RNA tetraplex as a primordial peptide synthesis scaffold

Umehara, Takuya; Kitagawa, Takahiro; Nakazawa, Yu; Yoshino, Hinako; Nemoto, Ryohei; Tamura, Koji

doi:10.1016/j.biosystems.2012.03.003

Cited by 7 publications

(5 citation statements)

References 51 publications

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“…The CD spectra [ 30 ] of the R3C ligase ribozyme and its mutants dissolved in Ultrapure water (Invitrogen) at room temperature were taken using a J-805 Circular Dichroism Spectrometer (JASCO Corporation, Tokyo, Japan). The cell path length was 1 mm with a 50 nm/min scanning speed.…”

Section: Methodsmentioning

confidence: 99%

Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis

Kurihara

Uchida

Umehara

et al. 2014

Biology

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The R3C ligase ribozyme is an artificial ligase ribozyme produced by modification of the ribozyme that lacks cytidine. Here, we attempted to modify the original R3C ribozyme (73 nucleotides) by reducing the number of nucleotides while maintaining the maximum possible catalytic efficiency. By partially deleting both the “grip” (P4 + P5) and “hammer” (P3) stem-loops, we found the critical border to retain activity comparable to that of full-length R3C. The three-way junction structure was necessary to maintain enzymatic function and the stability of the “grip” (P4 + P5) stem had a large influence on the catalytic activity of R3C. The final minimized ribozyme we obtained comprised ~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Our findings suggest that the autocatalytic function in ribozymes is indeed possible to obtain using sequence lengths achievable with prebiotic synthesis.

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Section: Methodsmentioning

confidence: 99%

Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis

Kurihara

Uchida

Umehara

et al. 2014

Biology

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“…Interestingly, G-quadruplex motifs are found at both the 5′-termini of 5′-untranslated regions and immediately after the 3′-termini of coding sequences, suggesting their important role in translation as well as transcription [ 90 ]. In addition, G-quadruplex has been suggested to be a primordial scaffold for peptide bond formation using aminoacyl-tRNAs [ 91 ].…”

Section: Evolution Of the Genetic Code And Trnamentioning

confidence: 99%

Origins and Early Evolution of the tRNA Molecule

Tamura

2015

Life

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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.

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“…A model for primordial entropic RNA catalysis of peptide formation has been tested experimentally [ 118 ]. Specifically, two RNA minihelices with charged 3’-CCA terminals were used as tRNA precursors in conjunction with an RNA tetraplex (a duplex of two RNA duplexes) with four unpaired sequences complementary to the CCA sequences of the RNA minihelices.…”

Section: Place Of Rna In the Origin And Early Evolution Of Translamentioning

confidence: 99%

The Place of RNA in the Origin and Early Evolution of the Genetic Machinery

Wächtershäuser¹

2014

Life

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The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness.

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RNA tetraplex as a primordial peptide synthesis scaffold

Cited by 7 publications

References 51 publications

Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis

Development of a Functionally Minimized Mutant of the R3C Ligase Ribozyme Offers Insight into the Plausibility of the RNA World Hypothesis

Origins and Early Evolution of the tRNA Molecule

The Place of RNA in the Origin and Early Evolution of the Genetic Machinery

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