Molecular Mimicry Between Protein and tRNA

Nakamura, Yoshikazu

doi:10.1007/s002390010218

Cited by 17 publications

(12 citation statements)

References 43 publications

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“…This intriguing connection highlights the importance of molecular mimicry in the RNA-RNP (RNA plus protein) transition (Nakamura, 2001;Liang and Landweber, 2005;Delarue, 2007), and strongly supports our earlier hypothesis that the two complementary recognition patterns of acceptor stems by the class I and class II p-aaRSs were inherited from the two isofunctional ribozymes (Rodin et al, 1996). This is also relevant to the possible origin of the two p-aaRSs from the complementary strands of the same ancestral gene (Rodin and Ohno, 1995) that conceivably, directly recapitulates the preceding complementarity of the two r-aaRSs.…”

Section: Sn Rodin and As Rodinmentioning

confidence: 89%

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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Section: Sn Rodin and As Rodinmentioning

confidence: 89%

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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“…Moreover, the first aptamer-based therapeutic, Pegaptanib (Macugen), targeting vascular endothelial growth factor, was approved by the FDA in December 2004 for the treatment of age-related macular degeneration (AMD) (Ng et al 2006;Zhou and Wang 2006). Considering the basic principle of aptamer selection, the high potential of RNA to create a vast set of tertiary structures is conceivable from both the ''RNA world'' hypothesis (Gesteland et al 1999) and the concept of ''molecular mimicry'' between RNA and protein (Nakamura 2001).…”

Section: Introductionmentioning

confidence: 99%

Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G

Miyakawa¹,

Nomura²,

Sakamoto³

et al. 2008

RNA

Self Cite

109

107

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Potential applications for functional RNAs are rapidly expanding, not only to address functions based on primary nucleotide sequences, but also by RNA aptamer, which can suppress the activity of any target molecule. Aptamers are short DNA or RNA folded molecules that can be selected in vitro on the basis of their high affinity for a target molecule. Here, we demonstrate the ability of RNA aptamers to recognize-and bind to-human IgG with high specificity and affinity. An optimized 23-nucleotide aptamer, Apt8-2, was prepared, and was shown to bind to the Fc domain of human IgG, but not to other IgG's, with high affinity. Apt8-2 was observed to compete with protein A, but not with the Fcg receptor, for IgG binding. NMR chemical-shift analyses localized the aptamer-binding sites on the Fc subdomain, which partially overlaps the protein A binding site but not the Fcg receptor binding site. The tertiary structures of the predicted recognition sites on the Fc domain differ significantly between human IgG and other species of IgGs; this, in part, accounts for the high specificity of the selected aptamer. Apt8-2 can therefore be used as a protein A alternative for affinity purification of human IgG and therapeutic antibodies. Using Apt8-2 would have several potential advantages, raising the possibility of developing new applications based on aptamer design.

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“…The RNA world hypothesis (Gilbert 1986) leads to the conjecture that most or many proteins displaced RNA ancestors, allowing the transition from the RNA world to the protein-dominated world of today (Nakamura 2001). The fact that protein translation, a web of interactive RNAs and proteins, contains protein components that mimic tRNA implies that an important step in this transition was mimicry of functional or catalytic RNA by the proteins that usurped their role (Landweber 1999).…”

Section: Discussionmentioning

confidence: 99%

“…Among these proteins, the most striking ones are elongation factor G (EF-G) and the ribosome recycling factor (RRF). In terms of their size and shape, the EF-G molecule resembles strikingly well the ternary complex of the elongation factor Tu (EF-Tu) bound to a GTP analog and a tRNA molecule (Aevarsson et al 1994;Czworkowski et al 1994;Nissen et al 1995;Liljas 1996;Nakamura 2001). Both structures share a roughly globular GTPase domain and a similar long protrusion.…”

Section: Description Of Two Well-studied Protein-rna Examplesmentioning

confidence: 92%

“…In particular, domains III, IV, and V in EF-G appear respectively to mimic the shapes of the acceptor stem, the anti-codon helix, and the T stem of tRNA in the EF-Tu ternary complex (Fig. 1a,b) (Nakamura 2001). The structure of RRF when first solved was also found to be a near-perfect tRNA mimic (Selmer et al 1999).…”

Section: Description Of Two Well-studied Protein-rna Examplesmentioning

confidence: 95%

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Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA

Liang

Landweber

2005

RNA

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With rapidly increasing availability of three-dimensional structures, one major challenge for the post-genome era is to infer the functions of biological molecules based on their structural similarity. While quantitative studies of structural similarity between the same type of biological molecules (e.g., protein vs. protein) have been carried out intensively, the comparable study of structural similarity between different types of biological molecules (e.g., protein vs. RNA) remains unexplored. Here we have developed a new bioinformatics approach to quantitatively study the structural similarity between two different types of biopolymers-proteins and RNA-based on the spatial distribution of conserved elements. We applied it to two previously proposed tRNA-protein mimicry pairs whose functional relatedness between two molecules has been recently determined experimentally. Our method detected the biologically meaningful signals, which are consistent with experimental evidence.

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Molecular Mimicry Between Protein and tRNA

Cited by 17 publications

References 43 publications

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

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

Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G

Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA

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