The origin of the tRNA molecule: implications for the origin of protein synthesis

Giulio, Massimo Di

doi:10.1016/j.jtbi.2003.07.001

Cited by 94 publications

(79 citation statements)

References 32 publications

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“…1), that is to say, its origin might have been punctuated and not gradualistic. This also seems to be the case for the origin of the tRNA molecule (Di Giulio 1992Giulio , 2004Giulio , 2006Giulio , 2009 contrarily to the suggestions of other authors (Sun and Caetano-Anollés 2008;Rodin et al 2011). The V domain of the 23S rRNA seems also has had a segment of 110 nucleotides duplicated to place the P and A sites of the ribosome in the present evolutionary relationship (Bokov and Steinberg 2009).…”

Section: Introduction and Hypothesissupporting

confidence: 72%

The Origin of the 5S Ribosomal RNA Molecule Could Have Been Caused by a Single Inverse Duplication: Strong Evidence from Its Sequences

Branciamore

Giulio

2012

J Mol Evol

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The secondary structure of the 5S ribosomal RNA (5S rRNA) molecule shows a high degree of symmetry. In order to explain the origin of this symmetry, it has been conjectured that one half of the 5S rRNA molecule was its precursor and that an indirect duplication of this precursor created the other half and thus the current symmetry of the molecule. Here, we have subjected to an empirical test both the indirect duplication model, analysing a total of 684 5S rRNA sequences for complementarity between the two halves of the 5S rRNA, and the direct duplication model analysing in this case the similarity between the two halves of this molecule. In intra- and inter-molecule and intra- and inter-domain comparisons, we find a high statistical support to the hypothesis of a complementarity relationship between the two halves of the 5S rRNA molecule, denying vice versa the hypothesis of similarity between these halves. Therefore, these observations corroborate the indirect duplication model at the expense of the direct duplication model, as reason of the origin of the 5S rRNA molecule. More generally, we discuss and favour the hypothesis that all RNAs and proteins, which present symmetry, did so through gene duplication and not by gradualistic accumulation of few monomers or segments of molecule into a gradualistic growth process. This would be the consequence of the very high propensity that nucleic acids have to be subjected to duplications.

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Section: Introduction and Hypothesissupporting

confidence: 72%

The Origin of the 5S Ribosomal RNA Molecule Could Have Been Caused by a Single Inverse Duplication: Strong Evidence from Its Sequences

Branciamore

Giulio

2012

J Mol Evol

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“…24 Di Giulio 45,46 and Rodin & Ohno 47 have described models in which the anticodon loop arose from pre-existing, acceptor-stem RNA hairpins. The acceptor stem code may have helped mediate an early transitionfrom stereochemical coding of peptides directly by RNA to a rudimentary indirect coding mechanism 40,41,48 -paving the way for subsequent development of the universal genetic code and the interpretation of mRNAs by a ribosome.…”

Section: Independent Coding By the Trna Acceptor Stem And Anticodonmentioning

confidence: 99%

tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

Carter

Wolfenden

2015

RNA Biology

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The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyltRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology.

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“…It remains an open question whether ribozymes specific for different amino acids would evolve independently versus from a single promiscuous ancestor. The observed similarity among modern tRNAs has been suggested to be the result of diversification from a single ancestral ribozyme evolving specificity to a number of different amino acids [191][192][193].…”

Section: Inventing the Genetic Codementioning

confidence: 99%

The RNA World as a Model System to Study the Origin of Life

2015

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Understanding how life arose is a fundamental problem of biology. Much progress has been made by adopting a synthetic and mechanistic perspective on originating life. We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated informational and functional roles. There is cause for optimism on this difficult problem: the prebiotic chemical inventory may not have been as nightmarishly complex as previously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of self-replicating RNA; encapsulation in protocells provides evolutionary and biophysical advantages. Nevertheless, major issues remain unsolved, such as the origin of a genetic code. Attention to this field is particularly timely given the accelerating discovery and characterization of exoplanets.

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The origin of the tRNA molecule: implications for the origin of protein synthesis

Cited by 94 publications

References 32 publications

The Origin of the 5S Ribosomal RNA Molecule Could Have Been Caused by a Single Inverse Duplication: Strong Evidence from Its Sequences

The Origin of the 5S Ribosomal RNA Molecule Could Have Been Caused by a Single Inverse Duplication: Strong Evidence from Its Sequences

tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

The RNA World as a Model System to Study the Origin of Life

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