Open Access Research article

Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria

Lavanya Babujee1, Jennifer Apodaca1, Venkatesh Balakrishnan1, Paul Liss1, Patricia J Kiley2, Amy O Charkowski3, Jeremy D Glasner1 and Nicole T Perna14*

  • * Corresponding author: Nicole T Perna ntperna@wisc.edu

  • † Equal contributors

Author Affiliations

1 Biotechnology Center, University of Wisconsin-Madison, WI, USA

2 Department of Biomolecular Chemistry, University of Wisconsin-Madison, WI, USA

3 Department of Plant Pathology, University of Wisconsin-Madison, WI, USA

4 Department of Genetics, University of Wisconsin-Madison, WI, USA

For all author emails, please log on.

BMC Genomics 2012, 13:110  doi:10.1186/1471-2164-13-110

Published: 22 March 2012

Additional files

Additional file 1:

List of orthologous genes in D. dadantii and P. atrosepticum that are detected as differentially expressed using stringent criteria (cFDR = 0.01 and fold change > 3).

Format: XLS Size: 1.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

List of simple orthologs in the phytopathogens (P. atrosepticum and D. dadantii) that are detected as differentially expressed (cFDR = 0.01) in both phytopathogens, but one or the other, or even both have fold changes < 3. Orthologs that show congruent expression patterns as well as those that show divergent expression patterns are listed.

Format: XLS Size: 1.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

List of simple orthologs in all three organisms (E. coli, P. atrosepticum and D. dadantii) that are detected as differentially expressed in at least one using stringent criteria (cFDR = 0.01 and fold change > 3).

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

List of genes shared with E. coli and only one of the phytopathogens that are detected as differentially expressed using stringent criteria (cFDR = 0.01 and fold change > 3).

Format: XLS Size: 2.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

List of strain-specific genes in D. dadantii that are detected as differentially expressed using stringent criteria (cFDR = 0.01 and fold change > 3).

Format: XLS Size: 140KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

List of strain-specific genes in P. atrosepticum that are detected as differentially expressed using stringent criteria (cFDR = 0.01 and fold change > 3).

Format: XLS Size: 108KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Fold change patterns for P. atrosepticum and D. dadantii genes implicated in virulence and for their orthologs in E. coli predicted by OrthoMCL. Anaerobic growth in the presence of glucose alters expression of virulence-associated genes in both P. atrosepticum and D. dadantii. This includes genes associated with cell wall degradation and the Out system (down-regulated in D. dadantii only), T6SS (down-regulated in D. dadantii and up-regulated in P. atrosepticum), iron uptake (down-regulated in both), methyl-accepting chemotaxis and regulators associated with virulence. Fold change patterns and genome order are as follows: E. coli, P. atrosepticum and D. dadantii (see key within the figure). Each orthologous group of genes is represented by three blocks colored by fold change (dark blue: down-regulated, fold change > 3; light blue: down-regulated, fold change < 3; bright yellow: up-regulated, fold change > 3; dirty yellow: up-regulated, fold change < 3; black: no change in expression, X: ortholog absent in that organism). Genes are represented by their symbols, or by ASAP feature IDs (especially for strain-unique genes) or by OrthoMCL group designations ("G" followed by number).

Format: XLS Size: 71KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Complete OrthoMCL analysis.

Format: XLS Size: 51KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Normalized signals, fold changes and significance for features in D. dadantii 3937.

Format: XLS Size: 29KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

Normalized signals, fold changes and significance for features in P. atrosepticum SCRI1043.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Normalized signals, fold changes and significance for features in E. coli K12-MG1655.

Format: PDF Size: 523KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data