Transfer RNA, and its biogenesis

Transfer RNA, and its biogenesis

https://reasonandscience.catsboard.com/t2058-transfer-rna-and-its-biogenesis

tRNA's are very specific  and complex molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are by themselves also enormously complex, not only in their structure but as well in their " made of ". So the question in the end arises: did natural processes have the foresight of the end product, tRNA, to make this highly specific nanorobot - like molecular machines which remove, add and modify the nucleotides? If not, how could they have arisen, since, without end goal, there would be no function for them? these enzymes are all specifically made for the production of tRNAs. And tRNA is essential for life

JOSEF BERGER: THE GENETIC CODE AND THE ORIGIN OF LIFE 1976
If the t-RNA's of recent organisms have about 80 nucleotides, then the random origin of recent forms of tRNA's has a low probability because that of the origin of one definite t-RNA molecule is about 1: 10^54. The probability of the origin of one definite protein molecule is also slight, i.e. 1: 10^130 if we take into consideration small protein subunits with 100 amino acids. The probability of the random independent simultaneous origin of one definite protein
molecule and one definite nucleic acid molecule is even 1: 10^184 in  our case. These and others facts, taking into consideration that the age of the earth is 10^17 seconds. only, can be a basis for hypotheses on an extra-terrestrial origin of life. On the other hand Portelli (1975) defends that 'the complex and perfect information existing in the genetic code is (explained by) that the evolutionary cycles of the universe and the cycle of life are interconnected, namely the information accumulated by the development of life, within the framework of a cycle of the universe passes through the origin of the next universe in the new cosmic cycle. The actual genetic code represents just the informational message arising from the living systems of the previous universe'. However, we have not a single fact as indication for the existence of such a process.


Transfer RNA is an ancient molecule, central to every task a cell performs and thus essential to all life.
The enzyme is one of only two ribozymes which can be found in all kingdoms of life (Bacteria, Archaea, and Eukarya). 11

The three major RNAs involved in the flow of genetic information are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All these RNAs participate in the protein-synthesizing pathway in cells. tRNA has two distinct characteristics. It carries an anticodon corresponding to the mRNA codon and it binds to the corresponding amino acid in a reaction catalyzed by a specific aminoacyl-tRNA synthetase. In this sense, tRNA is a key bridging molecule between ribonucleotide information (RNA world) and peptide information (protein world). Therefore, tracing the evolution origin of tRNA molecules is likely to cast light on the processes that led to the establishment of the central dogma. 16

10
Of the thousands of RNAs so far identified, transfer RNA (tRNA) is the most direct intermediary between genes and proteins. Like many other RNAs (ribonucleic acids), tRNA aids in translating genes into the chains of amino acids that make up proteins. With the help of a highly targeted enzyme, each tRNA molecule recognizes and latches onto a specific amino acid, which it carries into the protein-building machinery. In order to successfully add its amino acid to the end of a growing protein, tRNA must also accurately read a coded segment of messenger RNA, which gives instructions for the exact sequence of amino acids in the protein. see here

tRNAs Are covalently modified before they exit from the Nucleus

Like most other eucaryotic RNAs, tRNAs are covalently modified before they are allowed to exit from the nucleus. Eucaryotic tRNAs are synthesized by RNA Polymerase III. Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, which are then trimmed to produce the mature tRNA. In addition, some tRNA precursors (from both bacteria and eucaryotes) contain introns that must be spliced out. This splicing reaction differs chemically from pre-mRNA splicing; rather than generating a lariat intermediate, tRNA splicing uses a cut-and-paste mechanism that is catalyzed by proteins See below:



Trimming and splicing both require the precursor tRNA to be correctly folded in its cloverleaf configuration. Because misfolded tRNA precursors will not be processed properly, the trimming and splicing reactions are thought to act as quality- control steps in the generation of tRNAs. All tRNAs are modified chemically—nearly 1 in 10 nucleotides in each mature tRNA molecule is an altered version of a standard G, U, C, or A ribonucleotide.Over 50 different types of tRNA modifications are known; a few are shown below:



Some of the modified nucleotides—most notably inosine, produced by the deamination of adenosine—affect the conformation and basepairing of the anticodon and thereby facilitate the recognition of the appropriate mRNA codon by the tRNA molecule. Others affect the accuracy with which the tRNA is attached to the correct amino acid.Some of the modified nucleotides—most notably inosine, produced by the deamination of adenosine—affect the conformation and basepairing of the anticodon and thereby facilitate the recognition of the appropriate mRNA codon by the tRNA molecule . Others affect the accuracy with which the tRNA is attached to the correct amino acid.[/b]


After tRNA is transcribed by RNA polymerase III as a precursor tRNA, it  must be processed into a mature tRNA

This happens through  the removal, addition and chemical modification of nucleotides. Processing for some tRNA involves 2

   1) removal of the leader sequence at the 5 prime end
   2) replacement of two nucleotides at the 3 prime end by the sequence CCA (with which all mature tRNA molecules terminate)
   3) chemical modification of certain bases and
   4) excision of an intron.

