular degradation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5296656/


Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function tofacilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery.

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Two proofreading steps amplify the accuracy of genetic code translation

http://www.pnas.org/content/113/48/13744.abstract

We have discovered that two proofreading steps amplify the accuracy of genetic code reading, not one step, as hitherto believed. We have characterized the molecular basis of each one of these steps, paving the way for structural analysis in conjunction with structure-based standard free energy computations. Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading. Our results have implications for the evolution of efficient and accurate genetic code reading through multistep proofreading, which attenuates the otherwise harmful effects of the obligatory tradeoff between efficiency and accuracy in substrate selection by enzymes.

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The ribosome as a missing link in the evolution of life 1

https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#5929

The title is already deceptive. There was no evolution prior to DNA replication. Why do the authors try to insert the mechanism of evolutionary change into a scenario pre-life, where it does not belong?

Hypothesize that ribosome was self-replicating intermediate between compositional or RNA-world and cellular life.

My comment: There is no explanation of what function the Ribosome would have without all the other parts required to make proteins.

rRNA contains genetic information encoding self-replication machinery: all 20 tRNAs and active sites of key ribosomal proteins.

My comment: the make of transfer RNA's ( tRNA's) requires ultracomplex molecular machinery and in a production line fashion, where several proteins and ribozymes work in a coordinated fashion to produce the twenty tRNA's used in life:

Transfer RNA, and its biogenesis, best explained through design
https://reasonandscience.catsboard.com/t2070-transfer-rna-and-its-biogenesis

tRNA's are very specific molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are often made of several subunits and ainded by essential co-factors and metals.

Statistical analyses demonstrate rRNA-encodings are very unlikely to have occurred by chance.

My comment: EXACTLY. But that is precisely the ONLY possible mechanism prior to DNA replication. 

The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-the-possible-mechanisms-to-explain-the-origin-of-life

Natural selection is not a possible mechanism to explain the origin of life, since evolution depends on DNA replication

When we consider how life might have arisen from nonliving matter, we must take into account the properties of the young Earth’s atmosphere, oceans, and climate, all of which were very different than they are today. Biologists postulate that complex biological molecules first arose through the random physical association of chemicals in that environment.
LIFE The Science of Biology, TENTH EDITION, page 3

Neither Evolution nor physical necessity are a driving force prior dna replication. The only two alternatives are either a) creation by an intelligent agency, or b) Random, unguided, undirected natural events by a lucky "accident".

Koonin, the logic of chance, page 266
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible . The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance abetted by chemical selection, such as the preferential survival of stable RNA species. Translation is thought to have evolved later via an ad hoc selective process.  Did you read this ???!! An ad-hoc process ??

Suggest that DNA and cells evolved to protect and optimize pre-existing ribosome functions.

My comment: There were no self-replicating cells without the Ribosome fully setup and operating....

Among the molecules that probably arose very early in the biological systems, the large subunit of the ribosomal RNA that composes the ribosomes in cellular organisms are considered as a possible turning point in molecular evolution (Fox, 2010). Even more specifically, a part of this molecule called the Peptidyl Transferase Center (PTC) is considered by some as having an essential role in evolution, since this catalytic ability of getting
together aminoacids is crucial for protein synthesis and thus, for a first transition fromaRNAworld to a Ribonucleoprotein world, as seen in modern organisms 2

1. https://www.sciencedirect.com/science/article/pii/S0022519314006778
2. http://sci-hub.tw/https://www.cambridge.org/core/journals/international-journal-of-astrobiology/article/buds-of-the-tree-the-highway-to-the-last-universal-common-ancestor/ED26AA7787BA5A152090913CC7C20067

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Assembly of the bacterial ribosome

Ribosome biogenesis is the process that leads to the assembly of translationally competent ribosomes. It is considered the most energy demanding mechanism in cell metabolism, accounting for more than half of a cell’s whole energy. Ribosome biogenesis starts in a dedicated organelle: the nucleolus, where ribosomal components accumulate. From the transcription of ribosomal RNA to the assembly of the last ribosomal proteins on the 80S ribosome, a plethora of maturation and assembly steps is required. These occur sequentially during the entire journey from the nucleolus fibrillar centre to the cytoplasm.

Biogenesis of the mature bacterial ribosome requires the stepwise association of ∼50 ribosomal proteins and intricately folded rRNA, and involves ∼100 molecular chaperones. Each bacterium can generate ∼100,000 ribosomes per hour 8

The translation machinery is, by far, the most complex part of a modern minimal cell, both in its biogenesis and its function. Therefore, it was not surprising that half of the previously classified as poorly characterized genes have been associated with the maturation of the translation apparatus.

Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. 15  The biosynthesis of ribosomes is, therefore, an essential process for all living organisms. A highly complex interaction of a multiplicity of non-ribosomal proteins and small nucleolar RNAs (snoRNAs) facilitates ribosome formation. Prokaryotic ribosome synthesis is a complex, multistep process requiring the coordinated synthesis, cleavage, post-transcriptional modification and folding of ribosomal RNA (rRNA), and the translation, post-translational modification, folding and binding of approximately 50 ribosomal proteins (r-proteins). 16  Ribosome biogenesis is energetically costly, with the majority of cellular transcription and translational capacity dedicated to the production of new ribosomes.   This process is both rapid, requiring ∼2 minutes for production of a single ribosome, and efficient, with the vast majority of assembly events resulting in mature, translationally active complexes. The assembly of ribosomes is tightly regulated in a growth-rate–dependent manner primarily at the level of rRNA synthesis 7


In the last step of the gene expression pathway, genomic information encoded in messenger RNAs is translated into protein by a ribonucleoprotein called the ribosome.
The bacterial ribosome is an extremely complex macromolecular machine capable of performing a fundamental and instrumental cellular process, protein translation. The ribosome comprises two ribonucleoprotein subunits.

Translation through ribosomes,  amazing nano machines WUmFJSIl
This is a 3D computer graphic model of a ribosome.
Ribosomes are composed of protein and RNA. They consist of subunits that fit together and work as one to translate mRNA (messenger RNA) into a polypeptide chain during protein synthesis (translation).

The ribosome is an essential ribonucleoprotein enzyme, and its biogenesis is a fundamental process in all living cells. 1  

Ongoing investigations are focused on elucidating the cellular processes that facilitate biogenesis of the ribosomal subunits, and many extraribosomal factors, including modification enzymes, remodelling enzymes and GTPases, are being uncovered.

The large, or 50S, subunit, which is responsible for the catalysis of peptide bonds linking the amino acid building blocks of protein, contains two RNA molecules, 23S and 5S, as well as 34 ribosomal proteins (r-proteins).

The small, or 30S, subunit (SSU) contains a 16S RNA molecule and 21 r-proteins and is the site of mRNA decoding.

Translation through ribosomes,  amazing nano machines 95RPuilm

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. 3
It is composed of 3045 nucleotides and 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure.

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The tertiary and secondary structures of the RNA in the H. marismortui large ribosomal subunit and its domains. 

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Large-subunit proteins from Haloarcula marismortui

Structure of the 30S ribosomal subunit
Protein synthesis is a complex, multistep process that requires, in addition to the ribosome, several extrinsic GTP-hydrolysing protein factors during each of the main stages of initiation, elongation and termination. The 30S ribosomal subunit has a crucial role in decoding mRNA by monitoring base pairing between the codon on mRNA and the anticodon on transfer RNA; the 50S subunit catalyses peptide bond formation. 4

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Overview of the 30S structure

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Structure and dynamics of bacterial ribosome biogenesis
The assembly and maturation of the ribosomal subunits are very complex and involve a series of events, such as processing and modification of rRNA, ordered binding of ribosomal proteins and metal ions, and sequential conformational changes. In vivo, this takes approximately 2 min at 37°C 5

The bacterial ribosome consists of three rRNA molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. Formation of the ribosomal particle involves a complex series of processes, i.e., synthesis, processing and modification of both rRNA and ribosomal proteins, and assembly of the components. The quality of the particle must also be checked and the amount of active ribosomes monitored. All of these events must be tightly regulated and coordinated to avoid energy losses and imbalances in cell physiology. 5

The small subunit, 30S, is made of 16S rRNA (1,542 nucleotides) and 21 ribosomal proteins (r-proteins), while 
the large subunit,  50S, is composed of two rRNAs, 23S (2,904 nt) and 5S (120 nt) rRNA, and 33 proteins. 

Nucleolytic processing of rRNA

Translation through ribosomes,  amazing nano machines Schema10
Schematic drawing of the rrnB operon.
(A) Nucleolytic processing of the rrnB primary transcript. The rRNA and tRNA species, promoters P1 and P2, and terminators T1 and T2 are indicated, as well as the processing sites of RNase III (III), RNase G (G), RNase E (E), RNase P (P), RNase T (T), and the unknown RNases (?).
(B) Promoter region of the rrnB operon. Locations of FIS- and H-NS-binding sites and the UP, discriminator, and nut sequences are marked. Arrows show the start sites of transcription.

The biogenesis of ribosomes begins with transcription of the 16S, 23S, and 5S rRNA, which are synthesized as one primary transcript (Figure above A). Maturation of the transcript begins before transcription is completed, with instant formation of local secondary structures and, as soon as their binding sites emerge from the polymerase, binding of ribosomal proteins. Simultaneously, rRNA becomes chemically modified at a number of positions and is processed by several RNases to generate mature rRNA species.

