Special Issue "Evolution of tRNA"

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (31 October 2015).

Special Issue Editors

Guest Editor
Prof. Dr. Lluís Ribas de Pouplana

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
Website | E-Mail
Interests: genetic code; genetic translation; codon usage; proteome control; tRNAs; ribosomes; proteome quality control in cell biology and disease; structure-function studies of protein-RNA interactions; biomedicine and biotechnology
Guest Editor
Dr. Adrian Gabriel Torres

Institute for Research in Biomedicine (IRB), Barcelona, Catalonia, Spain
Website | E-Mail
Interests: small non-coding RNA biology; nucleic acids-based therapeutics; post-transcriptional control of gene expression

Special Issue Information

Dear Colleagues,

Transfer RNAs (tRNAs) are the key adaptor molecules that translate information from codons in messenger RNAs (mRNAs) into a polypeptide chain that will ultimately form a newly synthesized protein. Because of the essential role of tRNAs in protein translation, these molecules are, from an evolutionary point of view, as old as life itself.

Despite being discovered more than 50 years ago, tRNAs continue to amaze us. New non-canonical functions of tRNAs are being described, physiological roles for post-transcriptional modifications on tRNA residues have started to emerge, and the overall biology of tRNAs, from their enzymatic processing to their cellular transport, is being revisited.

In this Special Issue, experts in the field will present their thoughts and views on the evolution of tRNAs and how this evolution has affected the decoding strategies that different species have chosen for efficient protein translation. The scope of this Special Issue encompasses not only analysis of the conservation and divergence of tRNA genes, but also of canonical and non-canonical tRNA functions (such as aminoacylation), post-transcriptional editing, the role of codon usage, cellular control of translation elongation, links to other cellular pathways, and the balance between translation fidelity and efficiency.

We hope to include multi-disciplinary articles. Molecular, cellular, biochemical, and bioinformatical approaches that focus on tRNA are all welcome. In this way, we hope to compile an up-to-date perspective on this exciting and ever-growing research “arena”.

Prof. Dr. Lluís Ribas de Pouplana
Dr. Adrian Gabriel Torres
Guest Editors

Manuscript Submission Information

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Keywords

  • protein translation
  • transfer RNA
  • messenger RNA
  • post-transcriptional modifications
  • aminoacylation
  • tRNA synthetase
  • codon usage
  • translation fidelity
  • translation efficiency
  • translation machinery

Published Papers (14 papers)

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Research

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Open AccessArticle
tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World
Received: 28 August 2015 / Revised: 29 February 2016 / Accepted: 18 March 2016 / Published: 23 March 2016
Cited by 6 | PDF Full-text (794 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs were at the core [...] Read more.
Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes then arose in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by three kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessFeature PaperArticle
Non-Conserved Residues in Clostridium acetobutylicum tRNAAla Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch
Life 2015, 5(4), 1567-1582; https://doi.org/10.3390/life5041567
Received: 24 August 2015 / Revised: 16 September 2015 / Accepted: 18 September 2015 / Published: 28 September 2015
Cited by 3 | PDF Full-text (2591 KB) | HTML Full-text | XML Full-text
Abstract
The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions [...] Read more.
The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions between the tRNA and the leader RNA have been demonstrated to be necessary, but not sufficient, for efficient antitermination. In this study, we used the Clostridium acetobutylicum alaS gene, which encodes alanyl-tRNA synthetase, to investigate the specificity of the tRNA response. We show that the homologous C. acetobutylicum tRNAAla directs antitermination of the C. acetobutylicum alaS gene in vitro, but the heterologous Bacillus subtilis tRNAAla (with the same anticodon and acceptor end) does not. Base substitutions at positions that vary between these two tRNAs revealed synergistic and antagonistic effects. Variation occurs primarily at positions that are not conserved in tRNAAla species, which indicates that these non-conserved residues contribute to optimal antitermination of the homologous alaS gene. This study suggests that elements in tRNAAla may have coevolved with the homologous alaS T box leader RNA for efficient antitermination. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Review

