On the origin of the transfer RNA molecule

Giulio, Massimo Di

doi:10.1016/s0022-5193(05)80702-7

Cited by 124 publications

(119 citation statements)

References 21 publications

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“…The relationship between these sequences/ structures in minihelices and specific amino acids constitutes an operational RNA code for amino acids (14,21,27,63). The duplication and recombination of minihelices can lead to the full two-domain tRNA structure, where the anticodon-containing domain originated from the original minihelix (14,64,65). In this scenario, the triplets of the code arose from nucleotides associated with the operational RNA code (14, 61, 64 -67).…”

Section: Discussionmentioning

confidence: 99%

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase

Steer¹,

Schimmel

1999

Journal of Biological Chemistry

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The small size of the archaebacterial Methanococcus jannaschii tyrosyl-tRNA synthetase may give insights into the historical development of tRNAs and tRNA synthetases. The L-shaped tRNA has two major arms-the acceptor⅐TC minihelix with the amino acid attachment site and the anticodon-containing arm. The structural organization of the tRNA synthetases parallels that of tRNAs. The more ancient synthetase domain contains the active site and insertions that interact with the minihelix portion of the tRNA. A second, presumably more recent, domain interacts with the anticodon-containing section of tRNA. The small size of the M. jannaschii enzyme is due to the absence of most of the second domain, including a segment thought to bind to the anticodon. Consistent with the absence of an anticodonbinding motif, a mutation of the central base of the anticodon had a relatively small effect on the aminoacylation efficiency of the M. jannaschii enzyme. In contrast, others showed earlier that the same mutation severely reduced charging by a normal-sized bacterial enzyme that has the aforementioned anticodon-binding motif. However, the M. jannaschii enzyme has a peptide insertion into its catalytic domain. This insertion is shared with all other tyrosyl-tRNA synthetases and is needed for a critical minihelix interaction. We show that the M. jannaschii enzyme is active on minihelix substrates over a wide temperature range and has preserved the same peptide-dependent minihelix specificity seen in other tyrosine enzymes. These findings are consistent with the concept that anticodon interactions of tRNA synthetases were later adaptations to the emerging synthetase-tRNA complex that was originally framed around the minihelix.The tRNA secondary structure consists of two domains: the acceptor⅐TC stem-loop and the anticodon⅐D stem-loop ( Fig. 1) (1-3). This secondary structure forms an L-shaped tertiary fold where one domain (the acceptor⅐TC minihelix) is formed by the coaxial stacking of the 5-bp 1 TC stem onto the 7-bp acceptor helix (1, 4, 5). It contains the amino acid attachment site at the 3Ј-end. For many aminoacyl-tRNA synthetases (aaRSs), the acceptor⅐TC minihelix alone is a substrate for specific aminoacylation where sequence and structural elements in the acceptor helix confer specific recognition by an aaRS (6 -14). The second domain contains the anticodon triplet of the genetic code and is formed by the stacking of the anticodon stem onto the D stem. The anticodon domain serves as the template (mRNA) reading head.Aminoacyl-tRNA synthetases are universal proteins believed to have arisen early during the development of the genetic code. They are organized into two classes designated as class I and class .This classification is based on the sequences and structures of their active site domains. Like tRNAs, aaRSs are comprised of two major domainsϪa conserved class-defining catalytic domain and a second domain that is not conserved even for synthetases in the same class (20 -23). These two domains of the synthetase interact wit...

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Section: Discussionmentioning

confidence: 99%

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase

Steer¹,

Schimmel

1999

Journal of Biological Chemistry

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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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“…This brings us to the only reasonable solution-a duplication of anticodon within the same tRNA molecule (Di Giulio, 1992), a duplication that actually means that these two, presently very different, codes (operational and classic) were originally one and the same (Rodin et al, 1996). And this, in turn, necessarily implies that the bottom (dumbbell) module of tRNA might have originated by duplication from the top (minihelix) module, or vice versa ( Figure 1b); (Szathmary, 1999).…”

Section: The Rna Operational Codementioning

confidence: 99%

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

Rodin

2008

Heredity

103

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If the table of the genetic code is rearranged to put complementary codons face-to-face, it becomes apparent that the code displays latent mirror symmetry with respect to two sterically different modes of tRNA recognition. These modes involve distinct classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the acceptor stem, respectively. We analyze the anticodon pairs complementary to the face-toface codon couplets. Taking into account the invariant nucleotides on either side (5 0 and 3 0 ), we consider the risk of anticodon confusion and subsequent erroneous aminoacylation in the ancestral coding system. This logic leads to the conclusion that ribozymic precursors of tRNA synthetases had the same two complementary modes of tRNA aminoacylation. This surprising case of molecular mimicry (1) shows a key potential selective advantage arising from the partitioning of aaRSs into two classes, (2) is consistent with the hypothesis that the two aaRS classes were originally encoded by the complementary strands of the same primordial gene and (3) provides a 'missing link' between the classic genetic code, embodied in the anticodon, and the second, or RNA operational, code that is embodied mostly in the acceptor stem and is directly responsible for proper tRNA aminoacylation.

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On the origin of the transfer RNA molecule

Cited by 124 publications

References 21 publications

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase

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

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

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