After the ribosome structures: How are the subunits assembled?
As if the intricacy of the RNA fold in the ribosome was not overwhelming enough, we are left to grapple with the question “By Jove, how does this thing get put together?” There is a vast amount of information concerning bacterial ribosome assembly. 6

Ribosome biogenesis in Escherichia coli begins with transcription of the ribosomal RNA operon, where the three ribosomal RNAs are synthesized as a single transcript. The subsequent steps surely begin before the entire transcript is completed. It is likely that extensive local secondary structure in the rRNA forms very quickly, and that ribosomal protein binding begins as the protein binding sites are completed. The rRNA transcript is chemically modified at a number of points, and it is processed by nucleolytic cleavage to ultimately generate the 16S, 23S, and 5S chains. 

The assembly process is a carefully choreographed series of RNA conformational changes, protein binding, ion binding, and processing events that occurs cotranscriptionally.

Bacterial ribosome biogenesis has been an active area of research for more than 30 years. Prokaryotic ribosome synthesis is a complex, multistep process requiring the coordinated synthesis, cleavage, post-transcriptional modification and folding of ribosomal RNA (rRNA), and the translation, post-translational modification, folding and binding of approximately 50 ribosomal proteins (r-proteins). Ribosome biogenesis is energetically costly, with the majority of cellular transcription and translational capacity dedicated to the production of new ribosomes. This process is both rapid, requiring 2 minutes for production of a single ribosome, and efficient, with the vast majority of assembly events resulting in mature, translationally active complexes. The assembly of ribosomes is tightly regulated in a growth-rate–dependent manner primarily at the level of rRNA synthesis, which, in turn, regulates r-protein synthesis through an elegant autoregulatory feedback translational control mechanism that prevents the r-proteins’ levels from exceeding the availability of rRNA. The net effect of this network of regulatory mechanisms is a linear relationship between cellular growth rate and ribosomal content that optimally allocates the proteome between catabolic enzymes that produce amino acids and ribosomes that convert these precursors into new biomass.

A co-transcriptional assembly process 
Despite the central cellular role of ribosome assembly in cell physiology and decades of study, the details of ribosome biogenesis are only beginning to emerge. There has been a trade-off between the detailed studies that can be accomplished by studying assembly in vitro, and less precise but more biologically relevant studies that can be carried out in cells. The primary difference between the in vitro and in vivo studies is the co-transcriptional assembly of rRNA that occurs in cells. Direct evidence for co-transcriptional assembly arose from observation of ultrastructure in the rRNA operons, known as ‘Miller spreads’. Miller found that gently fixing the chromatin of rapidly growing cells cross-linked the RNA polymerase (RNAP) and nascent rRNA transcripts, and that these preparations could be visualized by negative stain electron microscopy (EM), as shown in figure below. 

Translation through ribosomes,  amazing nano machines WLavqqkh
Co-transcriptional assembly of ribosomes in the E. coli ribosomal RNA operon. 
The negative-stain electron micrograph of fixed chromatin shows the high transcriptional level of the ribosomal operon, where over a hundred RNAP molecules can be seen over the 5.5 kb segment. The organization of the rRNA genes is shown below, where the primary rRNA precursor transcript is processed by a series of endonucleolytic cleavage reactions to produce the mature 16S, 23S and 5S rRNAs. The series of increasingly long nascent transcripts can be seen progressing from left to right, with evidence for co-transcriptional binding of ribosomal proteins. In addition, co-transcriptional rRNA processing is observed, indicated by the arrow, which liberates a pre-30S ribonucleoprotein complex prior to initiating the transcription of the 23S rRNA gene.

These images revealed high packing density of RNAP on the rRNA gene with clear evidence for association of additional protein components to the nascent rRNA as the polymerase moved through the operon. Furthermore, a discrete transition from long to short nascent chains at the approximate position of the 30 -terminus of the 16S rRNA coding region provided strong evidence for co-transcriptional rRNA cleavage and release of a 30S precursor early during transcription of the pre-23S rRNA (figure above ).

Assembly guided by RNA folding 
The assembly of the small ribosomal subunit (SSU) requires RNA folding and compaction, which occurs through both r-protein-dependent and independent events.   Ribosome assembly is effectively an RNA folding problem, wherein proteins are used to ‘lock in’ productive RNA folding and drive the structure towards its mature conformation. Much of the native rRNA secondary structure is formed in a protein-independent manner, whereas native tertiary rRNA contacts are often stabilized through protein-binding events.

In vitro ribosomal protein assembly maps 
Despite the highly complex and co-transcriptional nature of the assembly process, active subunits can be reconstituted in vitro using purified r-proteins and rRNA. While these in vitro assembly reactions are generally less efficient than the process in vivo, the success of in vitro assembly implies that the folding determinants are primarily encoded in the ribosomal components themselves. Extensive in vitro reconstitution experiments directly tested the interdependence of r-protein binding. By withholding specific r-proteins, they could classify the r-proteins into groups that bound to rRNA independently (primary binders) and those whose binding was improved by the addition of other r-proteins (secondary binders). These distinct protein-binding classes were the first evidence that ribosome assembly consists both of sequential and parallel processing steps.

The role of ribosome biogenesis factors 
Dozens of accessory biogenesis factors help guide the assembly process, including GTPases, rRNA modification enzymes, helicases and other maturation factors.

These are basically molecular machines required and helping the assembly of the Ribosome factory. These enzymes, evidently, would have no function unless the higher goal, that is to make functional ribosomes, is foreseen as a distant goal. 

Interestingly, many ribosome assembly factors indicate that redundant factors are present or that they are only necessary under particular environmental conditions like cold-stress.

Structure and composition of assembly intermediates 

Translation through ribosomes,  amazing nano machines DRNCXTrh
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Cooperative folding blocks of the bacterial large (LSU) and small (SSU) ribosomal subunits
(a) Heatmap of median folding block occupancy in various published SSU assembly intermediate structures. Blocks 1 – 4 were derived from hierarchical clustering of the calculated occupancy for each r-protein or rRNA helix across the set of available SSU assembly intermediate structures. 
(b) 16S secondary structure coloured and labelled by domain. Folding blocks as defined by hierarchical clustering in the electronic supplementary material, figure S1, are outlined and coloured according to (a). 
(c) SSU structure model (PDB: 4ybb) with blocks labelled and coloured according to (a). 
(d) Heatmap of median folding block occupancy in various published LSU assembly intermediate structures. Blocks 1 – 6 were derived from hierarchical clustering as in (a) using the set of available LSU assembly intermediate structures (electronic supplementary material, figure S2). 
(e) 23S secondary structure coloured and labelled by domain and folding blocks as in (b). (f ) LSU structure model (PDB: 4ybb) with blocks labelled and coloured according to (d).

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Bringing the maturation of ribosomal subunits into focus.
Illustrated are the biogenesis pathways of the functional bacterial ribosomal subunits 30S; RNA colored gray and r-proteins colored blue) and 50S  RNA colored gray and r-proteins colored purple). The biogenesis of these subunits commences with transcription of primary rRNA transcripts, which contain 16S, 23S and 5S rRNA sequences and intervening sequences, and proceeds through a series of ill-defined stages. Although a precise X-ray crystal structure of the ribosomal subunits has been solved, the cellular processes involved in ribosome maturation (presented within the gray box) remain incompletely understood. It is known that an array of ribosomal biogenesis factors facilitates processes through a coordinated series of maturation events. Some of these factors are listed in the middle of the gray box, but the temporal aspects of their function have not been resolved. Elucidating a more complete understanding of the specific processes involved in the biogenesis of ribosomes remains a formidable challenge in the field but would result in a lessening of the ‘gray haze’ overlaying the biogenesis cascade at this time.

Translation through ribosomes,  amazing nano machines Pre-rr10
Translation through ribosomes,  amazing nano machines Pre-rr11
. (A) Pre-rRNA processing scheme in Saccharomyces cerevisiae. (B) Pre-rRNA processing scheme in HeLa cells.

Translation through ribosomes,  amazing nano machines _pre-r10
Pre-ribosomal particles along the 40S assembly pathway. 
The major intermediates of 40S pre-ribosomes, their rRNA content (dark green) and the presence of ATP/GTPconsuming enzymes are depicted (DExD/H-box ATPases in green, kinases in light blue, GTPase in orange). The nascent 35S pre-rRNA is modified and folded to form a first precursor of the 40S subunit. The cleavages at site A0, A1, A2, which generate the 20S pre-rRNA, are accompanied by a major exchange of non-ribosomal factors. The formation of the beak and final 20S processing occurs in the cytoplasm. 7

Translation through ribosomes,  amazing nano machines _pre-r11
Pre-ribosomal particles along the 60S assembly pathway. 
The different 60S pre-ribosomes are depicted together with their rRNA content (blue). The presence of ATP/GTPconsuming enzymes (GTPases in orange, DExD/H-box ATPases in green, AAA-type ATPases in pink), prominent subcomplexes (purple/yellow), and export factors (red) is shown. Bait proteins purifying the corresponding, distinct particles are indicated on top.

“a multitude of transient assembly factors” regulate and systematically fold the proteins that will be used to construct the machine. The authors mention “21 ribosome assembly factors that stabilize and remodel” the RNA and proteins before the machine is even operational. Inside the growing ribosome, a scaffold holds factors for the exit tunnel in place. Everything is choreographed in time and space with “mechanisms driving… assembly in a unidirectional manner.”

Here we see numerous parts working together on a timeline. The parts alone do not work individually. You can have all the proteins delivered to the construction site, and nothing will happen without the programmed mechanisms to put them together in order. Some parts hold others in place, others guide the folding of protein parts, and some even prevent premature assembly. All the pathways for assembly of the subdomains are regulated by a master program, so that each group of steps follows a “unidirectional” plan toward the finished product.
https://evolutionnews.org/2018/03/irreducible-complexity-in-molecular-machine-assembly/




1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711711/
2. https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2016.0181
3. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/10937989/
4. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/11014182/
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168646/
6. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/12554857/
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311925/
8. https://www.nature.com/articles/nrmicro.2016.200
7. https://sci-hub.tw/https://www.sciencedirect.com/science/article/pii/S0167488909002651?via%3Dihub



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The ribosome is a vital machine in every cell. It is stunning in the details required to make this machine. I like the insight gained through new research. When it is made "It doesn't just go plop". It is a multistep process requiring perfect precision and timing.
Not something unintelligent processes can produce!!
Again glory to God for life!!