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Open AccessReview
Multiple Layers of Stress-Induced Regulation in tRNA Biology
Received: 25 January 2016 / Revised: 14 March 2016 / Accepted: 17 March 2016 / Published: 23 March 2016
Cited by 16 | PDF Full-text (788 KB) | HTML Full-text | XML Full-text
Abstract
tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple [...] Read more.
tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple layers of regulatory mechanisms in each step of tRNA biogenesis. For example, tRNA 3′ trailer processing is altered upon nutrient stress; tRNA modification is reprogrammed under various stresses; nuclear accumulation of tRNAs occurs upon nutrient deprivation; tRNA halves accumulate upon oxidative stress. Here we address how environmental stresses can affect nearly every step of tRNA biology and we describe the possible regulatory mechanisms that influence the function or expression of tRNAs under stress conditions. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications
Received: 11 January 2016 / Revised: 27 February 2016 / Accepted: 7 March 2016 / Published: 14 March 2016
Cited by 10 | PDF Full-text (2141 KB) | HTML Full-text | XML Full-text
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In [...] Read more.
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?
Received: 16 November 2015 / Revised: 26 January 2016 / Accepted: 5 February 2016 / Published: 17 February 2016
Cited by 6 | PDF Full-text (662 KB) | HTML Full-text | XML Full-text
Abstract
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection [...] Read more.
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Exploiting tRNAs to Boost Virulence
Received: 13 November 2015 / Revised: 8 January 2016 / Accepted: 14 January 2016 / Published: 19 January 2016
Cited by 4 | PDF Full-text (242 KB) | HTML Full-text | XML Full-text
Abstract
Transfer RNAs (tRNAs) are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it [...] Read more.
Transfer RNAs (tRNAs) are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it difficult to characterize individual species quantitatively. However, due to the central role of the tRNA pool in protein biosynthesis as well as newly emerging roles played by tRNAs, their quantitative assessment yields important information, particularly relevant for virus research. Viruses which depend on the host protein expression machinery have evolved various strategies to optimize tRNA usage—either by adapting to the host codon usage or encoding their own tRNAs. Additionally, several viruses bear tRNA-like elements (TLE) in the 5′- and 3′-UTR of their mRNAs. There are different hypotheses concerning the manner in which such structures boost viral protein expression. Furthermore, retroviruses use special tRNAs for packaging and initiating reverse transcription of their genetic material. Since there is a strong specificity of different viruses towards certain tRNAs, different strategies for recruitment are employed. Interestingly, modifications on tRNAs strongly impact their functionality in viruses. Here, we review those intersection points between virus and tRNA research and describe methods for assessing the tRNA pool in terms of concentration, aminoacylation and modification. Full article
(This article belongs to the Special Issue Evolution of tRNA)
Open AccessFeature PaperReview
The tRNA Elbow in Structure, Recognition and Evolution
Received: 18 November 2015 / Revised: 4 January 2016 / Accepted: 6 January 2016 / Published: 12 January 2016
Cited by 18 | PDF Full-text (5850 KB) | HTML Full-text | XML Full-text
Abstract
Prominent in the L-shaped three-dimensional structure of tRNAs is the “elbow” where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face [...] Read more.
Prominent in the L-shaped three-dimensional structure of tRNAs is the “elbow” where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation
Received: 1 December 2015 / Revised: 23 December 2015 / Accepted: 25 December 2015 / Published: 31 December 2015
Cited by 2 | PDF Full-text (1569 KB) | HTML Full-text | XML Full-text
Abstract
Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is [...] Read more.
Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition
Received: 29 October 2015 / Revised: 7 December 2015 / Accepted: 15 December 2015 / Published: 23 December 2015
Cited by 1 | PDF Full-text (739 KB) | HTML Full-text | XML Full-text
Abstract
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even [...] Read more.