The mature tRNA is often diagrammed as a flattened cloverleaf which clearly shows the base pairing between self-complementary stretches in the molecule.




tRNA maturation in Homo sapiens

Enzymatic  complexes involved in the process: 18

Proteins:
CCA tRNA nucleotidyltransferase 1
Zinc phosphodiesterase ELAC protein 2

Enzymatic  complexes:
Ribonuclease P
tRNA ligase complex
tRNA-splicing endonuclease


17


19

16




1)The transcription product, the pre-tRNA, contains additional RNA sequences at both the 5’ and 3’-ends.   These additional sequences are removed from the transcript during processing. The additional nucleotides at the 5’-end are removed by an unusual RNA containing enzyme called ribonuclease P (RNase P)


2.
Some tRNA precursors contain an intron located in the anticodon arm. These introns are spliced out during processing of the tRNA.

The cloverleaf structure of a single polynucleotide tRNA molecule is universally conserved among organisms. However, tRNA genes are often divided into parts on the chromosome; in bacteria, archaea, eukarya, and organelles, several tRNA genes are interrupted by various types of introns, which are removed by RNA splicing after transcription
Introns in nuclear and archaeal tRNAs are generally cleaved by tRNA-splicing endonuclease 13

tRNA splicing is a fundamental process required for cell growth and division. SEN2 is a subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns, the first step in tRNA splicing 14

The tRNA splicing reaction in yeast occurs in three steps; each step is catalyzed by a distinct enzyme, which can function interchangeably on all of the substrates 15

3.
All mature tRNAs contain the trinucleotide CCA at their 3’-end. These three bases are not coded for by the tRNA gene. Instead, these nucleotides are added during processing of the pre-tRNA transcript. The enzyme responsible for the addition of the CCA-end is tRNA nucleotidyl transferase and the reaction proceeds according to the following scheme:

tRNA +CTP --> tRNA-C + PPi (pyrophosphate)
tRNA-C +CTP --> tRNA-C-C + PPi
tRNA-C-C +ATP --> tRNA-C-C-A + PPi

4.
Mature tRNAs can contain up to 10% bases other than the usual adenine (A), guanine (G), cytidine (C) and uracil (U). These base modifications are introduced into the tRNA at the final processing step. The biological function of most of the modified bases is uncertain and the translation process seems normal in mutants lacking the enzymes responsible for modifying the bases.

Termination signals end the transcription of RNA by RNA polymerase I and RNA polymerase III without the activity of hairpin structures as seen in prokaryotes.
mRNA is cleaved 10 to 35 base-pairs downstream of a AAUAAA sequence (which acts as a poly-A tail addition signal).

The biogenesis of mature transfer (t)RNAs in cells has a complexity that belies the elegance of their function as the adaptor molecules of protein synthesis. They are synthesized as precursors which are converted to mature tRNA molecules by a sequence of events that includes processing of their 5′ and 3′ ends, modification of a number of bases, addition of the terminal CCA residues and, in the case of intron-containing tRNAs, splicing 1

Transfer RNAs (tRNAs) play an important role linking mRNA and amino acids during protein biogenesis. Four types of tRNA genes have been identified in living organisms. However, the evolutionary origin of tRNAs remains largely unknown.   Given their central role in life and their high level of conservation, tRNAs have stimulated extensive interest in their origin and evolution

This enzyme alone is like a small cogwheel in a watch in a complex clockwork mechanism. If you take it away, the whole mechanism of protein synthesis ceases to exist. No RNase, no protein synthesis, no life....... As with RNase, the Protein production needs hundreds, well, probably thousands of intricate fine-tuned parts, all doing their function in a precise way, and if you take away just one small apparently irrelevant part, bye-bye proteins, bye-bye life. These enzyme subparts have no use by their own, but only if correctly inserted in the intricate holoenzyme complexes exercising precisely their function.........

further readings :

http://journal.frontiersin.org/researchtopic/1729/molecular-biology-of-the-transfer-rna-revisited