"The synthesis of ribosomes is therefore an extremely complex, multistep process, which includes both assembly and maturation stages."

"The "emergence" of the 40S subunit entails an ordered series of reactions in which the outer shell of the 90S particle is progressively dissociated from the 40S. "It doesn't just go plop," Beckmann remarks. The process is actually reminiscent of the molting of an insect—shedding of the integument takes place layer by layer. "It's rather like those Russian dolls. When you open one, you find a smaller one nestled inside," says Beckmann"

https://phys.org/news/2020-09-ribosomes-russian-dolls.html?fbclid=IwAR0YcGlXqObFJAO3_RGxFNUIx271iXe43ljT4gPx-AhBqq2UxIWjbPWbvxc


Ribosome Biogenesis in Eukaryotes
Eukaryotic ribosomes are the 80S ribosomes, consisting of 60S large subunit and 40S small subunit. The large subunit consists of three types of rRNAs (25S in plants or 28S in mammals, 5.8S, and 5S) and about 47 ribosomal proteins. The small subunit consists of one rRNA (18S) and about 33 ribosomal proteins.

Ribosome Biogenesis in Prokaryotes
70S ribosomes, which consist of 50S large and 30S small subunits, are prokaryotic ribosomes. The large subunit consists of two types of rRNAs (23S and 5S) and 33 ribosomal proteins. The small subunit consists of only 16S rRNA and 20 ribosomal proteins.

52 genes of the prokaryotic genome encode the ribosomal proteins. They belong to 20 different operons. Transcription of the ribosome gene operons occurs in the cytoplasm. The synthesis of ribosomal proteins as well as the assembly of large and small subunits of the ribosome occurs in the cytoplasm in prokaryotes.

Epigenetic control of ribosome biogenesis homeostasis 2


1. https://pediaa.com/what-cellular-structure-is-responsible-for-manufacturing-ribosomes/
2. https://tel.archives-ouvertes.fr/tel-01878354/document



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19Translation through ribosomes,  amazing nano machines Empty Driving ribosome assembly on Sat Jul 18, 2020 7:43 am

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Driving ribosome assembly

The ribosome is a complex molecular machine that is composed of a small 40S and large 60S subunit. Despite their conserved molecular function, eukaryotic and prokaryotic ribosomal subunits differ significantly in size and complexity. Ribosome biogenesis faces the challenge to coordinate the processing and modification of ribosomal RNA (rRNA) with its correct structural assembly with ribosomal proteins (RP). Furthermore, this process has to be regulated according to the cellular environment, hence ribosome biogenesis is tightly coupled to growth rate: actively dividing cells, including cancer cells, depend on active ribosome biogenesis, whereas arrested or starving cells halt the production of new ribosomal subunits. Due to its easy experimental accessibility by genetic, biochemical, and cell biological methods, S. cerevisiae represents a suitable eukaryotic model organism to study ribosome assembly and the function of non-ribosomal factors. Over the past 20 years, it has been shown that a large number of non-ribosomal factors (N 200) and snoRNAs (75) are involved in ribosome assembly.  pre-ribosomal particles along their maturation path are also involved. The current challenge is to identify direct interaction partners of individual proteins and obtain structural information of single proteins and pre-ribosomal particles. 1

In eukaryotic cells, ribosomes are preassembled in the nucleus and exported to the cytoplasm where they undergo final maturation. This involves the release of trans-acting shuttling factors, transport factors, incorporation of the remaining ribosomal proteins, and final rRNA processing steps. Recent work, especially on the large (60S) ribosomal subunit, has made it abundantly clear that the 60S subunit is exported from the nucleus in a functionally inactive state. Its arrival in the cytoplasm triggers events that render it translationally competent. Here we focus on these cytoplasmic maturation events and speculate about why eukaryotic cells have evolved such an elaborate pathway of maturation.

The biogenesis of ribosomal subunits –“state of the art”
In all living cells, the ribosome is responsible for the final step of decoding genetic information into proteins. This universal “translating apparatus” comprises two subunits, each of which is a complex assemblage of RNA and proteins (. The two subunits display a distinct division of labor: the small 40S subunit (30S in prokaryotes) is responsible for decoding whereas the large 60S subunit (50S in prokaryotes) carries out the chemistry of polypeptide synthesis.  How do cells assemble such an intricate machine and ensure that it functions faithfully in the critical role of decoding a cell’s genome?  2

Ribosome biogenesis begins with transcription of the pre-rRNA, which undergoes co-transcriptional folding, modification, and assembly with ribosomal proteins (r-proteins) to form the two subunits. The assembly of ribosomal subunits in bacteria appears to require few (<25) trans-acting factors. By contrast, eukaryotic ribosome assembly is a complicated process that requires the concerted efforts of all three RNA polymerases and >200 trans-acting factors, that aid the assembly, maturation and intracellular transport of ribosomal subunits.

Eukaryotic ribosomes are initially assembled in the nucleolus, the site of rRNA transcription. Although the nascent pre-ribosomal particles released from the nucleolus appear to be largely preassembled, they require additional maturation steps in the nucleoplasm and/or cytoplasm. The pre-ribosome, the 90S particle, is subsequently processed to yield smaller 66S and 43S particles, the precursors to the mature 60S and 40S subunits, respectively. These particles contain pre-rRNA, r-proteins, and numerous trans-acting factors. There are multiple trans-acting factors.



1. https://sci-hub.tw/https://www.sciencedirect.com/science/article/pii/S0167488909002651?via%3Dihub
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866757/#:~:text=In%20eukaryotic%20cells%20ribosomes%20are,and%20final%20rRNA%20processing%20steps.

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Amino Esters and Ribosomes
DNA’s four-character alphabet is used to compose the larger twenty-character alphabet of alpha-amino acids (α-amino acids). Life needs this collection of twenty building blocks, each distinct, to make a protein. These building blocks must react with each other to form specific chemical connections called peptide bonds. Chemists have learned to use this reaction to make polymers like nylon, for which they used H2N- (CH2)6-COOH molecules as the specific building blocks. The reaction occurs without much guidance because NH2 has no option but to react with COOH. It’s much more complicated for proteins, however, since α-amino acids have twenty different side chains (called “R groups”; attached to their backbones. Each protein is a polymer, a chain made of many subunits linked together like nylon, but composed of amino acids. But the amino acid R groups pose a serious problem for protein synthesis, because they can react favorably with both themselves and the COOH and NH2 groups of the other α-amino acids. The desired peptide reactions, on the other hand, are usually unfavorable, requiring a positive change in free energy. All the other viable side reactions will interfere with the formation of a protein polymer. So how does life get around this severe competition problem? Life relies on a chemical trick often used in synthetic chemistry: derivatization. Ribosomes are large multimolecular machines that synthesize proteins from amino acids in living cells. But before going to ribosomes, each α-amino acid is converted into an amino ester, a process called “derivatization,” and attached to a “transfer RNA” (tRNA) by an enzyme called a t-RNA synthetase. There are distinct tRNAs and tRNA synthetases for each amino acid. Competition from energetically more favorable R-with-R or even R-with-NH2 or R-with-COOH reactions would be fatal to protein synthesis if it were not for the ribosome. Here’s what happens during the process of translation, as α-amino acids get attached to their specific t-RNA by their specific t-RNA synthetases. In a very elegant and ingenious process, amino esters are first phosphorylated by ATP and then, via a trans-esterification reaction, a t-RNA linked amino ester is formed. To ensure the desirable NH2-with-COOH reaction takes place, the amino acids are first esterified (which makes the chemical bond easier to form), then brought together by the mechanical hands of a ribosome, holding them in the correct position to prevent competing R reactions from taking place, and providing the necessary energy for the bond to form. Again, this ribosome-driven reaction does not seem to be an advantage that life could acquire little by little, by trial and error. Chemically, it is impossible to produce a functional protein without ribosomes that have already solved the competing reaction problem, or without the collection of twenty specific tRNAs and tRNA synthetases that would feed it with amino esters. As in so many other cases with the cell and its code, if this need is not foreseen and planned for, there will be no cell at all.

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21Translation through ribosomes,  amazing nano machines Empty Nervous-Like Circuits in the Ribosome on Tue Aug 18, 2020 7:32 pm

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Nervous-Like Circuits in the Ribosome

In the past few decades, studies on translation have converged towards the metaphor of a “ribosome nanomachine”;. Many studies have shown that to perform an accurate protein synthesis in a fluctuating cellular environment, ribosomes sense, transfer information, and even make decisions. This complex “behavior” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. We analyze here the significance of this analogy and establish a preliminary link between two fields: ribosome structure-function studies and the analysis of information processing systems. This cross-disciplinary analysis opens new perspectives about the mechanisms of information transfer and processing in ribosomes and may provide new conceptual frameworks for the understanding of the behaviors of unicellular organisms.

Proteins may constitute computational elements in cells. In unicellular organisms, protein-based circuits act in place of a nervous system to control the behavior. Because of the high degree of interconnection, systems of interacting proteins act as neural networks trained to respond appropriately to patterns of extracellular stimuli.  The recent analysis of r-protein networks in the ribosomes of the three kingdoms updates and further enhances this intriguing hypothesis. R-protein networks form complex circuits that differ from most known protein networks, in that they remain physically interconnected. These networks display some features of communication networks and an intriguing functional analogy with sensory-motor circuits found in simple organisms. These networks may play at a molecular scale, a role analogous to a sensory-motor nervous system, to assist and synchronize protein biosynthesis during translation. However, we must be aware that the nerve circuits do not have exactly the same properties that the ribosomal proteins circuits have, even in simple organisms having the most primitive nervous systems that are known.

