Error check and repair during messenger RNA translation in the ribosome: by chance, or design ?

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design? 

https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messengerrna-translation-in-the-ribosome-by-chance-or-design

Translation is the most error-prone step of protein synthesis. 14

The control of the error rate and its effects in biological processes of information transmission is one of the key requirements to have functional living cells.
When talking about error check and repair of translation in the cell, then we have to consider several aspects. First, in order to have a functional and error-prone translation, the components involved in translation must be correctly synthesized in the cell. In translation, messenger RNA, transfer RNA, Aminoacyl-tRNA synthetase, and the Ribosome are involved. Most, if not all, are carefully error checked, either repaired when errors are detected, or discarded when misfolding through proteostasis. 13
Secondly, the process of translation is a multistep process, and error check and repair occur all along the way. They will be listed as follows: 

Mistakes during DNA replication are on the order of ~10^8 and are kept to this extremely low level by a robust suite of error prevention, correction and repair mechanisms 12 Protein synthesis, offers the greatest opportunity for errors, with mistranslation events routinely occurring at a frequency of ~1 per 10,000 mRNA codons translated.  The ribosome must select the correct aminoacyl-transfer RNAs (aa-tRNAs) from a large pool of near-cognate substrates fast enough to sustain an elongation rate of 10–20 amino acids per second !!.
 Proofreading and editing processes are used throughout protein synthesis to ensure a faithful translation of genetic information. The maturation of tRNAs and mRNAs is monitored, as is the identity of amino acids attached to tRNAs. Accuracy is further enhanced during the selection of aminoacyl-tRNAs on the ribosome and their base-pairing with mRNA.

Ribosome biogenesis: quality control mechanisms must be in place to survey nascent ribosomes and ensure their functionality.
Chiral checkpoints during protein biosynthesis the ribosome act as “chiral checkpoints” by preferentially binding to L-amino acids or L-aminoacyl-tRNAs, thereby excluding D-amino acids 11
If misaminoacylated tRNA is successfully delivered to the ribosome, additional proofreading occurs within the A site of the ribosome based on aa-tRNA position and affinity
Ribosomal interactions with additional tRNA-specific sequences and modifications facilitate accurate selection of aa-tRNAs based on kinetic discrimination during the initial selection stage and subsequent proofreading stage.

mRNA translation regulation by nearly 100 epigenetic tRNA modifications.  The finer details in this sort of regulation have been proven to differ between prokaryotic and eukaryotic organisms. ( LUCA hello ??!! 10)

tRNA structure monitoring: Export of defective or immature tRNAs is avoided by monitoring both structure and function of tRNAs in the nucleus, and only tRNAs with mature 5′ and 3′ ends are exported. 6
tRNA synthesis quality control: RTD and other mechanisms that degrade hypomodified or mutated mature yeast tRNAs serve as a surveillance system to eliminate tRNA molecules that have incorrect nucleosides or conformations

Aminoacyl-tRNA synthetase error minimization by preferential binding of the right amino acids, and selective editing and proofreading of near cognate amino acids
Aminoacyl-tRNA synthetase Pre-transfer editing: Pre-transfer editing has been described in both class I and class II aaRSs and takes place after aa-AMP synthesis but before the aminoacyl moiety is transferred to the tRNA. 9
Aminoacyl-tRNA synthetase Post-transfer editing: Post-transfer editing takes place after the transfer of the amino acid to the tRNA and involves the hydrolysis of the ester bond, in a domain separated from the active site. 
Aminoacyl-tRNA synthetase Editing factors: Another important component of the translation quality control machinery is the trans-editing family, free-standing proteins that are not synthetases but are in some cases homologs to the editing domains of such enzymes. The role of these trans-editing factors is to clear the misacylated tRNA before it reaches the ribosome, acting as additional checkpoints to ensure fidelity. 
Aminoacyl-tRNA synthetases (aaRSs), selectively hydrolyze ( chemical reaction in which a molecule of water ruptures one or more chemical bonds )  incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. 12
In addition to misactivation of genetically encoded proteinogenic amino acids (GPAs), cells also encounter non-proteinogenic amino acids (NPAs) environmentally or as metabolic by-products, and must discriminate against these substrates to prevent aberrant use in protein synthesis.

