Multiple conversion between the genes encoding bacterial class-I release factors.

Sohta A Ishikawa,Yuji Inagaki,Ryoma Kamikawa

doi:10.1038/srep12406

Sohta A Ishikawa, Yuji Inagaki + Show 1 more

Open Access

https://doi.org/10.1038/srep12406

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Journal: Scientific reports	Publication Date: Aug 10, 2015
Citations: 1	License type: CC BY 4.0

Affiliation: University of Tsukuba, Kyoto University

Abstract

Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. However, we here report two independent cases of conversion between RF1 and RF2 genes (RF1-RF2 gene conversion), which were severely examined by procedures incorporating the maximum-likelihood phylogenetic method. In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues. Nevertheless, the ‘direction’ of gene conversion appeared to be opposite from one another—from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other. The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.

Highlights

During translation in Bacteria, Archaea, and Eukarya, codons in mRNAs are recognized by aminoacyl tRNAs with cognate anticodons, except three stop codons
We anticipated the separation between RF1 and RF2 sequences, as the two paralogues are most likely established through a single gene duplication followed by divergence of codon specificity in the last common ancestor of extant bacteria[12]
With respect to the ancient separation of the release factors (RFs) paralogues, it is unexpected to find that a unique motif of 12 aa in length (12 aa-motif) is shared between the RF paralogues sampled from the vast majority of the 57 members of the class Bacteroidia examined in this study (Fig. 1A,B; see below for the details)

Summary

Introduction

During translation in Bacteria, Archaea, and Eukarya, codons in mRNAs are recognized by aminoacyl tRNAs with cognate anticodons, except three stop codons. RF1 and RF2 were functionally diverged from one another to recognize different sets of stop codons, the two proteins share the significant sequence similarity at the primary to tertiary structural levels[9,10,11]. These observations strongly suggest that two distinct class-I RFs emerged via gene duplication followed by functional divergence in the last common ancestor of bacteria[12]. In addition to the ‘classical’ gene conversion between multiple gene copies described above, the ‘non-classical’ cases of gene conversion between evolutionarily distant sequences—orthologous sequences in different genomes and paralogous sequences in the same genome—were documented by analyzing bacterial[21], archaeal[22,23,24], and eukaryotic[25,26,27] genomes in literature

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