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Coding of Class I and II Aminoacyl-tRNA Synthetases

Part of the Advances in Experimental Medicine and Biology book series (PROTRE,volume 966)

Abstract

The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically-active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.

Keywords

  • Bi-directional genetic coding
  • Modular deconstruction
  • Protozymes
  • Reflexivity
  • Synthetase class division
  • Urzymes

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Abbreviations

aaRS:

aminoacyl-tRNA synthetase(s)

TrpRS:

tryptophanyl-tRNA synthetase

LeuRS:

Leucyl-tRNA synthetase

HisRS:

histidyl-tRNA synthetase

ATP:

adenosine 5′ triphosphate

PPi:

inorganic pyrophosphate

ASA:

Solvent-accessible surface area

HSQC:

Heteronuclear Single-Quantum Correlation

BEAST:

Bayesian Evolutionary Analysis Sampling Trees

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Acknowledgments

Research from the Carter laboratory was supported by the National Institutes of General Medical Sciences, GM 78228 and GM40906. I am grateful for the comments of an anonymous referee, and for similar input from E. First.

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The author is unaware of any conflicts of interest.

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Carter, C.W. (2017). Coding of Class I and II Aminoacyl-tRNA Synthetases. In: Atassi, M. (eds) Protein Reviews. Advances in Experimental Medicine and Biology(), vol 966. Springer, Singapore. https://doi.org/10.1007/5584_2017_93

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