This is a list of eleven different error check and repair mechanisms during translation. Consider, that life cannot start, unless these mechanisms are fully in place, and operational. Consider as well, that all this machinery is a pre-requirement for living cells to kick-start life. Their origin cannot be explained by evolution. The alternatives are either all these hypercomplex life essential error check and repair mechanisms emerged by a fortuitous accident, spontaneously through self-organization by unguided stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction, chemical non-biological, purely physico-dynamic kinetic processes and reactions influenced by environmental parameters, or through the direct intervention, creative force and activity of an intelligent agency, a powerful creator.  Which of the two makes more sense? 

1. https://www.pnas.org/content/113/12/3311
2. https://sci-hub.tw/https://www.annualreviews.org/doi/10.1146/annurev.micro.091208.073210
2. https://elifesciences.org/articles/54898
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570319/
4. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008017
5. https://www.labome.com/method/Aminoacyl-tRNA-Synthetases.html
6. https://sci-hub.tw/https://science.sciencemag.org/content/282/5396/2082?ijkey=ace41d59cbf20b8ca66e9a068342b45398645b9b&keytype2=tf_ipsecsha
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640646/
8. Quality Control Mechanisms During Translation
9. https://rnajournal.cshlp.org/content/early/2020/04/17/rna.071720.119.full.pdf
10. https://en.wikipedia.org/wiki/Translational_regulation
11. https://www.jbc.org/content/early/2019/10/07/jbc.REV119.008166.full.pdf
12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697424/
13. https://en.wikipedia.org/wiki/Proteostasis
14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764353/

aaRS come in two unrelated families; 10 of the 20 amino acids need a Class I aaRS, the other 10 a Class II aaRS. This landscape is thus littered with perplexing questions like these:
I. Why wasn’t one ancestor enough when they both do the same job?
II. How did the two types of ancestral synthetases avoid competition that might have eliminated the inferior Class? 12
https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids


Errors that occur during transcription and translation have substantial effects on gene function by producing misfolded and malfunctioning proteins. The rate of translation errors is typically an order of magnitude higher than the rate of transcription errors. 1 Errors occurring during transcription often elicit more dire consequences than those occurring during translation because individual mRNAs can be translated up to 40 times resulting in a burst of flawed proteins. Therefore, a single transcription error can result in many flawed proteins, whereas a translation error will disrupt only a single protein. Estimates of the rate of transcription errors in Escherichia coli have yielded variable estimates of transcription error rates of 10−4–10−5 per nucleotide, several orders of magnitude higher than the mutation rate . Transcript-error rates are 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates.  The general error rates of genomic replication (about 10− are estimated to be approximately 10,000-fold lower than those of protein synthesis (about 10−4), and thus in most instances, mRNA translation is the key process contributing to the inaccuracy of the cellular proteome 4

Gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. 3  Alterations in mRNA stability can have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have unique post-transcriptional control mechanisms to enact such adaptive responses through:

1) general mRNA decay,
2) differential mRNA degradation using small non-coding RNAs (sRNAs), and
3) selective mRNA degradation using the tmRNA quality control system.

As with other biomolecules, the great variety of RNA species produced by the bacterial cell requires quality control mechanisms to ensure proper folding and function. In addition, the role of mRNA as a template for protein synthesis adds greater significance to mRNA quality control. The translation of a faulty transcript without adequate quality assurance measures might lead to the accumulation of aberrant protein products that could be detrimental to the cell. Bacterial mRNAs are not post-transcriptionally spliced, nor do they exhibit the 5’-cap structures of their eukaryotic counterparts. As such, post-transcriptional quality control processes of prokaryotic mRNA are distinct from the corresponding processes in eukaryotes. This review focuses on issues related to post-transcriptional processing, targeting, and degradation of bacterial mRNAs including those facilitated by small regulatory RNAs, with special emphasis on tmRNA and trans-translation.

Variation in the stability of transcripts has an important role in the control of protein expression within the cell, as long-lived transcripts are generally subject to more rounds of translation than those with a shorter half-life. Several factors play a role in controlling the lifespan of specific mRNAs by regulating their propensity to be degraded.