Molecular biology of the transfer RNA revisited

Transcription of tRNA

tRNAs are transcribed by RNA polymerase III as pre-tRNAs in the nucleus. RNA polymerase III
recognizes two internal promoter sequences (A-box B internal promoter) inside tRNA genes.
The first promoter begins at nucleotide 8 of mature tRNAs and the second promoter is located 30-60
nucleotides downstream of the first promoter. The transcription terminates after a stretch of
four or more thymidines.12

RNA polymerase III is responsible for the production of pre-tRNAs, 5SrRNA and other small RNAs. 2

tRNA Synthesis & Processing 4

RNA polymerase III is responsible for the production of pre-tRNAs, 5SrRNA and other small RNAs. 2

RNA polymerase III:  The promoters for RNA polymerase III vary in structure but the ones for tRNA genes and 5S rRNA genes are located entirely downstream of the startpoint, within the transcribed sequence.  In tRNA genes, about 30-60 base-pairs of DNA separate promoter elements; in 5S rRNA genes, about 10-30 base-pairs promoter elements.



General transcription factors and the polymerase undergo a pattern of  sequential binding to initate transcription of nuclear genes.
1) TFIID binds to the TATA box followed by
2) the binding of TFIIA and TFIIB.
3) The resulting complex is now bound by the polymerase, to which TFIIF has already attached.
4) The initiation complex is completed by the addition of TFIIE, TFIIJ, and TFIIH.
5) After an activation step requiring ATP-dependent phosphorylation of the RNA polymerase molecule, the polymerase can initiate transcription at the startpoint.




The TATA-binding protein (TBP) is a subunit of the TFIID and plays a role in the activity of the  RNA polymerase III transcription.
TBP is also essential for transcription of TATA-less genes.
TBP differs from most DNA-binding proteins in that it interacts with the minor groove of DNA, rather than the major groove and imparts a sharp bend to the DNA.
The TBP is highly conserved.
When TBP is bound to DNA, other transcription-factor proteins can interact with the convex surface of the TBP saddle.
TBP is required for transcription initiation on all types of eukaryotic promoters.


In order to make tRNA, 1. the genetic information stored in DNA is required, as well as the information to make the machines that process the newly synthesized and unfinished pre-tRNAs strand, so as the RNA polymerase III complex , together with all subunits, co-factors, transcription factors etc. to transcribe DNA into pre-tRNAs, beside ATP, the fuel to make all happen. Well over one hundred sub units are required in such a complex process, that science even today does not fully understand the details.  That is a irreducible complex, and interdependent sophisticated and highly complex system,  which requires a enormous amount of complex, specified, coded information stored in DNA.


http://mol-biol4masters.masters.grkraj.org/html/Ribose_Nucleic_Acid3D-Processing_of_tRNA_Precursors.htm

2) http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-21/CB21.html
4) http://www.nobelprize.org/educational/medicine/dna/a/translation/trna_processing.html

CCA tRNA nucleotidyltransferase 1

FUNCTION:

Isoform 1: Adds and repairs the conserved 3'-CCA sequence necessary for the attachment of amino acids to the 3' terminus of tRNA molecules, using CTP and ATP as substrates. Ref.9
Isoform 2: Adds 2 C residues (CC-) to the 3' terminus of tRNA molecules instead of a complete CCA end as isoform 1 does (in vitro).

Recognition of 3' end without CCA by tRNA nucleotidyltransferase in Homo sapiens



Addition of CCA sequence to 3'end of intron-containing pre-tRNA in Homo sapiens





Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3′ end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3′ terminus of immature tRNAs without using a nucleic acid template. 1

The acylation of all tRNAs with an amino acid occurs at the terminal ribose of a 3' CCA sequence.
The CCA sequence is added to the tRNA precursor by stepwise nucleotide addition performed by a single enzyme that is ubiquitous in all living organisms.
Although the enzyme has the option of releasing the product after each addition, it prefers to stay bound to the product and proceed with the next addition.  4



tRNA-nucleotidyltransferases: Highly unusual RNA polymerases with vital functions 3

tRNA-nucleotidyltransferases are fascinating and unusual RNA polymerases responsible for the synthesis of the nucleotide triplet CCA at the 3′-terminus of tRNAs. As this CCA end represents an essential functional element for aminoacylation and translation, these polymerases (CCA-adding enzymes) are of vital importance in all organisms.

