Same-strand overlapping genes in bacteria: compositional determinants of phase bias.

Biology Direct
Niv SabathGiddy Landan

Abstract

Same-strand overlapping genes may occur in frameshifts of one (phase 1) or two nucleotides (phase 2). In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes. We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in...Continue Reading

References

Apr 6, 1978·Nature·T Miyata, T Yasunaga
Jan 1, 1983·Annual Review of Genetics·S NormarkO Olsson
May 3, 1996·Science·J R Lobry
May 1, 1996·Molecular Biology and Evolution·J R Lobry
Aug 11, 2000·Evolution; International Journal of Organic Evolution·D C Krakauer
Jun 6, 2002·Trends in Genetics : TIG·Igor B RogozinEugene V Koonin
Dec 9, 2003·Gene·Yoko FukudaMasaru Tomita
Nov 3, 2004·Genome Research·Zackary I Johnson, Sallie W Chisholm
Dec 9, 2004·DNA and Cell Biology·Hervé Seligmann, David D Pollock
Feb 1, 2005·Computational Biology and Chemistry·Izabela MakalowskaWojciech Makalowski
May 5, 2007·Journal of Molecular Evolution·Peter J A Cock, David E Whitworth
Jul 24, 2007·Molecular Biology and Evolution·Carl KingsfordSteven L Salzberg
Sep 6, 2007·Genome Research·Robert BelshawAndrew Rambaut
Sep 29, 2007·Journal of Molecular Biology·Elizabeth J SummerRy Young
Dec 7, 2007·Nature Reviews. Genetics·Massimo Pigliucci
Jan 13, 2010·International Journal of Obesity : Journal of the International Association for the Study of Obesity·P A GrazianoS P Keane

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Citations

Sep 8, 2010·Journal of Molecular Evolution·Niv Sabath, Dan Graur
Dec 17, 2009·Molecular Biology and Evolution·Peter J A Cock, David E Whitworth
Feb 26, 2013·BMC Research Notes·Arun Gupta, Tiratha Raj Singh
May 29, 2009·Computational Biology and Chemistry·Tiratha Raj Singh, Kamal Raj Pardasani
Dec 17, 2014·Extremophiles : Life Under Extreme Conditions·Deeya SahaTapash Chandra Ghosh
Oct 2, 2014·PloS One·Katharina Mir, Steffen Schober
Nov 7, 2013·G3 : Genes - Genomes - Genetics·Miguel M FonsecaDavid Posada
Nov 22, 2016·Frontiers in Microbiology·Deeya SahaTapash C Ghosh

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