Many of the ribosome functional properties go far beyond the skills of a simple mechanical machine.

Many experimental studies have shown that—as well summarized in the title of paper of Rhodin and Dinman—“an extensive network of information flow” through the ribosome during protein biosynthesis. First, growing evidence indicates that ribosome functional sites (RNA binding sites, decoding centre, peptidyl transferase centre (PTC), peptide exit tunnel) continually exchange and integrate information during the various steps of translation. For example, an allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. In addition, the overall ribosome dynamics are modulated by the three tRNA site occupancies and their aminoacylation status. Additionally, several studies have demonstrated long-range signaling between the decoding centre that monitors the correct geometry of the codon-anticodon and other distant sites such as the Sarcin Ricin Loop (SRL) or the E-tRNA site [16,17]. The peptidyl transferase centre (PTC), the large-subunit rRNA active site where peptide bond formation is catalyzed, is also a key node of allosteric communication. PTC and the A-site communicate and are coordinated through the universal protein uL3. Moreover, specific r-proteins of the ribosomal tunnel play an active role in the translation regulation or co-translational folding by sensing the nature of the nascent peptide and communicating to the PTC or the exit sites. In addition, recent studies have extended the scope of ribosome sensing systems to a higher level in describing the molecular mechanisms of a quality sensor of collided ribosomes in eukaryotes and showed that sensing may also involve higher-order ribosome architectures to monitor the translation status.

Ribosome Choreography during Protein Biosynthesis
Second, to perform the biosynthesis of proteins, the ribosome must synchronize extremely complex movements by combining small and large-scale motions such as the ratchet-like motion between the two subunits. More than 21 hinges have been identified within the rRNAs for accomplishing independent unit motions in bacterial ribosome. Could Brownian molecular motions be efficient and fast for a system with so many freedom degrees without control? Brownian motion is convincingly suggested to be at the ambient origin of the process driving the basic motions of the ribosome, then rotation and elongation can be thermally driven. It has also been suggested that an out of equilibrium stochastic process, a variant of Totally Asymmetric Exclusion Process (TASEP), can describe approximately the basic sequence of ribosome’s movements. However, this sequence is certainly of a more elaborate nature than a pure TASEP, needing the intervention of external factors for regulation and also an internal control and adaptation, probably helped by the rRNA, mRNA, tRNA and the r-proteins. Interestingly, remote communication processes have been recently shown to participate in the coordination of complex ribosomal movements during translation, thus suggesting that ribosomal motions may be helped by external synchronization systems.

How information transit between distant functional sites and how this information is integrated and processed to enable an optimized ribosome activity in a fluctuating cellular environment remains one of the major challenges in the research on the ribosome. Many studies have already addressed this question and revealed that long-range communication occurs in the ribosome and perform information transfer between remote functional sites. This allosteric communication has been shown to either involve rRNA or r-proteins. However, the vocabulary frequently used in these recent studies implicitly reveals the limits of the machine metaphor: “Sensing”, “communicating” and even “taking decisions” are indeed generally employed for describing autonomous organisms and are rarely used for a machine.

In view of the extraordinary ribosome properties, it could be asked today if the ribosome is a device, an “intelligent machine”, a “Turing machine” or just an organism instead of an organelle? The later view implies that the ribosome has autonomous “behaviour” in the cell and is fully adapted to perform translation in a fluctuating cellular context. This apparently naïve view has two hypothetical implications. First, it infers that the “ribosome behaviour” would be supported by the equivalent of a nervous system at a molecular scale. Second, in an evolutionary point of view, it would lead to generalizing the concept of a “primordial endosymbiosis” to an early prokaryotic cellular origin. This view fits well with recent papers that propose that the ribosome is a self-replicating intermediate between the RNA world and cellular life and may constitute a missing link in the evolution of life. These papers have shown indeed that the rRNA contains genetic information that encodes the self-replication machinery, all tRNAs and key ribosomal proteins. Thus, similar to the mitochondria endosymbiosis in eukaryotic cells, RNA/protein organisms like the ribosomes may have joined the cytoplasm of a primitive prokaryotic cell. Cells would have subsequently evolved to protect and optimize pre-existing functions.

My comment: How could ribosomes have joined the cytoplasm of a primitive prokaryotic cell, if prokaryotic cells need the very own ribosome in order to live? 

Our recent analysis of r-proteins networks formed by tiny but highly conserved contacts between r-protein extensions noticed an intriguing analogy of these networks with nervous circuits . This study proposed that in addition to the previously well-described allosteric mechanisms, r-protein networks could also contribute to transfer and process the “information flow” during translation. This provided an integrated framework that could be based, at least in part, on graph theory, to investigate information transfer and processing in the whole ribosome. 

D. Bray explicitly suggested the “neuron-protein equivalence” in protein circuits. Following Bray’s metaphor, r-proteins may be functionally comparable to neurons and their networks should, therefore, form nervous-like circuits able to transfer and process information at a molecular scale. We examined here this hypothesis knowing that if a protein behaves like a neuron at a molecular scale, it should have properties similar to a neuron: sensing, transferring and integrating information. R-protein networks would be also expected to display some similarities with an interacting ensemble of nervous circuits systems. We explore these analogies to evaluate their significance and their heuristic power in the understanding of the ribosome’s behaviour.

In fact, the metaphor is perhaps more appropriate and precise with the substructures of a central nervous system CNS, for instance, a collection of neuronal areas. This is indicated in particular by eukaryotic ribosomes: although there is a multiplication by ten of the number of bases in rRNA between C. elegans and primates and a corresponding growing complexity of the elements of the proteins, there are no noticeable changes of their r-protein networks. In comparison, the graph of the neuronal networks becomes more and more complex, the numbers of neurons and of their mutual connexions explode. However, in vertebrates, for instance, the whole plan of the CNS is relatively stable. Thus, a better analogy seems to occur between the r-proteins network and interconnected areas of the nervous central system (CNS). The neuronal assemblies become more complex as the individual proteins and their contacts do.

Many studies have already addressed this question and revealed that long-range communication occurs in the ribosome and perform information transfer between remote functional sites. This allosteric communication has been shown to either involve rRNA or r-proteins. However, the vocabulary frequently used in these recent studies implicitly reveals the limits of the machine metaphor: “Sensing”, “communicating” and even “taking decisions”

In the ribosome, the structural and functional organizations of the individual r-proteins suggest a close analogy with neurons in both the structural and functional points of view. Most ribosomal proteins are composed of a globular domain that is located at the surface of the ribosomal subunits and long filamentous extensions that penetrate deeply into the rRNA core. Some r-proteins are devoted to forming tiny interactions with substrates or products within the ribosome functional sites. A current view is that these interactions contribute to stabilizing the mRNA or tRNA substrates in their correct positions.

Sensing the functional sites to monitor the presence, the sequence or the correct orientation of the substrate may be, therefore, generalized to all the ribosomal functional sites.

My comment: In order to monitor the system, the ribosome must have previous knowledge of what should be, compare to what is, and if the error is detected, be able to act accordingly. This requires foresight and knowledge. 

It has been previously noted that the r-proteins “innervate” all the functional sites in a manner similar to a nervous system. The functions of sensing and stabilizing the substrates are not incompatible and may have co-evolved gradually for optimizing ribosome accuracy. 

My comment: First of all, the origin of the ribosome is a problem of abiogenesis, not evolution. Secondly, how could the ribosome work properly if accuracy was not established right from the get go, with all 11 different error check-and repair mechanisms in place? 

Many structural features and the electrostatic nature of the interactions suggest that common electrostatic mechanisms enable them to sense the different actors of translation through transient tiny interactions. The ribosome actively participates with the correct tRNA selection through the decoding centre. However, in contrast to polymerases, the recognition site that monitors the correct codon-anticodon pairing is about 70 Å away from the PTC where the polymerization takes place. The two sites must, therefore, communicate to perform accurate protein synthesis. 

My comment: Had this communication not to be fully set up and functional right from the start, otherwise, the right tRNA selection would not be established, and the entire system would break down and be non-functional? 

During the first step of decoding, the aminoacyl-tRNAs are delivered to the ribosome in a ternary complex with EF-Tu and GTP. The correct codon recognition induces a conformation change in EF-Tu and triggers the GTP hydrolysis leading to the dissociation of the EF-Tu-GDP complex from the ribosome, thus, freeing the aa-tRNA to accommodate into the PTC.  16S rRNA bases A1492, A1493, G530 and C1518 directly monitor the correct geometry of the codon-anticodon helix formed between the mRNA and the A-tRNA. It has been shown that these rRNA bases relay global structural changes of the small subunit that occur in response to the binding of cognate anticodon stem-loops in the decoding centre. This produces a “closed state” of the small subunit that, in turn, activates the EF-Tu GTP hydrolysis. Both biochemical and structural studies have demonstrated that uS12, uS3 and the interaction between uS4 and uS5 also play a key role in this process. r-proteins closely approach the decoding centre through electrostatic interactions involving conserved amino acids. Their side chains may, therefore, sense and transmit the local structural and electrostatic changes associated with the correct tRNA-mRNA pairing.

Molecular Synapses and Wires
In addition to sensing and/or stabilizing the tRNAs and the nascent peptides in the functional sites, r-protein extensions are systematically involved in r-protein contacts and form complex networks. Most of the r-protein interactions display well-defined interfaces that remain stable once the mature ribosome structure has been formed. With an average area of 200 A2, which is too tiny to be rationalized in terms of dimer stabilization, these highly phylogenetically conserved interfaces have play a specific role in inter-protein communication. Their analysis revealed that most of them share aromatic and basic residues involved in cation-π interactions that were interpreted as the “necessary minimum for communication”.