Translational decoding of the mRNA codons is constrained by factors during codon-anticodon recognition and often constitutes the rate-limiting step during protein synthesis. Besides the abundance of tRNA species, mRNA translation is regulated by nearly 100 epigenetic tRNA modifications, especially at the wobble position 4  Faithful translation of the mRNA codons into protein is essential for cellular physiology. The fidelity of the translation machinery firstly depends on the specific coupling of amino acids to their cognate tRNA species, which is catalyzed by aminoacyl-tRNA synthetases (aaRSs). Eukaryotic elongation factor 1A (eEF-1A) or prokaryotic EF-Tu delivers the aminoacyl-tRNA to the ribosome A site for elongation of nascent peptide chain after proper codon-anticodon recognition. Thus, aminoacyl-tRNA synthetase (aaRSs) are cardinal in protecting protein synthesis against misacylation ( incorrectly adding an acyl group to a compound).

tRNA synthesis quality control
Hypomodified tRNAs (modified to an abnormally small degree) can be degraded by the RNA degradosome, a multicomponent RNA degradation complex. Thus, the degradosome serves as a previously unrecognized bacterial tRNA quality control system that mediates clearance of hypomodified tRNAs.can be degraded by the RNA degradosome, a multicomponent RNA degradation complex. Thus, the degradosome serves as a bacterial tRNA quality control system that mediates clearance of hypomodified tRNAs. 1  Within the anticodon, the first or “wobble” position is particularly subject to modification, and these modifications are often critical for efficient translation; consequently, mutations that prevent such modification can result in loss of viability.  tRNAs’ highly stable structures are thought to contribute to their intracellular stability; in general, tRNAs exhibit a high melting temperature in vitro and a long half-life within the cell. RTD and other mechanisms that degrade hypomodified or mutated mature yeast tRNAs serve as a surveillance system to eliminate tRNA molecules that have incorrect nucleosides or conformations
In order to ensure fidelity, some of the synthetases perform editing functions to reduce the occurrence of errors during protein synthesis. 5

Quality control mechanisms during ribosome maturation
Protein synthesis on ribosomes is carefully quality controlled to ensure the faithful transmission of genetic information from mRNA to protein. Many of these mechanisms rely on communication between distant sites on the ribosomes, and thus on the integrity of the ribosome structure. Furthermore, haploinsufficiency of ribosomal proteins, which increases the chances of forming incompletely assembled ribosomes, can predispose to cancer. Finally, release of inactive ribosomes into the translating pool will lead to their degradation together with the degradation of the bound mRNA. Together, these findings suggest that quality control mechanisms must be in place to survey nascent ribosomes and ensure their functionality. This review gives an account of these mechanisms as currently known. 7

Proof-reading
Yeast employs structural proofreading of ribosome functional centres during nuclear steps of assembly
Accumulating evidence indicates a tight coupling between nuclear export, cytoplasmic maturation, and final proofreading of the ribosome. 
We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.
To minimize production of dysfunctional ribosomes, yeast employs structural proofreading of ribosome functional centres during nuclear steps of assembly
Arx1 binding may serve to proofread the proper accommodation of these ribosomal proteins into the tunnel exit
time window for the quality-control machinery to functionally proofread preribosomes. 

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?

Translation is the most error-prone step of protein synthesis. 14

Wikipedia: Proteostasis
The control of the error rate and its effects in biological processes of information transmission is one of the key requirements to have functional living cells.
When talking about error check and repair of translation in the cell, then we have to consider several aspects. First, in order to have a functional and error-prone translation, the components involved in translation must be correctly synthesized in the cell. In translation, messenger RNA, transfer RNA, Aminoacyl-tRNA synthetase, and the Ribosome are involved. Most, if not all, are carefully error checked, either repaired when errors are detected, or discarded when misfolding through proteostasis. 
https://en.wikipedia.org/wiki/Proteostasis

The process of translation is a multistep process, and error check and repair occur all along the way.

Kyle Mohler Translational fidelity and mistranslation in the cellular response to stress 2017 Nov 21.
Mistakes during DNA replication are on the order of ~10^8 and are kept to this extremely low level by a robust suite of error prevention, correction and repair mechanisms. Protein synthesis, offers the greatest opportunity for errors, with mistranslation events routinely occurring at a frequency of ~1 per 10,000 mRNA codons translated.  The ribosome must select the correct aminoacyl-transfer RNAs (aa-tRNAs) from a large pool of near-cognate substrates fast enough to sustain an elongation rate of 10–20 amino acids per second !!. Proofreading and editing processes are used throughout protein synthesis to ensure a faithful translation of genetic information. The maturation of tRNAs and mRNAs is monitored, as is the identity of amino acids attached to tRNAs. Accuracy is further enhanced during the selection of aminoacyl-tRNAs on the ribosome and their base-pairing with mRNA.
In addition to misactivation of genetically encoded proteinogenic amino acids (GPAs), cells also encounter non-proteinogenic amino acids (NPAs) environmentally or as metabolic by-products, and must discriminate against these substrates to prevent aberrant use in protein synthesis. This is a list of eleven different error check and repair mechanisms during translation. Consider, that life cannot start, unless these mechanisms are fully in place, and operational. Consider as well, that all this machinery is a pre-requirement for living cells to kick-start life. Their origin cannot be explained by evolution. The alternatives are either all these hypercomplex life essential error check and repair mechanisms emerged by a fortuitous accident, spontaneously through self-organization by unguided stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction, chemical non-biological, purely physico-dynamic kinetic processes and reactions influenced by environmental parameters, or through the direct intervention, creative force and activity of an intelligent agency, a powerful creator.  Which of the two makes more sense? 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697424/