CCA-adding enzymes obviously can count until three: after the addition of three nucleotides, the polymerization reaction is efficiently stopped Additionally, and most interestingly, the CCA-adding enzymes recognize if nucleotides are previously added to a tRNA primer and incorporate then only the missing ones, completing thereby the CCA triplet. A tRNA that carries already the first C residue of the CCA terminus is elongated only by one C and one A, while on a tRNA ending with CC, only the terminal A residue is added. This feature shows that CCA-adding enzymes are not only responsible for the de novo synthesis of CCA ends but have an important maintenance and repair function for tRNA ends. This stringent sequence and length control of the tRNA CCA end reflects the recognition requirements for aminoacylation and translation. ( this is amazing. How did it " learn "  that feat ? trial and error ?  )

Furthermore, positioning in the ribosome during translation and even peptide release from the ribosome depend on an intact CCA end, which is critical for water coordination and efficient hydrolysis of the ester bound translation product

These facts indicate that an accurate CCA end participates, beyond simple recognition and binding, as an integral part in several reaction mechanisms and is therefore of vital importance for the cell.

Surprisingly, these polymerases with such unusual features evolved twice in evolution, leading to classes 1 and 2 CCA-adding enzymes

Convergence is evidence against evolution, and the author supposes evolution prior the existence of a replicating cell 5

While class 1 is exclusively found in archaea, class 2 tRNA-nucleotidyltransferases are present in eukaryotes and bacteria, where they fulfill identical functions.




Structural organization of classes 1 and 2 CCA-adding enzymes. While both enzyme versions have a hook-like shape of similar size, the allocation of secondary structure elements in neck, body and tail domains are quite different. In class 1 enzymes, these regions contain alpha-helical as well as beta-sheet elements. Class 2, on the other hand, has exclusively alpha-helical structures in these domains. The catalytic cores, located in head and neck domains of both enzyme versions, are indicated by the grey arrows. The rainbow color bar represents the consecutive protein regions from N- (blue) to C-terminus (red).

One of the most fascinating aspects of both classes of tRNA-nucleotidyltransferases is the fact that CCA-addition does not require an external nucleic acid as a template – somehow these enzymes “know” when to incorporate which nucleotide.

Indeed. Isn't that a magnificient example and evidence of design ?

Crystal structures of both classes 1 and 2 enzymes revealed a set of highly conserved amino acid residues located in the single nucleotide binding pocket that interact with the incoming nucleotide by forming Watson/Crick-like hydrogen bonds

So these enzymes do not only " know " when to incorporate which nucleotide, but also " know " how to bind each nucleotide to the next through hydrogen bonds..... amazing.


The 3′-terminal CCA nucleotide sequence  of transfer RNA is essential for amino acid attachment and interaction with the ribosome during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, ‘CCA-adding enzyme’, using CTP and ATP as substrates

tRNA nucleotidyltransferase

In eukaryotes, multiple forms of tRNA nucleotidyltransferases are synthesized from a single gene and are distributed to different subcellular compartments in the cell. There are multiple in-frame start codons which allow for the production of variant forms of the enzyme containing different targeting information predominantly found in the N-terminal sequence of the protein 2

5) http://reasonandscience.heavenforum.org/t2014-convergence-another-problem-for-evolution

CCA addition : http://onlinelibrary.wiley.com/doi/10.1002/iub.301/pdf

Elucidation of the role of the CCA enzyme in the cellular network of tRNA quality control and the identities of the RNases accompanying the CCA enzyme constitute new questions that warrant active investigation.

Zinc phosphodiesterase ELAC protein 2

Function 1

Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA.

Catalytic activity

Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.

Processing of 3' end by RNase Z in Homo sapiens



Processing of 3' end by RNase Z in Homo sapiens

´

Recognition of 3' end by RNase Z in Homo sapiens




1) http://www.genesilico.pl/rnapathwaysdb/proteins/195/

Ribonuclease P

Structure of Ribonuclease P (Homo sapiens):

Human nuclear RNase P consists of 10 Protein subunits and one RNA subunit.

Protein components:

Ribonuclease P protein subunit p14
Ribonuclease P protein subunit p20
Ribonuclease P protein subunit p21
Ribonuclease P protein subunit p25
Ribonuclease P protein subunit p29
Ribonuclease P protein subunit p30
Ribonuclease P protein subunit p38
Ribonuclease P protein subunit p40
Ribonucleases P/MRP protein subunit POP1
Ribonuclease P/MRP protein subunit POP5

RNA components:

H1 RNA




Reactions in which Ribonuclease P is involved:

Recognition of 5' end by RNase P in Homo sapiens



Processing of 5' end by RNase P in Homo sapiens



Ribonuclease P (EC 3.1.26.5, RNase P) is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. 6




RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome), the discovery of which earned Sidney Altman and Thomas Cech the Nobel Prize in Chemistry in 1989

Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein

Sidney Altman of Department of Molecular, Cellular and Developmental Biology Yale University, writes in his paper: Ribonuclease P following:

It seems unreasonable that ribosomes, with three RNAs and about 50 proteins, would exist without less complex RNPs having come into existence first and having persisted
throughout evolution. 5

And for what reason would Ribonuclease P have evolved to make tRNA, if tRNA would provide no function, unless embedded in the Ribosome used as physical link between the nucleotide sequence of nucleic acids (DNA and RNA) and the amino acid sequence of proteins ? Furthermore, its second component , C5 protein, is made not made of RNA, but amino acids, that is, tRNA are required to make the machine that makes tRNA. Another example of catch22 situation  

In eukaryotes, such as humans and yeast, most RNase P consists of an RNA chain that is structurally similar to that found in bacteria  as well as nine to ten associated proteins (as opposed to the single bacterial RNase P protein, C5)

In archaea and eukarya the enzyme has evolved an increasingly more complex protein composition, whilst retaining a structurally related RNA subunit. The reasons for this additional complexity are not currently understood. Furthermore, the eukaryotic RNase P has evolved into several different enzymes including a nuclear activity, organellar activities, and the evolution of a distinct but closely related enzyme, RNase MRP, which has different substrate specificities, primarily involved in ribosomal RNA biogenesis. 11

In eukaryotes, RNase P appears to have split into a number of distinct activities, including diverse pre-tRNA cleavage activities found in eukaryotic organelles, such as mitochondria and chloroplasts

Eukaryotes possess both a nuclear RNase P, and another related essential endoribonuclease, RNase MRP, which is found only in eukaryotes and cleaves at least three distinct substrates.

The majority of RNase MRP is located in the nucleus where it processes precursor ribosomal RNA (pre-rRNA)

Other characterized functions are the processing of mitochondrial RNAs (mtRNAs) leading to the generation of primers for mitochondrial DNA (mtDNA) replication

RNase MRP also plays a role in the degradation of the mRNA of a B-type cyclin, an activity which appears to be important for cell cycle progression

A second issue of interest to biochemists and “evolutionists” is the puzzle presented by the different compositions of RNase P from eubacteria (one catalytic RNA and one protein subunit) and from eukaryotes (one RNA subunit and several protein subunits: no understanding yet of which subunit is responsible for catalysis).The complexity of eukaryotic RNase P presents the questions of why there are so many subunits and what relation this complexity might have to the intracellular localization of the enzyme, possible isoforms , and its relation to other enzymes with which it might interact in vivo. RNase P in organelles, e.g., chloroplasts and mitochondria, present their own complexities in terms of the origin and function of their subunits . More generally, the role of RNase P in the regulation of tRNA and rRNA biosynthesis in both prokaryotes and eukaryotes has not yet been fully explored.

Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that cleaves precursor tRNA transcripts to give mature 5′ ends. RNase P in eubacteria has a large, catalytic RNA subunit and a small protein subunit that are required for precursor tRNA cleavage in vivo. Although the eukaryotic holoenzymes have similar, large RNA subunits, previous work in a number of systems has suggested that the eukaryotic enzymes require a greater protein content. We have purified the Saccharomyces cerevisiae nuclear RNase P to apparent homogeneity, allowing the first comprehensive analysis of an unexpectedly complex subunit composition.


Function of Rnase P

In E. coli, RNase P processes not only ptRNAs, but also, at the very least, the precursors to 4.5S RNA

Signal recognition particle RNA 4.5S RNA   7

The signal recognition particle RNA, also known as  4.5S RNA, is the RNA component of the signal recognition particle (SRP) ribonucleoprotein complex.SRP is a universally conserved ribonucleoprotein that directs the traffic of proteins within the cell and allows them to be secreted. The signal recognition particle, SRP RNA, together with one or more SRP proteins contributes to the binding and release of the signal peptide. 8

A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway

In prokaryotes, signal peptides direct the newly synthesized protein to the SecYEG protein-conducting channel, which is present in the plasma membrane.

