Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

Peter T S van der Gulik; Wouter D Hoff

doi:10.1371/journal.pone.0158342

Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

PLoS One. 2016 Jul 25;11(7):e0158342. doi: 10.1371/journal.pone.0158342. eCollection 2016.

Authors

Peter T S van der Gulik¹, Wouter D Hoff^{2

3}

Affiliations

¹ Centrum Wiskunde & Informatica, P.O. Box 94079, 1090 GB Amsterdam, The Netherlands.
² Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America.
³ Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America.

Abstract

Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA.

MeSH terms

Anticodon*
Archaea / genetics
Bacteria / genetics
Codon*
Eukaryota / genetics
Evolution, Molecular*
Genetic Code
Genetic Variation
RNA, Transfer / genetics*

Substances

Anticodon
Codon
RNA, Transfer

Grants and funding

This work was supported by the National Science Foundation grants MCB-1051590, MRI-1338097, and CHE-1412500: WDH (http://www.nsf.gov). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.