Molecular Communication
How the information is distributed in the network and between functional sites still remains to be determined. In the “classic” allostery, locally induced conformational changes are propagated to remote protein sites and modulate their properties. Ribosome allostery has been well documented. There are many communication rRNA and r-protein pathways between remote ribosome functional sites.   

One of the best analogies between ribosomal networks and simple neuronal networks is their modular structure. Even in simple organisms, as tunicates having a few hundred neurons, but being close to the vertebrates, several distinct sensori-systems work together. A similar modular organization is observed in the r-protein networks. Figure 9 shows that in the bacterial ribosome, r-proteins are organized into a few interconnected sub-networks grouped around the functional sites: decoding centre, tRNA sites, factor binding, PTC and tunnel. This r-protein network organization, therefore, suggests that the r-proteins not only sense the functional sites but also collectively share the information that circulates during translation. It is likely that the information about the occupancy/orientation of substrates in the different functional sites is locally integrated into the sub-networks and then transmitted and processed between the different sub-networks

Allostery: How Cells Do Remote Control
https://evolutionnews.org/2020/08/allostery-how-cells-do-remote-control/
And yet the high-fidelity cooperative action between the RNA and protein parts in the ribosome require allostery over vast distances (on the cellular scale). This is astonishing. How can they believe this level of remote control just happened?

The size and complexity of its structure and the diversity of covalent and noncovalent interactions required to execute 10 to 20 translation cycles per second with high fidelity demand the coordinated interactions of bases that span more than 390,000 Å of molecular surface. But how does the ribosome actually work? How is molecular information transferred between functional centers? What are the allosteric pathways and conduits of communication, and how do specific residues in the structure contribute to this communication? In this work, we apply a global coevolution method (SCA) to show that, despite differences in fundamental chemistry, RNA and protein appear to use a common logic of interaction and assembly.

Assembly! It’s not just the interaction to consider, but the assembly, too. The ribosome parts had to be translated first, and then the building blocks, consisting of two very different molecules (RNA and protein), have to be assembled to work. And that work involves remote controls, where “molecular information” is “transferred between functional centers” by means of “allosteric pathways and conduits of communication.” Those pathways, moreover, rely on “specific residues in the structure” that contribute to the communication. The authors are clearly in awe of what they are seeing. What does the talk about “co-evolution” contribute, other than fanciful storytelling? Let the “logic of interaction and assembly” speak for itself.


Translation through ribosomes,  amazing nano machines Riboso11

The possible communication pathways depicted by the blue, yellow and red arrays, between the functional sites within the r-protein network.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627100/



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Nervous-Like Circuits in the Ribosome come to light

1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.


Ribosomes have been called “intelligent machines”,  “Turing machines”, and "molecular factories". And a recent science paper, from 2019, has now even unraveled, that they contain nervous-like circuits. Ribosomes carefully sense, transfer, and process information, and amazingly, even make decisions. Ribosomal protein networks form complex circuits that differ from most known protein networks, in that they remain physically interconnected. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They have nodes of allosteric communication in a coordinated manner, remote communication processes, and information is integrated and processed to enable an optimized ribosome activity.  They, “Sense”, “communicate” and even “take decisions”. Isn't that awe-inspiring?  These networks are analogous with nervous circuits - the “neuron-protein equivalence” in protein circuits. They transfer and process information within itself at a molecular scale. These networks display some features of communication networks and an intriguing functional analogy with sensory-motor circuits found in simple organisms.  Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. Remarkably, they continually exchange and integrate information during the various steps of translation.

Through their superb integrated communication networks, ribosomes choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, which may also involve higher-order ribosome architectures, synchronize and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. A recent Science paper: The last universal common ancestor between ancient Earth chemistry and the onset of genetics, published: August 16, 2018, informed that: LUCA had a ribosome and had the genetic code. This means the origin of the Ribosome cannot be explained by Darwinian evolution. 1 No wonder, does science confess, as in this paper: The Double Life of Ribosomal Proteins, for example: The origins and evolutionary history of these polypeptides remain an enigma. 2 But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, during the creation week, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.  

More:
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#7900

A recent science paper, from 2019, has given further light in regards of how Ribosomes perform their life-essential tasks, translating the information from messenger RNA to amino acids.  Ribosomes masterfully sense, transfer information, and, awe-inspiringly, even make decisions. This complex “behavior” that goes far beyond the skills of a simple mechanical machine has suggested that the ribosomal protein networks could play a role equivalent to nervous circuits at a molecular scale to enable information transfer and processing during translation. 

Proteins may constitute ingenious computational elements in cells. In unicellular organisms, protein-based circuits act strikingly in place of a nervous system to control the behavior. Because of the high degree of interconnection, systems of interacting proteins act as neural networks trained to respond appropriately to patterns of extracellular stimuli.  The recent analysis of ribosomal proteins (r-protein) networks in the ribosomes of the three kingdoms updates and further enhances this intriguing hypothesis. R-protein networks form complex circuits that differ from most known protein networks, in that they remain physically interconnected. These networks display some features of communication networks and an intriguing functional analogy with sensory-motor circuits found in simple organisms. These networks may play at a molecular scale, a role analogous to a sensory-motor nervous system, to assist and synchronize protein biosynthesis during translation. 

Many of the ribosome functional properties go far beyond the skills of a simple mechanical machine.

There is a superb extensive network of information flow” through the ribosome during protein biosynthesis. Ribosome functional sites (RNA binding sites, decoding centre, peptidyl transferase centre (PTC), peptide exit tunnel) continually exchange and integrate information during the various steps of translation. Long-range signaling between the decoding centre that monitors the correct geometry of the codon-anticodon and other distant sites.  The peptidyl transferase centre (PTC), the large-subunit rRNA active site where peptide bond formation is catalyzed, is also a key node of allosteric communication. In addition, recent studies have extended the scope of ribosome sensing systems to a higher level in describing the molecular mechanisms of a quality sensor of collided ribosomes in eukaryotes and showed that sensing may also involve higher-order ribosome architectures to monitor the translation status.

Ribosome Choreography during Protein Biosynthesis
To perform the biosynthesis of proteins, the ribosome must synchronize extremely complex movements with exquisite precision, by combining small and large-scale motions such as the ratchet-like motion between the two subunits. More than 21 hinges have been identified within the rRNAs for accomplishing independent unit motions in bacterial ribosome. Could Brownian molecular motions be efficient and fast for a system with so many freedom degrees without control?  Interestingly, remote communication processes have been recently shown to participate in the coordination of complex ribosomal movements during translation, thus suggesting that ribosomal motions may be helped by external synchronization systems.

In view of the extraordinary ribosome properties, it could be asked today if the ribosome is a device, an “intelligent machine”, a “Turing machine” or just an organism instead of an organelle? The later view implies that the ribosome has autonomous “behavior” in the cell. This apparently naïve view has two hypothetical implications. First, it infers that the “ribosome behavior” would be supported by the equivalent of a nervous system at a molecular scale. Second, in an evolutionary point of view, it would lead to generalizing the concept of a “primordial endosymbiosis” to an early prokaryotic cellular origin. This view fits well with recent papers that propose that the ribosome is a self-replicating intermediate between the RNA world and cellular life and may constitute a missing link in the evolution of life. These papers have shown indeed that the rRNA contains genetic information that encodes the self-replication machinery, all tRNAs, and key ribosomal proteins. Thus, similar to the mitochondria endosymbiosis in eukaryotic cells, RNA/protein organisms like the ribosomes may have joined the cytoplasm of a primitive prokaryotic cell. Cells would have subsequently evolved to protect and optimize pre-existing functions.

My comment: How could ribosomes have joined the cytoplasm of a primitive prokaryotic cell, if prokaryotic cells need the very own ribosome in order to live? 

Our recent analysis of r-proteins networks formed by tiny but highly conserved contacts between r-protein extensions noticed an intriguing analogy of these networks with nervous circuits . This study proposed that in addition to the previously well-described allosteric mechanisms, r-protein networks could also contribute to transfer and process the “information flow” during translation. This provided an integrated framework that could be based, at least in part, on graph theory, to investigate information transfer and processing in the whole ribosome. 

D. Bray explicitly suggested the “neuron-protein equivalence” in protein circuits. Following Bray’s metaphor, r-proteins may be functionally comparable to neurons and their networks should, therefore, form nervous-like circuits able to transfer and process information at a molecular scale. We examined here this hypothesis knowing that if a protein behaves like a neuron at a molecular scale, it should have properties similar to a neuron: sensing, transferring and integrating information. R-protein networks would be also expected to display some similarities with an interacting ensemble of nervous circuits systems. We explore these analogies to evaluate their significance and their heuristic power in the understanding of the ribosome’s behavior.

In fact, the metaphor is perhaps more appropriate and precise with the substructures of a central nervous system CNS, for instance, a collection of neuronal areas. This is indicated in particular by eukaryotic ribosomes: although there is a multiplication by ten of the number of bases in rRNA between C. elegans and primates and a corresponding growing complexity of the elements of the proteins, there are no noticeable changes of their r-protein networks.  Sensing the functional sites to monitor the presence, the sequence, or the correct orientation of the substrate may be, therefore, generalized to all the ribosomal functional sites.

My comment: In order to monitor the system, the ribosome must have previous knowledge of what should be, compare to what is, and if the error is detected, be able to act accordingly. This requires foresight and knowledge. 

It has been previously noted that the r-proteins “innervate” all the functional sites in a manner similar to a nervous system. The functions of sensing and stabilizing the substrates are not incompatible and may have co-evolved gradually for optimizing ribosome accuracy. 

