Open Access Research article

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

Neus Sanchez-Alberola12, Susana Campoy1, Jordi Barbé1 and Ivan Erill2*

Author Affiliations

1 Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain

2 Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21228, USA

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BMC Genomics 2012, 13:58  doi:10.1186/1471-2164-13-58

Published: 3 February 2012

Additional files

Additional file 1:

Analysis of rstR promoter regions. (A) Comparison of the rstR-rstA intergenic region of V. cholerae O395 classical O1 serotype and V. cholerae O1 biovar El Tor str. N16961. Predicted (O395) and known (N16961) promoter elements (-35 and -10) are highlighted in grey. Known (N16961, [72]) and predicted (O395) half-site operator sequences are highlighted in orange. Known (N16961) and predicted (O395) LexA-binding sites are shown in bold blue and underlined. RstR operators [36] are indicated by green boxes. (B) Alignment of 9 representative V. cholerae rstR-rstA intergenic regions. The LexA-binding site is shown in a blue box. The alignment shows a clear-cut distinction between El Tor and classical biotypes, but remarkably little divergence within each group, consistent with a recent dissemination of these phages. Sequence alignment was carried out using CLUSTALW [94] and default parameters. Adobe Portable Document File.

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Additional file 2:

Analysis of setR promoter regions. Alignment of the setR promoter region in different Vibrio cholerae strains. The SetR-binding sites [95] are highlighted in yellow. The putative promoter elements (-10 and -35) are bolded in blue. The translation start site for setR is bolded in red. Sequence alignment was carried out using CLUSTALW [94] and default parameters. Adobe Portable Document File.

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Additional file 3:

EMSA competition experiments. The lanes show, respectively, the standard EMSA using V. parahaemolyticus LexA and lexA promoter, the competition assay adding 200-fold excess of unlabelled lexA promoter, and the competition assay adding 200-fold excess of unlabelled non-specific DNA. JPEG image.

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Additional file 4:

LexA-binding site searches. Results for the LexA-binding site searches for the three phylogenetic groups analyzed in this work. The results are organized by organism and gene, providing information on the gene locus identifier (no identifier indicates absence in that organism), the predicted LexA-binding site sequence and its distance to the gene translation start site. Microsoft Excel format.

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Additional file 5:

Oligonucleotides. List of all oligonucleotides used in this work. Microsoft Word format.

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Additional file 6:

Strains and plasmids. List of all strains and plasmids used in this work. Microsoft Word format.

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