Ribosome biogenesis: quality control mechanisms must be in place to survey nascent ribosomes and ensure their functionality.
1. Chiral checkpoints during protein biosynthesis the ribosome act as “chiral checkpoints” by preferentially binding to L-amino acids or L-aminoacyl-tRNAs, thereby excluding D-amino acids 11
2. If misaminoacylated tRNA is successfully delivered to the ribosome, additional proofreading occurs within the A site of the ribosome based on aa-tRNA position and affinity
Ribosomal interactions with additional tRNA-specific sequences and modifications facilitate accurate selection of aa-tRNAs based on kinetic discrimination during the initial selection stage and subsequent proofreading stage.
3. mRNA translation regulation by nearly 100 epigenetic tRNA modifications.  The finer details in this sort of regulation have been proven to differ between prokaryotic and eukaryotic organisms. ( LUCA hello ??!! 10)
4. tRNA structure monitoring: Export of defective or immature tRNAs is avoided by monitoring both structure and function of tRNAs in the nucleus, and only tRNAs with mature 5′ and 3′ ends are exported. 6
5. tRNA synthesis quality control: RTD and other mechanisms that degrade hypomodified or mutated mature yeast tRNAs serve as a surveillance system to eliminate tRNA molecules that have incorrect nucleosides or conformations
6. Aminoacyl-tRNA synthetase error minimization by preferential binding of the right amino acids, and selective editing and proofreading of near cognate amino acids
7. Aminoacyl-tRNA synthetase Pre-transfer editing: Pre-transfer editing has been described in both class I and class II aaRSs and takes place after aa-AMP synthesis but before the aminoacyl moiety is transferred to the tRNA. 9
8. Aminoacyl-tRNA synthetase Post-transfer editing: Post-transfer editing takes place after the transfer of the amino acid to the tRNA and involves the hydrolysis of the ester bond, in a domain separated from the active site. 
9. Aminoacyl-tRNA synthetase Editing factors: Another important component of the translation quality control machinery is the trans-editing family, free-standing proteins that are not synthetases but are in some cases homologs to the editing domains of such enzymes. The role of these trans-editing factors is to clear the misacylated tRNA before it reaches the ribosome, acting as additional checkpoints to ensure fidelity. 
10. Aminoacyl-tRNA synthetases (aaRSs), selectively hydrolyze ( chemical reaction in which a molecule of water ruptures one or more chemical bonds )  incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. 12

B.Alberts Molecular Biology of the Cell. 4th edition: From RNA to Protein 2002
aaRS come in two unrelated families; 10 of the 20 amino acids need a Class I aaRS, the other 10 a Class II aaRS. This landscape is thus littered with perplexing questions like these:
I. Why wasn’t one ancestor enough when they both do the same job?
II. How did the two types of ancestral synthetases avoid competition that might have eliminated the inferior Class? 12
https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids

Errors that occur during transcription and translation have substantial effects on gene function by producing misfolded and malfunctioning proteins. The rate of translation errors is typically an order of magnitude higher than the rate of transcription errors. 1 Errors occurring during transcription often elicit more dire consequences than those occurring during translation because individual mRNAs can be translated up to 40 times resulting in a burst of flawed proteins. Therefore, a single transcription error can result in many flawed proteins, whereas a translation error will disrupt only a single protein. Estimates of the rate of transcription errors in Escherichia coli have yielded variable estimates of transcription error rates of 10−4–10−5 per nucleotide, several orders of magnitude higher than the mutation rate . Transcript-error rates are 3 to 4 orders of magnitude higher than the corresponding genetic mutation rates.  The general error rates of genomic replication (about 10− are estimated to be approximately 10,000-fold lower than those of protein synthesis (about 10−4), and thus in most instances, mRNA translation is the key process contributing to the inaccuracy of the cellular proteome 4

Gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. 3  Alterations in mRNA stability can have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have unique post-transcriptional control mechanisms to enact such adaptive responses through:

1) general mRNA decay,
2) differential mRNA degradation using small non-coding RNAs (sRNAs), and
3) selective mRNA degradation using the tmRNA quality control system.