My comment: First of all, the origin of the ribosome is a problem of abiogenesis, not evolution. Secondly, how could the ribosome work properly if accuracy was not established right from the get-go, with all 11 different error check-and repair mechanisms in place? 

Many structural features and the electrostatic nature of the interactions suggest that common electrostatic mechanisms enable them to sense the different actors of translation through transient tiny interactions. The ribosome actively participates with the correct tRNA selection through the decoding centre. However, in contrast to polymerases, the recognition site that monitors the correct codon-anticodon pairing is about 70 Å away from the PTC where the polymerization takes place. The two sites must, therefore, communicate to perform accurate protein synthesis. 

My comment: Had this communication not to be fully set up and functional right from the start, otherwise, the right tRNA selection would not be established, and the entire system would break down and be non-functional? 

Molecular Synapses and Wires
In addition to sensing and/or stabilizing the tRNAs and the nascent peptides in the functional sites, r-protein extensions are systematically involved in r-protein contacts and form complex networks. Most of the r-protein interactions display well-defined interfaces that remain stable once the mature ribosome structure has been formed. With an average area of 200 A2, which is too tiny to be rationalized in terms of dimer stabilization, these highly phylogenetically conserved interfaces have play a specific role in inter-protein communication. Their analysis revealed that most of them share aromatic and basic residues involved in cation-π interactions that were interpreted as the “necessary minimum for communication”.

Molecular Communication
How the information is distributed in the network and between functional sites still remains to be determined. In the “classic” allostery, locally induced conformational changes are propagated to remote protein sites and modulate their properties. Ribosome allostery has been well documented. There are many communication rRNA and r-protein pathways between remote ribosome functional sites.   

One of the best analogies between ribosomal networks and simple neuronal networks is their modular structure. Even in simple organisms, as tunicates having a few hundred neurons, but being close to the vertebrates, several distinct sensory-systems works together. A similar modular organization is observed in the r-protein networks. Figure 9 shows that in the bacterial ribosome, r-proteins are organized into a few interconnected sub-networks grouped around the functional sites: decoding center, tRNA sites, factor binding, PTC, and tunnel. This r-protein network organization, therefore, suggests that the r-proteins not only sense the functional sites but also collectively share the information that circulates during translation. It is likely that the information about the occupancy/orientation of substrates in the different functional sites is locally integrated into the sub-networks and then transmitted and processed between the different sub-networks.


Question: How did this awe-inspiring macromolecular nanomachine come to be? Could it acquire its amazing functionalities little by little, by trial and error. ?  

1. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007518
2. https://www.cell.com/fulltext/S0092-8674(03)00804-3
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627100/

Translation through ribosomes,  amazing nano machines Riboso12



Last edited by Admin on Fri Sep 04, 2020 3:12 am; edited 3 times in total

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1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency. 

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. 

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder, does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

http://elshamah.heavenforum.com

Admin


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90S pre-ribosome transformation into the primordial 40S subunit

Production of small ribosomal subunits initially requires the formation of a 90S precursor followed by an enigmatic process of restructuring into the primordial pre-40S subunit. .

1. the remodeling RNA helicase Dhr1 engages the 90S pre-ribosome, followed by
2. Utp24 endonuclease–driven RNA cleavage at site A1, thereby
3. separating the 5′-external transcribed spacer (ETS) from 18S ribosomal RNA. Next,
4. the 5′-ETS and 90S assembly factors become dislodged, but this occurs sequentially, not en bloc.
5. Eventually, the primordial pre-40S emerges, still retaining some 90S factors including Dhr1, now ready to
6. unwind the final small nucleolar U3–18S RNA hybrid.

Our data shed light on the elusive 90S to pre-40S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins. The formation of eukaryotic ribosomes requires transcription, processing, and modification of ribosomal RNA (rRNA) and the integration of ~80 ribosomal proteins. This highly complex process starts in the nucleolus with the transcription of a large rRNA precursor (35S in yeast, 47S in human), which contains the 18S rRNA of the 40S small subunit and the 5.8S and 25S rRNAs of the 60S large subunit, separated by the internal transcribed spacers ITS1 and ITS2 and flanked by the external transcribed spacers 5′-ETS and 3′-ETS. During transcription of the 35S pre-rRNA by RNA polymerase I, the earliest stable assembly intermediate, called the 90S pre-ribosome or small subunit processome, forms. This comprises more than 50 assembly factors, the U3 small nucleolar ribonucleoprotein (U3 snoRNP), the nascent pre-rRNA, and dozens of the small subunit ribosomal proteins. In the subsequent maturation steps, coordinated endonucleolytic cleavage at site A1 within the 5′-ETS and at A2 within the ITS1 is key to the separation of the 18S rRNA and 5.8S/25S rRNA (Fig. 1A), 

Translation through ribosomes,  amazing nano machines Riboso14
Fig. 1. Pre-rRNA processing and purification of 90S to pre-40S transition intermediates. 
(A) Sequence of rRNA processing events during 40S biogenesis in yeast with A0, A1, A2, A3, and D as cleavage sites on the pre-rRNA. 
(B) Analysis of splittag (Noc4-TAP–Dhr1-Flag) affinity-purified assembly intermediates by sucrose gradient centrifugation, followed by SDS–polyacrylamide gel electrophoresis (PAGE) and Coomassie staining or Northern blotting, using the RNA probes a, b, and c to detect the various indicated pre-rRNA forms (23S, 21S, 20S, 5′-ETS-A0). 
(C) SDS-PAGE of sucrose gradient fractions containing the pre-40S and 90S intermediates, with ribosome assembly factors identified by mass spectrometry indicated (bait proteins in red, factors shared by pre-40S and 90S in blue). See fig. S1B for the whole sucrose gradient.

which then follow independent biogenesis pathways. The remaining 5′-ETS is degraded by RNA nucleases, including the nuclear exosome. The four subdomains of the 18S rRNA (5′, central, 3′ major, and 3′ minor)  fold independently and to associate with their set of early ribosomal proteins of the small subunit (S-proteins) cotranscriptionally, before integrating into the 90S pre-ribosome. This integration happens in a reverse order, in which the 3′ major and 3′ minor domains incorporate first, followed by the central and 5′ domain. Together with its numerous associated 90S assembly factors, which predominantly are organized in modules (e.g., UTP-A, UTP-B, UTP-C, U3 snoRNP, Mpp10 complex, Bms1-Rcl1 complex, Kre33 module, Noc4 module, Krr1-Faf1 complex), the 90S preribosome is fully assembled and primed for subsequent A1 cleavage. After this cleavage, the 90S pre-ribosome is transformed into a primordial pre-40S intermediate (a process hereafter referred to as 90S transition) by a still-elusive mechanism; only later pre-40S intermediates have been described so far. The early 90S transition was initially uncovered by biochemical studies of Enp1, a ribosome assembly factor that is present in both early 90S and late pre-40S intermediates. However, many additional proteins have since been suggested to be intimately involved in this transition. Candidate factors include the methyltransferase Dim1, the KH domain proteins Krr1 and Pno1 (previously called Dim2), RNA helicase Dhr1, and the nuclear RNA exosome system. To decipher the mechanisms of this transition, we aimed at a structural analysis of 90S transition intermediates by cryo-EM.

 90S to pre-40S transition
The Noc4- Dhr1 and Dhr1-Dim1 have seven well-defined and distinct classes of pre-ribosomal particles, which were put in a temporal order covering the 90S transition (Fig. 2).

Translation through ribosomes,  amazing nano machines Riboso15
Figure 2: Cryo-EM analysis of 90S to pre-40S transition intermediates. 
CryoEM maps (top) and molecular models (middle) of distinct states of yeast 90S to pre-40S transition observed after split-tag affinity purification using Noc4-Dhr1 (all states) and Dhr1-Dim1 (states B2, Post-A1, Dis-A, Dis-B, Dis-C) are shown. Assembly factors and modules are labeled and compositional changes indicated. Bottom: Depiction of pre-18S rRNA density using 90S views with corresponding rRNA secondary structures; 40S views are shown in boxes (color code: magenta, 5′ domain; orange, central domain; cyan, 3′ major domain; green, 3′ minor domain).

These states are called B2, Pre-A1, Post-A1, and Dis-C. There are other three states :A, Dis-A, and Dis-B) permit rigid-body docking of molecular models (Fig. 2, figs. S2 to S6, and table S1). The first two particles in this series, states A and B2, closely resemble previously described 90S assembly intermediates, with a noncleaved A1 site as a characteristic feature (Fig. 2 and fig. S6). In the next state, Pre-A1, which is the last state preceding A1 processing, we observed the integration of helix 21 (h21) of the pre-18S rRNA at its mature position (Fig. 2 and fig. S6). Subsequently and concomitant with cleavage at site A1, major structural changes lead to the Post-A1 intermediate. Specifically, Pno1, together with h45 of the 18S rRNA, replaces the Krr1-Faf1 complex, bringing h45 from a peripheral to an integrated mature position. Furthermore, the remodeling helicase Dhr1 is observed for the first time in this post-A1 state intermediate, positioned at the site vacated by Pno1 (Fig. 2 and fig. S6). The succeeding group of intermediates comprises states Dis-A, Dis-B, and Dis-C (where Dis stands for dissociation), which represent the actual 90S to pre-40S transition intermediate states. Unexpectedly, the canonical pre-40S is not released as a whole entity after A1 cleavage by leaving a presumed 5′-ETS particle behind. Instead, several prominent 90S assembly factor modules dissociate one after the other, leading to a progressive simplification of these complexes (Fig. 2 and fig. S6). The last state of this series, Dis-C, after ultimately losing the conspicuous UTP-B module, resembles a 40S shape for the first time, clearly displaying the 5′, central (platform), and flexible and immature 3′ major and 3′ minor domains. Here, the characteristic h44 of the 3′ minor domain, which in preceding states is held in a defined immature position by UTP-B and UTP-C, is mostly delocalized. This is because the immature conformation is no longer stabilized by the 90S modules, and the mature position is still masked by the Bms1-Rcl1 complex (Fig. 2 and fig. S6). Conformational changes and mechanism of A1 cleavage In contrast to the expected en bloc release of a 5′-ETS particle upon A1 cleavage, we observed that the 5′-ETS RNA becomes increasingly disordered during a stepwise 90S transition. Helix H9 at the 3′ end of the 5′-ETS is the first to become detached from Utp20 (fig. S7, A to F). Next, after A1 cleavage, other prominent 5′-ETS helices (H3 to H8) disappear, leaving behind empty cavities in this part of the 90S intermediate (Fig. 3A and fig. S7, A to C). 

