Abstract
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved.
Highlights
A sequence record has been maintained of some of the first and most central events in evolution of life on Earth
Synthetases (aaRS; i.e., GlyRS-IIA) [1,2,3,4,5]. tRNAs are charged with amino acids by aminoacyl-tRNA synthetase (aaRS) enzymes, so aaRS were some of the first enzymes to evolve [6]
The query sequence was from Pyrococcus furiosis, which is an ancient archaea that is closely related to the last universal common ancestor (LUCA) for translation functions [1,2,4,5]
Summary
A sequence record has been maintained of some of the first and most central events in evolution of life on Earth. TRNAs and minihelices were probably charged with ribozyme aaRS enzymes [11,12,13]. Analyzing sequences and structures of aaRS enzymes, in ancient archaea, the pathways of aaRS enzyme radiation were determined with little or no ambiguity. GlyRS-IIA appears to be closest to the primordial aaRS Despite their alternate folds, ValRS-IA and IleRS-IA enzymes have been shown to be sequence homologs of GlyRS-IIA [2]. N-terminus of a class IIA enzyme via an in-frame upstream transcription and translation start and by refolding of the aaRS structure nucleated by the N-terminal extension, which forms part of the class I aaRS active site. AaRS enzymes recognize the tRNA, the amino acid, and ATP [6]. Other ribozymes generated in vitro adenylate amino acids [17,18]
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