As with other biomolecules, the great variety of RNA species produced by the bacterial cell requires quality control mechanisms to ensure proper folding and function. In addition, the role of mRNA as a template for protein synthesis adds greater significance to mRNA quality control. The translation of a faulty transcript without adequate quality assurance measures might lead to the accumulation of aberrant protein products that could be detrimental to the cell. Bacterial mRNAs are not post-transcriptionally spliced, nor do they exhibit the 5’-cap structures of their eukaryotic counterparts. As such, post-transcriptional quality control processes of prokaryotic mRNA are distinct from the corresponding processes in eukaryotes. This review focuses on issues related to post-transcriptional processing, targeting, and degradation of bacterial mRNAs including those facilitated by small regulatory RNAs, with special emphasis on tmRNA and trans-translation.

Variation in the stability of transcripts has an important role in the control of protein expression within the cell, as long-lived transcripts are generally subject to more rounds of translation than those with a shorter half-life. Several factors play a role in controlling the lifespan of specific mRNAs by regulating their propensity to be degraded.

Translational decoding of the mRNA codons is constrained by factors during codon-anticodon recognition and often constitutes the rate-limiting step during protein synthesis. Besides the abundance of tRNA species, mRNA translation is regulated by nearly 100 epigenetic tRNA modifications, especially at the wobble position 4  Faithful translation of the mRNA codons into protein is essential for cellular physiology. The fidelity of the translation machinery firstly depends on the specific coupling of amino acids to their cognate tRNA species, which is catalyzed by aminoacyl-tRNA synthetases (aaRSs). Eukaryotic elongation factor 1A (eEF-1A) or prokaryotic EF-Tu delivers the aminoacyl-tRNA to the ribosome A site for elongation of nascent peptide chain after proper codon-anticodon recognition. Thus, aminoacyl-tRNA synthetase (aaRSs) are cardinal in protecting protein synthesis against misacylation ( incorrectly adding an acyl group to a compound).

tRNA synthesis quality control
Hypomodified tRNAs (modified to an abnormally small degree) can be degraded by the RNA degradosome, a multicomponent RNA degradation complex. Thus, the degradosome serves as a previously unrecognized bacterial tRNA quality control system that mediates clearance of hypomodified tRNAs.can be degraded by the RNA degradosome, a multicomponent RNA degradation complex. Thus, the degradosome serves as a bacterial tRNA quality control system that mediates clearance of hypomodified tRNAs. 1  Within the anticodon, the first or “wobble” position is particularly subject to modification, and these modifications are often critical for efficient translation; consequently, mutations that prevent such modification can result in loss of viability.  tRNAs’ highly stable structures are thought to contribute to their intracellular stability; in general, tRNAs exhibit a high melting temperature in vitro and a long half-life within the cell. RTD and other mechanisms that degrade hypomodified or mutated mature yeast tRNAs serve as a surveillance system to eliminate tRNA molecules that have incorrect nucleosides or conformations
In order to ensure fidelity, some of the synthetases perform editing functions to reduce the occurrence of errors during protein synthesis. 5

Quality control mechanisms during ribosome maturation
Protein synthesis on ribosomes is carefully quality controlled to ensure the faithful transmission of genetic information from mRNA to protein. Many of these mechanisms rely on communication between distant sites on the ribosomes, and thus on the integrity of the ribosome structure. Furthermore, haploinsufficiency of ribosomal proteins, which increases the chances of forming incompletely assembled ribosomes, can predispose to cancer. Finally, release of inactive ribosomes into the translating pool will lead to their degradation together with the degradation of the bound mRNA. Together, these findings suggest that quality control mechanisms must be in place to survey nascent ribosomes and ensure their functionality. This review gives an account of these mechanisms as currently known. 7

Proof-reading Yeast employs structural proofreading of ribosome functional centres during nuclear steps of assembly
Accumulating evidence indicates a tight coupling between nuclear export, cytoplasmic maturation, and final proofreading of the ribosome. 
We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.
To minimize production of dysfunctional ribosomes, yeast employs structural proofreading of ribosome functional centres during nuclear steps of assembly
Arx1 binding may serve to proofread the proper accommodation of these ribosomal proteins into the tunnel exit
time window for the quality-control machinery to functionally proofread preribosomes. 