Translation through ribosomes,  amazing nano machines Riboso16
Fig. 3. Conformational, positional, and compositional changes upon A1 cleavage. 
(A and B) Dismantling of 5′-ETS RNA helices (yellow) from Pre-A1 (A) and Post-A1 (B) is shown with interacting U3 snoRNA (green) in transparent 90S density. The secondary structure of the 5′-ETS RNA is shown with observed helices in yellow and the dislodged helices in gray. (C and D) Volume representation of Utp20, the Kre33 module, and the 5′ and central domains of the 18S pre-RNA highlights the compaction from state Pre-A1 (C) to Post-A1 (D). Dashed lines indicate the movement of Utp20. (E and F) Model of the h1 region of the 18S pre-rRNA aligned at Utp24 shown before (E) and after (F) A1 cleavage. The catalytic center of Utp24 and the A1 cleavage site are indicated by dashed circles. (G) Differences in the 18S central domain region are highlighted in states Pre-A1 and Post-A1. (H) Ribbon representation of the platform region in state Post-A1. Nucleotides 1021 to 1025 of
the 18S rRNA are shown in magenta. (I) Model of Dim1 bound to its substrate adenosine 1782 of the pre-18S in state Post-A1. (J) Model of Pno1 in state Post-A1 with the 3′ end of the 18S pre-rRNA and interacting segments of Mpp10, Utp7, Utp14, and Utp21. (K and L) Models of yeast and human Pno1 bound to Utp14 (K) and NOB1 [(L), PDB ID 6G18], respectively, highlight overlapping interaction sites. Key residues are shown as sticks. (M) Ribbon representation showing the interaction of Dhr1 with Utp21 and Utp13 in state Post-A1. Amino acid abbreviations: F, Phe; I, Ile; K, Lys; L, Leu; M, Met; Q, Gln; R, Arg; S, Ser; T, Thr; W, Trp; Y, Tyr.


Only the first two helices, H1 and H2, and two distinct internal 5′-ETS segments that form short heteroduplexes with the 3′ hinge and 5′ hinge of U3 snoRNA remain in position (Fig. 3B and figs. S4 and S7C). The cause for the increased structural freedom or partial degradation of the 5′-ETS is not clear. Notably, despite the dismantling of the 5′-ETS RNA, the overall shape and composition of this 90S intermediate remained largely unchanged at first. 

During this 90S transition, a clear structural compaction was observed. Initially, in state B2, the C terminus of Utp20 exhibits a superhelical HEAT repeat structure that wraps around the rRNA expansion segment ES6c (fig. S7D). Then, after transition to the Pre-A1 state, the Utp20 superhelix adopts a more closed conformation (changing from a “C” to an “O” shape), caused by the movement of the immature 5′ domain toward the central domain. As a consequence, binding of Lcp5 and H9 to Utp20 is disrupted, allowing h21 (ES6d) to enter this previously occupied site (fig. S7, E and F). Similar to Utp20, the prominent Kre33 module also moves with the 5′ domain during this transition; however, the Kre33 module finally dissociates when the intermediate reaches the Post-A1 state (Fig. 3, C and D, and fig. S7, G to I). This brings the 5′ domain even closer to the central domain (fig. S7H), and when state Post-A1 is reached, the 5′ and central domains eventually interact and adopt a mature-like conformation (Fig. 3D and fig. S7I). This apparent domain compaction—together with the 5′-ETS RNA remodeling, which takes place during the first steps of 90S transition— results in a conformational state sufficiently dynamic to facilitate A1 processing: The state Pre-A1 shows the noncleaved A1 site ~50 Å away from the catalytic center of the PIN domain endonuclease Utp24, which was suggested to carry out this cut (Fig. 3E) (38–41). The Post-A1 state reveals the formation of a short RNA stemloop (h1) at the 5′ end of the mature 18S rRNA. The initial formation of this helix may have triggered endonucleolytic cleavage, because it results in repositioning the A1 site close to the catalytic center of the Utp24 endonuclease (Fig. 3F). Consistent with this interpretation, at the base of the newly formed h1 we can retrace theRNA sequence until the thirdnucleotide (uridine 3) of the cleaved and mature 5′ end of 18S rRNA. Such a sequence-independent but h1 stem-loop–dependent mechanism for A1 cleavage, requiring an arbitrary threenucleotide spacer relative to the h1 base, has been predicted by genetic studies from the Tollervey lab (42). Unexpectedly, A1 cleavage does not require unwinding of the Box A and Box A′ heteroduplexes formed by pre-18S rRNA and U3 snoRNA, the latter two being retained in the Post-A1 state (Fig. 3F). Together, the data show that A1 cleavage is initiated by remodeling and relocation of the pre-18S rRNA substrate rather than by movement of the endonuclease Utp24 toward the A1 cleavage site.

A1 cleavage coupled to Pno1 and 90S remodeling
A series of additional remodeling events can be observed when comparing the Pre-A1 and Post-A1 states, which includes the release of the Krr1-Faf1 complex and its replacement by the relocated Pno1 and h45 (Fig. 3, G and H, and fig. S8). With the translocation of Pno1 and the associated h45, the RNA platform region adopts a mature-like conformation, typically seen in both yeast and human later cytoplasmic pre-40S intermediates. This results in the formation of rRNA helices h19 and h25 (Fig. 3H), and, as a consequence, a new interface is formed and stabilized by the newly recruited methyltransferase Dim1 (Fig. 3I, fig. S9, and supplementary text), thereby rendering these rearrangements irreversible. The binding mode of Pno1 to h45 differs between the Pre-A1 and Post-A1 states (Fig. 3J and fig. S8B). Relocation of h45 relative to Pno1 is stabilized by the long C-terminal a helix of Utp7, which previously was bound to H7 of the 5′-ETS before its dismantling (Fig. 3J and fig. S8C). The interaction of Utp14 with Pno1 prevents premature recruitment of the endonuclease Nob1, which later catalyzes the last processing step of the pre-18S rRNA at site D (Fig. 3, K and L) (28). Finally, by relocating to the central platform, Pno1 and its clamped h45 dissociate from Utp21 and Utp13 of the UTP-B module (fig. S8B), allowing for the first time the recruitment of the RNA helicase Dhr1 to the 90S via a two-site contact to Utp21 and Utp13 (see below and Fig. 3M).

Successive factor shedding during 90S transition to primordial pre-40S
Following the formation of state Post-A1, the dismantled 5′-ETS allows for a cascade of structural and compositional changes that result in a stepwise reduction of the 90S complex (Fig. 4). 

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Fig. 4. Successive shedding of factors during transition from 90S to primordial pre-40S. 
EM densities reveal the shedding process of major 90S assembly factor modules during transition from state Post-A1 to state Dis-C. Proteins, modules, and the U3 snoRNP are colored and labeled accordingly. The last remaining
helices of the 5′-ETS (H1, H2) and Dhr1 are shown in yellow. A local resolution-filtered map of Dhr1 was used in state Dis-C. The color-coded 18S pre-rRNA and the dismantled modules are shown below.

First, the Sof1 module (Utp7, Utp14, and Sof1) is released together with Utp6 from its binding site close to the former helix H9 at the 3′ region of the 5′-ETS, resulting in the state Dis-A. Then, in the second step, the UTP-A complex dissociates together with Utp18 and all protein components of the U3 snoRNP, leading to state Dis-B. In the last transition step from Dis-B to Dis-C, the core of the UTP-B complex and the remains of UTP-C are released. Also, the 5′-ETS, which served as RNA scaffold for all bindingmodules (UTP-A, UTP-B, UTP-C, and Imp3), is no longer detectable in this final intermediate. Of the U3 snoRNP, only a short segment of its RNA remains localized in states Dis-B and Dis-C, in particular the heteroduplexes with 18S rRNA; the rest becomes detached from these intermediates (Figs. 1B and 4). Interestingly, the domains of the pre-40S undergo rather limited maturation rearrangements during this shedding phase. Only rRNA expansion segments ES3a, ES3b, and ES6a to ES6d on the solvent side of the subunit adopt mature conformations, whereas the rest of the domains remain essentially unchanged (see boxes in Fig. 4 and fig. S10A).

