Genes under positive selection in Escherichia coli

Lise Petersen, J.P. Bollback, Matt Dimmic, Melissa Hubisch, Rasmus Nielsen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.
OriginalsprogDansk
Artikelnummer 10.1101/gr.6254707
TidsskriftGenome Research
Vol/bind17
Udgave nummer9
Sider (fra-til)1336-1343
Antal sider7
ISSN1088-9051
StatusUdgivet - sep. 2007

Citer dette

Petersen, L., Bollback, J. P., Dimmic, M., Hubisch, M., & Nielsen, R. (2007). Genes under positive selection in Escherichia coli. Genome Research, 17(9), 1336-1343. [ 10.1101/gr.6254707].
Petersen, Lise ; Bollback, J.P. ; Dimmic, Matt ; Hubisch, Melissa ; Nielsen, Rasmus. / Genes under positive selection in Escherichia coli. I: Genome Research. 2007 ; Bind 17, Nr. 9. s. 1336-1343.
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abstract = "We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.",
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Petersen, L, Bollback, JP, Dimmic, M, Hubisch, M & Nielsen, R 2007, 'Genes under positive selection in Escherichia coli', Genome Research, bind 17, nr. 9, 10.1101/gr.6254707, s. 1336-1343.

Genes under positive selection in Escherichia coli. / Petersen, Lise; Bollback, J.P.; Dimmic, Matt; Hubisch, Melissa; Nielsen, Rasmus.

I: Genome Research, Bind 17, Nr. 9, 10.1101/gr.6254707, 09.2007, s. 1336-1343.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Genes under positive selection in Escherichia coli

AU - Petersen, Lise

AU - Bollback, J.P.

AU - Dimmic, Matt

AU - Hubisch, Melissa

AU - Nielsen, Rasmus

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N2 - We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.

AB - We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence for positive selection, such as the enigmatic rhs elements and transposases. Based on structural evidence, we hypothesize that the selection acting on transposases is related to the genomic conflict between transposable elements and the host genome.

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Petersen L, Bollback JP, Dimmic M, Hubisch M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 2007 sep;17(9):1336-1343. 10.1101/gr.6254707.