Error check and repair in the Ribosome: More details come to light
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. 

https://www.youtube.com/watch?v=8Hsz_Vmcy-Y&feature=emb_title

Carnegie Institution for Science Quality control mechanism closes the protein production 'on-ramps' in cells OCTOBER 8, 2020
Quality control mechanism closes the protein production 'on-ramps' in cells
Recent work led by Carnegie's Kamena Kostova revealed a new quality control system in the protein production assembly line with possible implications for understanding neurogenerative disease.
The DNA that comprises the chromosomes housed in each cell's nucleus encodes the recipes for how to make proteins, which are responsible for the majority of the physiological actions that sustain life. Individual recipes are transcribed using messenger RNA, which carries this piece of code to a piece of cellular machinery called the ribosome. The ribosome translates the message into amino acids—the building blocks of proteins.
But sometimes messages get garbled. The resulting incomplete protein products can be toxic to cells. So how do cells clean up in the aftermath of a botched translation?
Some quality assurance mechanisms were already known—including systems that degrade the half-finished protein product and the messenger RNA that led to its creation. But Kostova led a team that identified a new tool in the cell's kit for preventing damage when protein assembly goes awry. Their work was published by Molecular Cell.
Using CRISPR-Cas9-based genetic screening, the researchers discovered a separate, and much needed, device by which the cell prevents that particular faulty message from being translated again. They found two factors, called GIGYF2 and 4EHP, which prevent translation from being initiated on problematic messenger RNA fragments.
"Imagine that the protein assembly process is a highway and the ribosomes are cars traveling on it," Kostova explained. "If there's a bad message producing incomplete protein products, it's like having a stalled car or two on the road, clogging traffic. Think of GIGYF2 and 4EHP as closing the on-ramp, so that there is time to clear everything away and additional cars don't get stalled, exacerbating the problem."
Loss of GIGYF2 has previously been associated with neurodegenerative and neurodevelopmental problems. It is possible that these issues are caused by the buildup of defective proteins that occurs without the ability to prevent translation on faulty messenger RNAs.
https://phys.org/news/2020-10-quality-mechanism-protein-production-on-ramps.html?fbclid=IwAR2LGlA78YPImmk44TTaKTgwsDEYA3hVKOny8J4XY3c7lHeejUYqxErjFA4

Amazing surveillance pathways that rescue ribosomes lost in translation point to intelligently designed mechanisms

https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messenger-rna-translation-in-the-ribosome-by-chance-or-design#8048

The final step of the central dogma is the most complex, where the information in RNA is translated to build proteins in the ribosome.  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. The ribosome uses an incredible peace of bio-engineering to rescue a stalled situation when they get stuck at the end of the truncated chain. They use a mechanism called Trans-translation. It is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. This mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frame shifting. Trans-Translation is performed by a ribonucleoprotein complex. A strangely shaped RNA molecule mimics both a transfer RNA and a messenger RNA, restarting the process and cleaning up the mess. A proteolysis-inducing tag is added at the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. Trans-translation relies on two main factors: small stable 10S RNA (ssrA), an aminoacylated transfer-messenger RNA (tmRNA) with properties both of a tRNA and an mRNA; and SmpB (small protein B). 

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.
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

Transfer-messenger RNA
https://en.wikipedia.org/wiki/Transfer-messenger_RNA

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

Biology of trans-Translation
The trans-translation mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. trans-Translation is performed by a ribonucleoprotein complex composed of tmRNA, a specialized RNA with properties of both a tRNA and an mRNA, and the small protein SmpB. tmRNA-SmpB interacts with translational complexes stalled at the 3prime end of anmRNA to release the stalled ribosomes and target the nascent polypeptides and mRNAs for degradation. In addition to quality control pathways, some genetic regulatory circuits use transtranslation to control gene expression. Diverse bacteria require transtranslation when they execute large changes in their genetic programs, including responding to stress, pathogenesis, and differentiation. 1

Genes encoding tmRNA and SmpB are present throughout the bacterial kingdom.