Although this successive shedding of large protein modules is the distinct hallmark of the 90S transition, several structural changes occur in addition. First, Dhr1 moves from its previous UTP-B binding site (Fig. 3M) toward Box A in state Dis-C, thereby bringing the helicase into an ideal position to dismantle the last remaining U3::18S rRNA hybrid on the intermediate (fig. S10, B and C). Concomitantly, the Utp24 endonuclease becomes detectable
again in this state, where it occupies the binding site for the uS5 ribosomal protein. Moreover,Utp14, previously bound to Utp6 and helix H9 of the 5′ETS, relocates to a new position in state Dis-C, where it binds Pno1 and Dhr1 via four a helices (fig. S10, D to F). Notably, two arginine residues of Utp14 inhibit the endonuclease activity of Utp24 by coordinating active-site residues, thus allowing Utp24 to serve as an endonuclease-inactive placeholder (fig. S10, G to I). Sequential Dhr1 helicase function during the 90S to pre-40S transition Finally, the Dis-C intermediate sheds light on the diverse functioning of the Dhr1 helicase during the 90S transition by showing how it
is primed to remove the U3 snoRNA from its last contact point to the 18S rRNA, Box A. From state Post-A1 to state Dis-C, Dhr1 is tethered to the assembly intermediates via two invariant N-terminal helices: one that interacts with rRNA helix h13 at a site that is later occupied by Tsr1 (Fig. 5, A to C, and fig. S11, A and B), and another that binds to the methyltransferase Dim1 (Fig. 5D and fig. S9B). The catalytic C-terminal domain, however, binds distantly fromits N-terminal anchor region (Fig. 5, A and B, and fig. S11A). From state Post-A1 to state Dis-B, this globular part is bound to Utp13 and Utp21, which is mediated by a b barrel– like domain of Dhr1 (fig. S11C). In state Dis- C, however, after dissociation of Utp21, Dhr1 relocates to the Box A and h1 region, close to its U3 snoRNA substrate.Here, its b barrel–like domain is bound to the interface formed by Utp14, Pno1, and the 3′ region of the pre-18S rRNA (Fig. 5, E and F). The observed interplay between Utp14 and Dhr1 highlights the importance of Utp14 for the recruitment and relocation of Dhr1 during the 90S transition (36, 43–45). In our ensemble of 90S transition structures, Dhr1 was observed in two distinct conformations. First, between states Post-A1 and Dis-B, Dhr1 was in a conformation with an open RNA binding tunnel. Here, the N terminus of Pno1 prevents substrate binding and closing of the catalytic domain (Fig. 5G). This suggests that Dhr1 is bound to the 90S pre-ribosome in an adenosine diphosphate–bound, open conformation after A1 cleavage (fig. S11D). After the transition to state Dis-C and relocation of Dhr1 toward the Box A duplex, however, the helicase domain engages a segment of the U3 snoRNA as substrate (Fig. 5F). Furthermore, Dhr1 appears now in a closed conformation, resembling the adenosine triphosphate (ATP)–free form of previously reported RNA-bound DHX37, the human homolog of Dhr1 (Fig. 5H and fig. S11E) (18). We conclude from these data that after the transition from state Dis-B to state Dis-C, Dhr1 is in a closed apo-state, awaiting ATP binding, and through successive cycles of ATP hydrolysis could exert its pulling force to completely expel the U3 snoRNA from this primordial pre-40S intermediate.

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How ribosomes are like Russian dolls

https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#8006

https://phys.org/news/2020-09-ribosomes-russian-dolls.html?fbclid=IwAR1nu4z70IXwlOloRrUTRLlkvNYulz1imSZoAADAAC0rPqP4M67w5dI0phM

Maturation ( biogenesis)  of the ribosome is a complex operation. The 90S precursor of the small 40S subunit undergoes a "molting" process, during which it progressively discards its outermost components.

Protein synthesis, programmed by the genetic information encoded in the DNA, is perhaps the most crucial process that takes place in biological cells. Proteins are indispensable for all organisms, because they are responsible for performing a vast range of biological functions. Indeed, the molecular machines that put proteins together—which are known as ribosomes—are themselves partly made up of specific proteins. The second vital ingredient of every ribosome is a small set of specific RNAs, which serve as scaffolds to which ribosomal proteins can be specifically attached. The synthesis of ribosomes is therefore an extremely complex, multistep process, which includes both assembly and maturation stages. This complexity explains why many of the details of the whole operation are still incompletely understood. Now a group of researchers led by Professor Roland Beckmann at LMU's Gene Center has obtained new insights into the maturation phase that gives rise to the small subunit of the functional ribosome in brewer's yeast. The study, which was carried out in collaboration with colleagues based in Heidelberg, appears in the journal Science.

In the cells of higher organisms, mature ribosomes are composed of two distinct subunits, each of which contains a long ribosomal RNA (rRNA) molecule (called 18S in the small and 25S in the large subunit in yeast). The subunits interact with one another and with the messenger RNAs that program the synthesis of each protein.

My comment: Consider that the biogenesis and maturation process of the first Ribosome had to emerge prebiotically, since the Ribosome is life essential. This is like the assembly of a complex machine, where each part must fit and must have interface compatibility. The Ribosome is a factory where many machine-like movements and actions occur in incredibly fast manner.   


For a working biological system to be built, the five following conditions would all have to be met:
1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.
2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time, they are needed.
4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if subsystems or parts are put together in the right order, they also need to interface correctly.
( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. In other words : Why would natural selection select an intermediate biosynthesis product or a scaffold protein, which has by its own no use for the organism, unless there is a distant goal, as in this case, to make a ribosome? And that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system ?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal.


In yeast, the smaller 40S subunit is derived from a much larger precursor complex called the 90S pre-ribosome. The 90S precursor particle contains a single (35S) RNA molecule. The RNAs ultimately associated with each mature subunit are produced by the removal of specific internal and end-fragments. However, one of the segments the RNA found in the 90S precursor plays an important role in ensuring that the mature 18S rRNA in the 40S subunit folds into its correct three-dimensional form.

How the processing of the 35S rRNA is achieved has so far been unclear. The general idea was that, as the 40S subunit matures, the processing steps that give rise to the 18S rRNA take place, and the mature 40S particle eventually 'emerges' from the 90S precursor. The new study adds new details, which reveal that the process is rather more complicated than that. For a start, a specific enzyme (Dhr1) is required to ensure that the initial cleavage of the 35S rRNA precursor occurs at the right position. Dhr1 first exposes the cleavage site, enabling it to interact with the enzyme Utp24, which cuts the correct fragment off one end of the 35S rRNA.

Shedding takes place stepwise

In addition, the "emergence" of the 40S subunit entails an ordered series of reactions in which the outer shell of the 90S particle is progressively dissociated from the 40S. "It doesn't just go plop," Beckmann remarks. The process is actually reminiscent of the molting of an insect—shedding of the integument takes place layer by layer. "It's rather like those Russian dolls. When you open one, you find a smaller one nestled inside," says Beckmann. And with the aid of cryo-electron microscopy, the specialists in Munich were able to discriminate between the different three-dimensional complexes characteristic of each step in the process. Earlier biochemical experiments performed by a team at the Center for Biochemistry at Heidelberg University (BZH), led by Professor Ed Hurt, had already cast doubt on the previous en bloc model by providing evidence for the idea that shedding of the outer layers of the 90S particle took place stepwise.

The elucidation of such mechanisms is not only of interest from the point of view of basic research. As Beckmann points out, more and more disorders have been shown to be related to a lack of intact ribosomes. When errors occur in the assembly and maturation of these delicate and intricate molecular machines, they may ultimately lead to a relative death of ribosomes, which then perturbs the delicate equilibrium between protein synthesis and degradation. Among the resulting syndromes are diverse forms of muscle atrophy, growth anomalies, anemias and certain cancers.

My comment: How can someone deny that this is a goal oriented process? 

90S pre-ribosome transformation into the primordial 40S subunit

The eukaryotic small ribosomal subunit (40S) is the smaller subunit of the eukaryotic 80S ribosomes, with the other major component being the large ribosomal subunit (60S). Production of small ribosomal subunits initially requires the formation of a 90S precursor followed by an enigmatic process of restructuring into the primordial pre-40S subunit. .

1. the remodeling RNA helicase Dhr1 engages the 90S pre-ribosome, followed by
2. Utp24 endonuclease–driven RNA cleavage at site A1, thereby
3. separating the 5′-external transcribed spacer (ETS) from 18S ribosomal RNA. Next,
4. the 5′-ETS and 90S assembly factors become dislodged, but this occurs sequentially, not en bloc.
5. Eventually, the primordial pre-40S emerges, still retaining some 90S factors including Dhr1, now ready to
6. unwind the final small nucleolar U3–18S RNA hybrid.

The principles of assembly and remodeling of large ribonucleoproteins requires transcription, processing, and modification of ribosomal RNA (rRNA) and the integration of ~80 ribosomal proteins. It is a  highly complex process which comprises more than 50 assembly factors. Many different actions have to be performed during the assembly process. These include

adoping
binding
cleaving
coordinating
cutting
closing
dissociating
dismantling
forming
processing,
interacting
integrating
interacting
interplaying
moving
processing
preventing premature recruitment
priming
replacing
rearranging
recruiting
remodeling
removing
relocating
releasing
relocating
replacing
shedding
stabilizing
stepwise reducing
translocating.

The huge 90S pre-ribosome transforms into its next major biogenesis intermediate, the primordial pre-40S, by large structural rearrangements, including the successive shedding of assembly factor modules. Several findings support the notion that the observed transition states are of physiological relevance and are not merely the products of random disintegration. Defects in ribosome biogenesis can have
drastic consequences for human health as ribosomopathies. Therefore, gaining more mechanistic insights into this elaborate maturation process and its integration into cellular signaling pathways is desirable.

My comment: Consider that the description refers just to the maturation and biogenesis of the small subunit of the Ribosome. Could such cutting edge, highly ordered and complex synthesis process have occurred prebiotically, by random unguided chemical reactions ? Consider that there was neither a genome present to instruct the information to make all the parts, and how the assembly could take place. And we are also facing a chicken egg problem. The ribosome is required to make the translation of the genetic information to make the polymers that constitute the Ribosome. What came first ? 

Translation through ribosomes,  amazing nano machines Riboso19

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