Open Access Research article

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Christof Francke1246*, Tom Groot Kormelink1236, Yanick Hagemeijer6, Lex Overmars136, Vincent Sluijter6, Roy Moezelaar15 and Roland J Siezen1246

Author Affiliations

1 TI Food and Nutrition, P.O.Box 557, 6700AN Wageningen, The Netherlands

2 Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67 2628 BC Delft, The Netherlands

3 Wageningen University and Research Center, Laboratory of Microbiology, Dreijenplein 10, 6703 HB Wageningen, the Netherlands

4 Netherlands Bioinformatics Centre, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands

5 Wageningen University and Research Center, Food and Biobased Research, PO Box 17, 6700 AA The Netherlands

6 Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O.Box 9101, 6500HB Nijmegen, The Netherlands

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BMC Genomics 2011, 12:385  doi:10.1186/1471-2164-12-385

Published: 1 August 2011

Additional files

Additional file 1:

Presence-Absence analysis for genes encoding Sigma-54 and the related Enhancers. The file contains: sheet 1 with the results of the presence analysis of Sigma-54 and the related Enhancers in all bacterial genomes published before November 2009 listed in the GOLD database and with NCBI NC-code; and sheet 2, which provides a summary of the presence and absence in relation to genome size.

Format: XLS Size: 1.3MB Download file

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Additional file 2:

All collected Sigma-54 related EBPs with annotation. The file contains: sheet 1, which gives the complete list of putative Sigma-54 related EBPs for the studied genomes (given in additional file 1) in order of product of BLAST e-values related to experimentally verified EBPs (given in additional file 3); sheet 2, which provides the putative annotations; and sheet 3, which gives the annotation summary.

Format: XLS Size: 14.7MB Download file

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Additional file 3:

List of experimentally validated EBPs and a multiple sequence alignment of the 'GAFTGA' region. The file contains: sheet 1, which provides the list of EBPs that was used to search EBP homologs with BLASTP; sheet 2, which gives the list of EBPs that was used to annotate EBP homologs with reference to relevant experimental data in second column; sheet 3, which shows a snapshot of the multiple sequence alignment of the EBPs from sheet two in the GAFTGA region; sheet 4, which gives the list of EBPs with a defective GAFTGA sequence; and sheet 5, providing a summary of the related numbers.

Format: XLS Size: 1.5MB Download file

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Additional file 4:

Promoter predictions for model organaisms. The file contains: the promoter predictions for Bacillus subtilis (sheet 1), Escherichia coli (sheet 2), Lactobacillus plantarum (sheet 3) and Pseudomonas putida (sheet 4); and a summary of the predictions (sheet 5).

Format: XLS Size: 2MB Download file

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Additional file 5:

Representation of the gene annotations in the context of the Sigma-54 encoding genes. The file contains: sheet 1, giving the annotations present in the context of the Sigma-54 encoding genes in all species (10 genes upstream and 10 genes downstream); and a summary sheet 2.

Format: XLS Size: 2.6MB Download file

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Additional file 6:

Representation of the gene annotations in the context of the EBP encoding genes. The file contains: sheet 1, giving the annotations present in the context of the operons and divergons that contain a gene encoding an EBP (max 10 genes upstream and 10 genes downstream and max 300 nucleotides intergenic distance); and a summary sheet 2.

Format: XLS Size: 7.6MB Download file

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Additional file 7:

Representation of the gene annotations in the context of the Sigma-54 promoters. The file contains: sheet 1, giving the annotations present in the genes and operons that follow a correctly spaced and oriented Sigma-54 promoter (member of top 15 ranked hits)(1 gene upstream and max 10 genes downstream); and a summary sheet 2.

Format: XLS Size: 8.3MB Download file

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Additional file 8:

Validation of the Similar Motif Search Procedure. The file contains: sheets 1, 2 and 3, with the outcome of a comparison between SMS and MAST in the identification of CcpA and Spo0A regulon members in Bacillus subtilis; and sheet 4 with a summary of the comparison.

Format: XLS Size: 105KB Download file

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