Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting

Abstract

BackgroundGene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented.ResultsRNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the −2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5’ rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria.ConclusionsSince nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli’s central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0558-z) contains supplementary material, which is available to authorized users.

Are Antisense Proteins in Prokaryotes Functional?

“…While the evolutionary analysis of antisense proteins in prokaryotes awaits further investigation of strong overlapping gene candidates, those discovered so far are typically relatively young (e.g. (Fellner et al, 2014, Fellner et al, 2015, Hücker et al, 2018a. This may be seen as a point against their functionality, particularly for candidates limited to just one species.…”

Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation

“…In alternative, the gene novelty hypothesis argues that the birth of overlapping genes is driven by selection pressures favoring evolutionary innovation (Brandes and Linial, 2016). This hypothesis is supported by the finding that overlaps, thought for a long time to be restricted to viruses, also occur in the large genomes of prokaryotic (Delaye et al, 2008;Fellner et al, 2015) and eukaryotic organisms (Szklarczyk et al, 2007;Bergeron et al, 2013;Vanderperre et al, 2013).…”

New insights into the evolutionary features of viral overlapping genes by discriminant analysis

“…Overlapping genes were first detected in the genome of the bacteriophage ΦX174 by Barrell et al (1976). For many years they were thought to be limited to viruses, but experimental (Michel et al, 2012;Bergeron et al, 2013;Vanderperre et al, 2013;Fellner et al, 2015) and computational studies (Chung et al, 2007;Delaye et al, 2008;Ribrioux et al, 2008;Vanderperre et al, 2012) indicate that they also occur in prokaryotes and eukaryotes.…”