Protein Localization in the Cell 9

Proteins are the workhorses of the typical cell. Originally coded for by DNA and composed of a sequence of amino acids, proteins serve a variety of roles including binding other molecules and/or transporting them, serving as 'switches' for cellular activity, catalyzing chemical reactions, and even acting as structural building blocks. It should come as no surprise then that in order to accomplish all these goals, proteins are needed in a variety of locations both inside and outside of the cell. Therefore, a variety of mechanisms have evolved in order to correctly localize proteins, helping to guide them from their point of synthesis (at the ribosome) to their destination.One such set of mechanisms is the secretory pathway. Also ubiquitous in biological systems are membranes, barriers between the cell and the outside world. Membranes also serve to divide compartments within some cells (those of eukaryotes). In order for proteins to get to where they are needed inside these compartments or outside the cell, they need a way to cross the membrane without rupturing it at the same time. The secretory pathway consists in part of a channel for just this purpose: the translocon

So, interestingly, PNase processes various  completely different molecules, namely tRNA, and the precursors of the signal recognition particle, beside others. How could that be explained from a naturalistic/evolutionary standpoint ? Lets assume, evolution were a driving force at this stage ( which it couldn't be ), for what reason would such a enzyme involve in the manufacturing process of two completely different molecular parts ? From a naturalistic standpoint, thats hard to grasp. From a intelligent design standpoint however, that makes perfectly sense. Designers sometimes create machines, involved in the manufacturing of different parts for various reasons. BTW. Pnase P would have no function, until fully developed, and working in concert and synchronisation with other manufacturing machines inside the cell, to produce molecular parts , required for the functioning of the cell.

Ribonuclease P(EC 3.1.26.5, RNase P) is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules.


1) http://www.genesilico.pl/rnapathwaysdb/EnzymaticComplex/6/

further readings :

http://rna.cshl.edu/content/free/chapters/14_rna_world_2nd.pdf

Ribonuclease P (RNase P) has been hitherto well known as a catalytic ribonucleoprotein that processes the 5' leader sequence of precursor tRNA. Recent studies, however, reveal a new role for nuclear forms of RNase P in the transcription of tRNA genes by RNA polymerase (pol) III, thus linking transcription with processing in the regulation of tRNA gene expression. However, RNase P is also essential for the transcription of other small noncoding RNA genes, whose precursor transcripts are not recognized as substrates for this holoenzyme. Accordingly, RNase P can act solely as a transcription factor for pol III, a role that seems to be conserved in eukarya.

http://www.ncbi.nlm.nih.gov/pubmed/11017184?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

In 1989, Sidney Altman and Thomas R. Cech shared the Nobel Prize in Chemistry for their discovery of catalytic properties of RNA. Cech was studying the splicing of RNA in a unicellular organism called Tetrahymena thermophila. He found that the precursor RNA could splice in vitro in the absence of proteins. Altman studied ribonuclease P (RNase P), a ribonucleoprotein that is a key enzyme in the biosynthesis of tRNA. RNase P is an RNA processing endonuclease that specifically cleaves precursors of tRNA, releasing 5' precursor sequences and mature tRNAs. RNase P is involved in processing all species of tRNA and is present in all cells and organelles that carry out tRNA synthesis. What follows is a personal recollection by Altman of how he came to study this remarkable enzyme.

http://www.ncbi.nlm.nih.gov/pubmed/16679018?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

Ribonuclease P (RNase P) is an endonuclease involved in processing tRNA. It contains both RNA and protein subunits and occurs in all three domains of life: namely, Archaea, Bacteria and Eukarya. The RNase P RNA subunits from bacteria and some archaea are catalytically active in vitro, whereas those from eukaryotes and most archaea require protein subunits for activity. RNase P has been characterized biochemically and genetically in several systems, and detailed structural information is emerging for both RNA and protein subunits from phylogenetically diverse organisms. In vitro reconstitution of activity is providing insight into the role of proteins in the RNase P holoenzyme. Together, these findings are beginning to impart an understanding of the coevolution of the RNA and protein worlds.

http://www.ncbi.nlm.nih.gov/pubmed/11871657?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

Catalytic complexes of nuclear ribonuclease P (RNase P) ribonucleoproteins are composed of several protein subunits that appear to have specific roles in enzyme function in tRNA processing. This review describes recent progress made in the characterization of human RNase P, its relationship with the ribosomal RNA processing ribonucleoprotein RNase MRP, and the unexpected evolutionary conservation of its subunits. A new model for the biosynthesis of human RNase P is presented, in which this process is dynamic, transcription-dependent, and implicates functionally distinct nuclear compartments in tRNA biogenesis.

more :

http://www.genesilico.pl/rnapathwaysdb/EnzymaticComplex/6/

tRNA ligase complex

Protein components: 1

tRNA-splicing ligase RtcB homolog
ATP-dependent RNA helicase DDX1
Protein FAM98B
Ashwin
UPF0568 protein C14orf166
Protein archease



Reactions in which tRNA ligase complex is involved:

Recognition of spliced pre-tRNA by tRNA ligase complex in Homo sapiens



Ligation of exon ends in Homo sapiens




Diversity and roles of (t)RNA ligases.

