ArticleJournal of molecular evolution2011
Evolution of prokaryotic genes by shift of stop codons.
Article in Journal of molecular evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
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- Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation.Molecular ecology · 2024Article
- Pairs of Mutually Compensatory Frameshifting Mutations Contribute to Protein Evolution.Molecular biology and evolution · 2022Article
- Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences.Molecular biology and evolution · 2020Article
- Impact of C-terminal amino acid composition on protein expression in bacteria.Molecular systems biology · 2020Article
- In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons.PLoS genetics · 2019Article
- Genotyping and Bio-Sensing Chemosensory Proteins in Insects.Sensors (Basel, Switzerland) · 2017Review
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- In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes.BMC genomics · 2016Article
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- The Recent De Novo Origin of Protein C-Termini.Genome biology and evolution · 2015Article
- Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon.Scientific reports · 2015Article
- Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.BioMed research international · 2015Article
- Overlapping genes: a window on gene evolvability.BMC genomics · 2014Article
- Compensatory evolution and the origins of innovations.Genetics · 2013Article
- Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont.Genome biology and evolution · 2013Article
- Stop codons in bacteria are not selectively equivalent.Biology direct · 2012Article
- Evolutionary pressures on simple sequence repeats in prokaryotic coding regions.Nucleic acids research · 2012Article
- Methods of combinatorial optimization to reveal factors affecting gene length.Bioinformatics and biology insights · 2012Article
- Putatively noncoding transcripts show extensive association with ribosomes.Genome biology and evolution · 2011Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
De novo origin of coding sequence remains an obscure issue in molecular evolution. One of the possible paths for addition (subtraction) of DNA segments to (from) a gene is stop codon shift. Single nucleotide substitutions can destroy the existing stop codon, leading to uninterrupted translation up to the next stop codon in the gene's reading frame, or create a premature stop codon via a nonsense mutation. Furthermore, short indels-caused frameshifts near gene's end may lead to premature stop codons or to translation past the existing stop codon. Here, we describe the evolution of the length of coding sequence of prokaryotic genes by change of positions of stop codons. We observed cases of addition of regions of 3'UTR to genes due to mutations at the existing stop codon, and cases of subtraction of C-terminal coding segments due to nonsense mutations upstream of the stop codon. Many of the observed stop codon shifts cannot be attributed to sequencing errors or rare deleterious variants segregating within bacterial populations. The additions of regions of 3'UTR tend to occur in those genes in which they are facilitated by nearby downstream in-frame triplets which may serve as new stop codons. Conversely, subtractions of coding sequence often give rise to in-frame stop codons located nearby. The amino acid composition of the added region is significantly biased, compared to the overall amino acid composition of the genes. Our results show that in prokaryotes, shift of stop codon is an underappreciated contributor to functional evolution of gene length.
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