trans-Translation removes all components of stalled translation complexes. 
tmRNA binds to SmpB and is aminoacylated by alanyl-tRNA synthetase (AlaRS). EF-Tu in the GTP state binds to alanyl-tmRNA, activating the complex for ribosome interaction. The alanyl-tmRNA/SmpB/EF-Tu complex recognizes ribosomes at the 3' end of an mRNA and enters the A-site as though it were a tRNA. The nascent polypeptide is transferred to tmRNA, and the tmRNA tag reading frame replaces the mRNA in the decoding center. The mRNA is rapidly degraded. Translation resumes, using tmRNA as a message, resulting in addition of the tmRNA-encoded peptide tag to the C terminus of the nascent polypeptide. Translation terminates at a stop codon in tmRNA, releasing the ribosomal subunits and the tagged protein. Multiple proteases recognize the tmRNA tag sequence and rapidly degrade the protein (box 3).



1. https://sci-hub.st/https://www.annualreviews.org/doi/10.1146/annurev.micro.62.081307.162948
2. https://sci-hub.st/https://www.nature.com/articles/nrm3457?proof=t

Claudia Müller  Ribosome Rescue Pathways in Bacteria 18 March 2021 1

Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes.

My comment: Ribosomes are life-essential and had to be fully developed, and in operation, when life started. That includes the diverse rescue arrays that remove the stalled aberrant mRNA's.
That means evolution is an inadequate explanation. There was no evolution prior to DNA replication.

In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation.

My comment: in addition, if these degradation mechanisms were not fully in place either right from the beginning, the cell would be soon full of aberrant mRNA's, which would be toxic to the cell, and the cell would die.

Bacteria have evolved a diverse array of mechanisms to rescue no-go and non-stop ribosomal complexes. This is critical for survival in bacteria since otherwise ribosomes and tRNAs become sequestered from the pool of free translational components and the capacity of the cell to produce proteins rapidly diminishes

1. https://www.frontiersin.org/articles/10.3389/fmicb.2021.652980/full

How Cells Keep Right-Handed Amino Acids Out
https://evolutionnews.org/2015/04/how_cells_keep/


Michael T. Englander: The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center April 27, 2015
https://www.pnas.org/doi/10.1073/pnas.1424712112

Questions to ChatGTP about the origin of the error check and repair mechanisms of the Ribosome

https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messenger-rna-translation-in-the-ribosome-by-chance-or-design#9839

Question: How many error check and repair systems are in the ribosome ?
Response ChatGTP: The ribosome has several error check and repair systems that help to ensure the fidelity of protein synthesis. These systems include proofreading and editing mechanisms that can detect and correct errors in the process of translation. Here are some of the key error check and repair systems in the ribosome:

1. Codon-anticodon base pairing: The ribosome relies on the precise base pairing between codons on the mRNA and anticodons on tRNA to ensure that the correct amino acid is incorporated into the growing protein chain. This process is highly selective and helps to prevent errors in translation.

2. Ribosome-associated proofreading: The ribosome has a proofreading mechanism that can detect errors in codon-anticodon base pairing. If an incorrect amino acid is added to the growing protein chain, the ribosome can stall and allow time for the incorrect tRNA to dissociate and be replaced with the correct tRNA.

3. Peptidyl transferase center (PTC): The PTC is the active site of the ribosome where peptide bond formation occurs. The PTC has a highly selective mechanism that helps to prevent errors in peptide bond formation, ensuring that only correct amino acids are incorporated into the protein.

4. Quality control mechanisms: In addition to proofreading and editing mechanisms, the ribosome also has quality control mechanisms that can recognize and correct errors in protein synthesis. For example, the ribosome-associated quality control (RQC) system can recognize and degrade proteins that are stalled during translation due to errors in codon-anticodon pairing or other factors.

5. Overall, the ribosome has multiple error check and repair systems that help to ensure the accuracy of protein synthesis. These mechanisms are critical for the proper functioning of cells and organisms, and they play an important role in maintaining the fidelity of the genetic code.

Question: Are aminoacyl tRNA synthetases also under error check and repair?
Response ChatGTP:  Yes, aminoacyl tRNA synthetases are also under error check and repair mechanisms.

Aminoacyl tRNA synthetases (aaRS) are enzymes that are responsible for attaching the correct amino acid to its corresponding transfer RNA (tRNA) molecule during protein synthesis. The accuracy of this process is essential for maintaining the fidelity of the genetic code and preventing errors in protein synthesis.

