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What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention.

Carter CW - Life (Basel) (2015)

Bottom Line: We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code.Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene.Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA. carter@med.unc.edu.

ABSTRACT
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule.

No MeSH data available.


Related in: MedlinePlus

Amino acid specificity spectra of Class I LeuRS and Class II HisRS2 Urzymes. The net free energy for specificity of Class I and II Urzymes for homologous vs. heterologous substrates, i.e., ΔG(kcat/KM)ref – ΔG(kcat/KM)amino acid (i), where ref is the cognate amino acid, is approximately 1 kcal/mole for both Class I and II Urzymes (center). Class I amino acids are colored blue; Class II amino acids are colored green. Bold colors denote substrates from the homologous Class; pastel colors denote heterologous substrates.
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life-05-00294-f006: Amino acid specificity spectra of Class I LeuRS and Class II HisRS2 Urzymes. The net free energy for specificity of Class I and II Urzymes for homologous vs. heterologous substrates, i.e., ΔG(kcat/KM)ref – ΔG(kcat/KM)amino acid (i), where ref is the cognate amino acid, is approximately 1 kcal/mole for both Class I and II Urzymes (center). Class I amino acids are colored blue; Class II amino acids are colored green. Bold colors denote substrates from the homologous Class; pastel colors denote heterologous substrates.

Mentions: The small sample of two aaRS Urzymes examined thus far retains ~20% of the Gibbs energy by which the full length enzymes achieve specific amino acid recognition ([20]; Figure 6). Urzymes derived from the two Classes favor amino acid substrates from their own class by ~1 kcal/mol. These unprecedented experimental data are the first to frame in quantitative terms the suggestion of Woese that the first coded peptides were probably statistical ensembles [42,43] with homologous sequences, and varying ranges of functionality. That situation highlights a key stage in the evolutionary development of specificity required for any acceptable scenario describing continuous emergence of complexity from randomness. In this light, it seems far more likely that the complexity of nucleic acids and proteins grew together than it is that one polymer emerged first without the aid of the other.


What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention.

Carter CW - Life (Basel) (2015)

Amino acid specificity spectra of Class I LeuRS and Class II HisRS2 Urzymes. The net free energy for specificity of Class I and II Urzymes for homologous vs. heterologous substrates, i.e., ΔG(kcat/KM)ref – ΔG(kcat/KM)amino acid (i), where ref is the cognate amino acid, is approximately 1 kcal/mole for both Class I and II Urzymes (center). Class I amino acids are colored blue; Class II amino acids are colored green. Bold colors denote substrates from the homologous Class; pastel colors denote heterologous substrates.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390853&req=5

life-05-00294-f006: Amino acid specificity spectra of Class I LeuRS and Class II HisRS2 Urzymes. The net free energy for specificity of Class I and II Urzymes for homologous vs. heterologous substrates, i.e., ΔG(kcat/KM)ref – ΔG(kcat/KM)amino acid (i), where ref is the cognate amino acid, is approximately 1 kcal/mole for both Class I and II Urzymes (center). Class I amino acids are colored blue; Class II amino acids are colored green. Bold colors denote substrates from the homologous Class; pastel colors denote heterologous substrates.
Mentions: The small sample of two aaRS Urzymes examined thus far retains ~20% of the Gibbs energy by which the full length enzymes achieve specific amino acid recognition ([20]; Figure 6). Urzymes derived from the two Classes favor amino acid substrates from their own class by ~1 kcal/mol. These unprecedented experimental data are the first to frame in quantitative terms the suggestion of Woese that the first coded peptides were probably statistical ensembles [42,43] with homologous sequences, and varying ranges of functionality. That situation highlights a key stage in the evolutionary development of specificity required for any acceptable scenario describing continuous emergence of complexity from randomness. In this light, it seems far more likely that the complexity of nucleic acids and proteins grew together than it is that one polymer emerged first without the aid of the other.

Bottom Line: We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code.Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene.Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA. carter@med.unc.edu.

ABSTRACT
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule.

No MeSH data available.


Related in: MedlinePlus