Genes under positive selection in Escherichia coli

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

In: Genome Research, Vol. 17, No. 9, 2007, p. 1336-43.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Petersen, L, Bollback, JP, Dimmic, M, Hubisz, M & Nielsen, R 2007, 'Genes under positive selection in Escherichia coli', Genome Research, vol. 17, no. 9, pp. 1336-43. https://doi.org/10.1101/gr.6254707

APA

Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007). Genes under positive selection in Escherichia coli. Genome Research, 17(9), 1336-43. https://doi.org/10.1101/gr.6254707

Vancouver

Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 2007;17(9):1336-43. https://doi.org/10.1101/gr.6254707

Author

Petersen, Lise ; Bollback, Jonathan P ; Dimmic, Matt ; Hubisz, Melissa ; Nielsen, Rasmus. / Genes under positive selection in Escherichia coli. In: Genome Research. 2007 ; Vol. 17, No. 9. pp. 1336-43.

Bibtex

@article{7055d080194a11deb43e000ea68e967b,
title = "Genes under positive selection in Escherichia coli",
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.",
author = "Lise Petersen and Bollback, {Jonathan P} and Matt Dimmic and Melissa Hubisz and Rasmus Nielsen",
note = "Keywords: Amino Acid Sequence; Bacterial Proteins; Escherichia coli K12; Genes, Bacterial; Genome, Bacterial; Molecular Sequence Data; Recombination, Genetic; Selection (Genetics); Sequence Analysis, DNA; Sequence Homology, Amino Acid",
year = "2007",
doi = "10.1101/gr.6254707",
language = "English",
volume = "17",
pages = "1336--43",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "9",

}

RIS

TY - JOUR

T1 - Genes under positive selection in Escherichia coli

AU - Petersen, Lise

AU - Bollback, Jonathan P

AU - Dimmic, Matt

AU - Hubisz, Melissa

AU - Nielsen, Rasmus

N1 - Keywords: Amino Acid Sequence; Bacterial Proteins; Escherichia coli K12; Genes, Bacterial; Genome, Bacterial; Molecular Sequence Data; Recombination, Genetic; Selection (Genetics); Sequence Analysis, DNA; Sequence Homology, Amino Acid

PY - 2007

Y1 - 2007

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.

U2 - 10.1101/gr.6254707

DO - 10.1101/gr.6254707

M3 - Journal article

C2 - 17675366

VL - 17

SP - 1336

EP - 1343

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 9

ER -

ID: 11529270