The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.



The human tRNA ligase complex 3′–5′ RNA ligation appears to be the prevalent human tRNA splicing pathway  and relies on HSPC117 as the essential ligase component Human HSPC117, together with the proteins DDX1, CGI-99, FAM98B, and ASW, forms a stable complex of about 200 kDa

HSPC117 is the essential subunit of a human tRNA splicing ligase complex.

Splicing of mammalian precursor transfer RNA (tRNA) molecules involves two enzymatic steps. First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. In animals, the second step predominantly entails direct exon ligation by an elusive RNA ligase. Using activity-guided purification of tRNA ligase from HeLa cell extracts, we identified HSPC117, a member of the UPF0027 (RtcB) family, as the essential subunit of a tRNA ligase complex. RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells. The high sequence conservation of HSPC117/RtcB proteins is suggestive of RNA ligase roles of this protein family in various organisms.

Transfer RNAs (tRNAs) are essential adaptor molecules in the translation of the genetic transcript into proteins. During their posttranscriptional maturation (1), intron-containing tRNA precursor transcripts (pre-tRNAs) undergo splicing, which is accomplished by a specialized endonuclease that excises the intron (2, 3) and a ligase that joins the resulting exon halves

Transfer RNAs (tRNA) are transcribed as precursor transcripts and are subjected to a series of posttranscriptional processing events before they are matured to fulfill their biological functions Sequence analysis of tRNA genes in mammals, revealed the existence of tRNA genes disrupted by intervening sequences. Intron harboring tRNA genes are now known to occur in the genomes of organisms from all three domains of life. After the discovery of intron-containing tRNAs, the mechanistic features of tRNA splicing were extensively studied. Eukaryal pre-tRNA transcripts undergo enzymatic splicing. The latter achieves intron removal by endoribonucleolytic cleavage and subsequent ligation rather than by two consecutive transesterification events as employed by self-splicing introns or the spliceosome.

1) http://www.genesilico.pl/rnapathwaysdb/EnzymaticComplex/39/

tRNA-splicing endonuclease

Protein components:

tRNA-splicing endonuclease subunit Sen54
tRNA-splicing endonuclease subunit Sen2
tRNA-splicing endonuclease subunit Sen15
tRNA-splicing endonuclease subunit Sen34




Reactions in which tRNA-splicing endonuclease is involved:

Recognition of intron-containing tRNA by tRNA-splicing endonuclease in Homo sapiens



http://www.ncbi.nlm.nih.gov/pubmed/015109492

Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation.

Both human endonuclease complexes are associated with pre-mRNA 3' end processing factors. Furthermore, siRNA-mediated depletion of SEN2 exhibited defects in maturation of both pre-tRNA and pre-mRNA. These findings demonstrate a link between pre-tRNA splicing and pre-mRNA 3' end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events.

The enigma of ribonuclease P evolution

1) http://www.northwestern.edu/newscenter/stories/2010/11/rna-structure-mondragon.html#sthash.ljRIodto.dpuf
2) http://users.sdsc.edu/~youkha/duplication/_B_BARRELS/b137_RnaseP_29/Enigma_RNaseP.pdf

tRNA Biology in Mitochondria

Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.



1) http://www.mdpi.com/1422-0067/16/3/4518/htm

Evolution of transfer RNA and the origin of the translation system

The origin of the translation system is at the center of discussions about the evolution of biological systems.

In this context, molecules of transfer RNA (tRNA) are highlighted due to its ability to convey the information contained in nucleic acids with the functional information contained in the proteins. Despite many characteristics shared among tRNAs in various organisms, suggesting a monophyletic origin for this group of molecules, recent discussions have proposed a polyphyletic origin for this group, thus indicating that the shared features are products of evolutionary convergence

A polyphyletic  group is characterized by one or more homoplasies: phenotypes which have converged or reverted so as to appear to be the same but which have not been inherited from common ancestors. Alternatively, polyphyletic is used to describe multiple ancestral sources regardless of convergence.

Discussions on the initial emergence of the acceptor arm or anticodon arm remain open.

Sun and Caetano-Anollés (2008) proposed from structural analysis that the acceptor arm could have arisen first and the anticodon loop is a later event in the evolutionary history of tRNAs.

If that were the case, tRNA would have lost its function.

According to the data discussed, these molecules have had this function since the beginning of the formation and organization of biological systems.