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even highly sophisticated features such as human cognition. RNA mediated RNA-aminoacylation can be seen as a first landmark on the path from the RNA world to modern DNA- and protein-based life. Likewise, the generation of the RNA modifications that can be found in various RNA species today may already have started in the RNA world, where such modifications most likely entailed functional advantages. This association of modification patterns with functional features was apparently maintained throughout the further course of evolution, and particularly tRNAs can now be seen as paradigms for the developing interdependence between structure, modification and function. It is in this spirit that this review highlights important stepping stones of the development of (t)RNAs and their modifications (including aminoacylation) from the ancient RNA world up until their present role in the development and maintenance of human cognition. The latter can be seen as a high point of evolution at its present stage, and the susceptibility of cognitive features to even small alterations in the proper structure and functioning of tRNAs underscores the evolutionary relevance of this RNA species. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification
Life 2015, 5(4), 1703-1725; https://doi.org/10.3390/life5041703
Received: 1 November 2015 / Revised: 24 November 2015 / Accepted: 25 November 2015 / Published: 8 December 2015
Cited by 7 | PDF Full-text (2840 KB) | HTML Full-text | XML Full-text
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, [...] Read more.
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Origins and Early Evolution of the tRNA Molecule
Life 2015, 5(4), 1687-1699; https://doi.org/10.3390/life5041687
Received: 14 October 2015 / Revised: 25 November 2015 / Accepted: 26 November 2015 / Published: 3 December 2015
Cited by 14 | PDF Full-text (3695 KB) | HTML Full-text | XML Full-text
Abstract
Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important role as “adaptor” molecules that mediate the translation of information from messenger RNAs (mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like [...] Read more.
Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important role as “adaptor” molecules that mediate the translation of information from messenger RNAs (mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA) can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3′ terminus of tRNA is also a typical characteristic of the molecule. “Why CCA?” is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC). The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression
Life 2015, 5(4), 1638-1651; https://doi.org/10.3390/life5041638
Received: 28 October 2015 / Revised: 17 November 2015 / Accepted: 17 November 2015 / Published: 27 November 2015
Cited by 38 | PDF Full-text (581 KB) | HTML Full-text | XML Full-text
Abstract
This review will summarise the recent discoveries and current state of research on short noncoding RNAs derived from tRNAs—known as tRNA-derived fragments (tRFs). It will describe the features of the known subtypes of these RNAs; including sequence characteristics, protein interactors, expression characteristics, biogenesis, [...] Read more.
This review will summarise the recent discoveries and current state of research on short noncoding RNAs derived from tRNAs—known as tRNA-derived fragments (tRFs). It will describe the features of the known subtypes of these RNAs; including sequence characteristics, protein interactors, expression characteristics, biogenesis, and similarity to canonical miRNA pathways. Also their role in regulating gene expression; including mediating translational suppression, will be discussed. We also highlight their potential use as biomarkers, functions in gene regulation and links to disease. Finally, this review will speculate as to the origin and rationale for the conservation of this novel class of noncoding RNAs amongst both prokaryotes and eukaryotes. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Open AccessReview
Non-Standard Genetic Codes Define New Concepts for Protein Engineering
Life 2015, 5(4), 1610-1628; https://doi.org/10.3390/life5041610
Received: 24 August 2015 / Revised: 12 October 2015 / Accepted: 21 October 2015 / Published: 12 November 2015
Cited by 11 | PDF Full-text (1555 KB) | HTML Full-text | XML Full-text
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally [...] Read more.
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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Other

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Open AccessHypothesis
Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code
Received: 1 December 2015 / Revised: 20 February 2016 / Accepted: 22 February 2016 / Published: 24 February 2016
Cited by 3 | PDF Full-text (922 KB) | HTML Full-text | XML Full-text
Abstract
We have previously proposed that tRNAGly was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, [...] Read more.
We have previously proposed that tRNAGly was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNAGly sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNASer has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNASer is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNASer and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio’s recent criticism of our proposal that tRNAGly was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers. Full article
(This article belongs to the Special Issue Evolution of tRNA)
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