To ensure the accuracy of aminoacylation, aaRSs have evolved several mechanisms to detect and correct errors. One such mechanism is the "proofreading" activity, which involves the hydrolysis of incorrectly charged tRNAs by the aaRS enzyme. This ensures that only the correct amino acid is attached to the tRNA, and any errors are corrected.

In addition to proofreading, other error correction mechanisms have been identified, including editing by separate domains within the aaRS enzymes, as well as mechanisms that involve additional proteins that help to detect and correct errors.

Overall, the accuracy of aminoacylation by aaRSs is critical for the proper functioning of the genetic code, and error check and repair mechanisms have evolved to ensure the fidelity of this process.

Question: How accurate is protein synthesis by the ribosome ? how often is a wrong amino acid incorporated in the nascent polymer strand?
Response ChatGTP: Protein synthesis by the ribosome is highly accurate, with an error rate estimated to be around 1 in 10,000 to 1 in 100,000 amino acids incorporated.

The accuracy of protein synthesis is ensured by several mechanisms, including the proofreading activity of aminoacyl-tRNA synthetases (which attach the correct amino acid to the corresponding tRNA), the fidelity of codon-anticodon base pairing between the mRNA and tRNA, and the accuracy of peptide bond formation by the ribosome.

Despite these error-checking mechanisms, mistakes can still occur during protein synthesis. The incorporation of a wrong amino acid can result from various factors, including errors in tRNA charging by aminoacyl-tRNA synthetases, errors in codon recognition by tRNA, or mistakes in the peptide bond formation by the ribosome.

However, the frequency of these errors is relatively low, with studies suggesting that the error rate is typically less than 0.1% for most amino acids. Additionally, the ribosome has additional proofreading mechanisms that can detect and correct some of these errors, further reducing the frequency of errors in protein synthesis.

Overall, while errors in protein synthesis can occur, the ribosome's accuracy is quite high, and the fidelity of the process is critical for the proper functioning of the cell.

Question:  You informed that those error check and repairs evolved. But the proper funcion of the ribosome had to be guaranteed for life to start. That means, the origin of these error check and repair mechanisms  had to be fully functional when life started. That means, evolution could not have plaid a role in its origin.
Response ChatGTP: It is true that the proper functioning of the ribosome is essential for life, and that the error-checking and repair mechanisms that ensure the fidelity of protein synthesis had to be present and functional at the time life began. However, it is important to note that the evolution of these mechanisms did not necessarily have to occur after the origin of life.

It is widely accepted that the origin of life involved a complex series of chemical and physical processes that eventually gave rise to the first living organisms. The exact nature of these processes is still not fully understood, but it is likely that they involved the gradual emergence and refinement of the molecular machinery that underlies the fundamental processes of life.

In this context, it is possible that the error-checking and repair mechanisms that are present in modern organisms arose through gradual evolution from simpler systems that were present at the time life began. While the exact details of this evolutionary process are not known, it is thought that the high accuracy of modern protein synthesis is the result of a long history of evolutionary refinement and optimization of the molecular machinery involved.

In summary, while the error-checking and repair mechanisms that ensure the fidelity of protein synthesis had to be present and functional at the time life began, it is still possible that they arose through the process of evolution, which may have played a role in the emergence and refinement of the molecular machinery that underlies the fundamental processes of life.

Question: But a high degree of fidelity had to be guaranteed right from the beginning. And its origin cannot be explained by evolution, since the origin of life has nothing to do with evolution.
Response ChatGTP:  While the origin of life and the subsequent evolution of living organisms are distinct processes, it is important to recognize that they are closely related and are not completely independent of each other. The emergence of the first living organisms from non-living matter was likely a gradual process that involved a series of chemical and physical events that eventually gave rise to the first self-replicating systems. Once self-replication was established, evolution by natural selection could have taken place.

Regarding the origin of the error-checking and repair mechanisms that ensure the fidelity of protein synthesis, it is possible that these mechanisms were present in the first self-replicating systems, as they would have been essential for the accurate transmission of genetic information from one generation to the next. The exact nature of these mechanisms is not known, but it is likely that they evolved gradually through a series of genetic and biochemical changes that increased the fidelity of protein synthesis over time.

Therefore, while the origin of life and the evolution of living organisms are distinct processes, they are not completely independent, and it is possible that the error-checking and repair mechanisms that ensure the fidelity of protein synthesis arose through a combination of both processes.