The similarity observed between the tRNA molecules and ribosomal RNAs, especially the PTC, suggest the importance of the tRNAs molecules in the assembly of the translation system, which certainly was a key event for the emergence of life on Earth.

15 enzymes required in tRNA synthesis

https://www.frontiersin.org/articles/10.3389/fevo.2015.00123/full

Complexity of tRNAs reinforces that the genetic system is irreducibly complex
 
tRNAs are primarily encoded by dedicated tRNA genes which are transcribed by RNA polymerase III. They serve as adaptor molecules to translate mRNA sequences into protein sequences. But first, tRNA precursors must be extensively processed by protein-based molecular machines. For example, 5' leader sequences and 3' extensions must be removed using complex ribonucleases. The ribonucleases involved have little similarity between prokaryotes, mitochondria and eukaryotes. In plants, RNase P (which removes 5' leaders) is a protein-only enzyme, unlike in other organisms. Introns must be removed from some tRNA precursors, with splice junction sites differing between eukaryotes and archaea (but no such introns are present in bacteria).

All tRNAs require a CCA sequence at their 3' end for aminoacylation and ribosome processing. In E. coli and some related bacteria, the CCA sequence is encoded in tRNA genes. In most eukaryotes and archaea, the CCA sequence is not encoded and must be added post-transcriptionally. All cells have an enzyme to repair damaged CCA sequences in tRNAs. Remarkably, a quality control process in all domains of life involves adding a second CCA to defective tRNAs as a degradation tag.

All tRNAs require numerous biochemical modifications to function properly, carried out by many different enzymes. Each of these enzymes are exquisitely precise, avoiding targeting the same kind of nucleotide in the wrong position. The modifications then ensure proper folding of the tRNA, correct codon recognition, prevent frameshift during translation, and discrimination between different types of tRNAs.

It is worth emphasizing, that unless the anticodon region has been precisely structured in advance the mRNA codons cannot distinguish it from similar trinucleotide pattern on any tRNA or other RNAs. All the tRNAs, despite their considerable sequence differences, must possess the correct geometry thanks to internal H-bonding and the chemical editing enzymes. This is a prerequisite for the genetic code to function.
Some of the modification processes are very complex, requiring several enzymes to work sequentially. The modifications and the responsible enzymes appear to be finely tuned to work together in a coordinated system
Cells also have sophisticated systems for identifying and eliminating incorrectly formed tRNAs, using two main degradation pathways: 3'-5' exonucleolytic degradation by the nuclear exosome and 5'-3' exonucleolytic degradation by the RTD pathway. Tu elongation factor screening also distinguishes incorrectly charged precursors and tRNAs.
There are several proofreading steps to ensure correct codon-anticodon pairing during translation, improving accuracy from about 100:1 to 3000:1.
In eukaryotes, tRNA processing occurs in different cellular locations, with tRNAs moving between the nucleus and cytoplasm. This provides additional quality control. Charged tRNAs can participate in the autoregulation of their own synthetases. These complex quality control systems could not have emerged gradually, as they rely on proteins that could not exist without a functional genetic code and tRNA system already in place.

Matching tRNAs to specific codons and activated amino acids requires a level of coordination that is impossible to adequately explain through gradual, unguided processes.
Dr. Truman elaborated on the chicken-and-egg problem at multiple levels: proteins require sequence information on DNA, but the DNA must be expressed and processed into mRNA using proteins; ribosomes require pre-existing proteins and rRNA; nothing works without ATP (which is produced using dozens of proteins). Now we discover that tRNAs require extensive processing by dozens of pre-existing proteins plus those needed to transcribe and regulate tRNA gene expression. In addition, complex aminoacyl-tRNA synthetases must already be present to ‘charge’ the correct amino acid to the right tRNA. Everything is precisely regulated by a several cellular programs. There is no feasible starting point to develop one part of the system and then another other later: they depend on each other mutually.
This is a novel conundrum that proponents of naturalistic mechanisms will need to face.

References:
Truman, R., The surprisingly complex tRNA subsystem: part 1 - generation and maturation, J. Creation 34(3):80–86, 2020.
Truman, R., The surprisingly complex tRNA subsystem: part 2 - biochemical modifications, J. Creation 34(3):87–94, 2020.
Truman, R., The surprisingly complex tRNA subsystem: part 3—quality control mechanisms, J. Creation 35(1):98–103, 2021.
Truman, R., The surprisingly complex tRNA subsystem: part 4—tRNA fragments regulate processes, J. Creation 35(1):104–110, 2021.
Truman, R., The surprisingly complex tRNA subsystem: part 5 - evolutionary implausibility, J. Creation 35(2):98–106 2021.