This article is part of the supplement: Validation methods for functional genome annotation

Open Access Research

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Dmitry A Rodionov12*, Pavel S Novichkov3, Elena D Stavrovskaya24, Irina A Rodionova1, Xiaoqing Li1, Marat D Kazanov12, Dmitry A Ravcheev12, Anna V Gerasimova3, Alexey E Kazakov23, Galina Yu Kovaleva2, Elizabeth A Permina5, Olga N Laikova5, Ross Overbeek6, Margaret F Romine7, James K Fredrickson7, Adam P Arkin3, Inna Dubchak38, Andrei L Osterman16 and Mikhail S Gelfand24

Author Affiliations

1 Sanford-Burnham Medical Research Institute, La Jolla, California, USA

2 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia

3 Lawrence Berkeley National Laboratory, Berkeley, California, USA

4 Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia

5 State Scientific Center GosNIIGenetika, Moscow, Russia

6 Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, USA

7 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA

8 Department of Energy Joint Genome Institute, Walnut Creek, California, USA

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BMC Genomics 2011, 12(Suppl 1):S3  doi:10.1186/1471-2164-12-S1-S3

Published: 15 June 2011

Additional files

Additional file 1:

Rodionov_AF1.xls - Repertoire of DNA-binding transcription factors identified in 16 genomes of Shewanella spp.

Format: XLS Size: 204KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Rodionov_AF2.xls - Transcription factors universally conserved in Shewanella spp.

Format: XLS Size: 42KB Download file

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Additional file 3:

Rodionov_AF3.xls - Functional classifiaction of 73 transcription factors conserved between E. coli and 16 Shewanella strains.

Format: XLS Size: 27KB Download file

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Additional file 4:

Rodionov_AF4.xls - Functional content and conservation of reconstructed TF and RNA regulons in Shewanella genomes.

Format: XLS Size: 261KB Download file

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Additional file 5:

Rodionov_AF5.pdf - Comparison of predicted TFBS motifs in Shewanella spp. to the previously characterized orthologous regulators in model species.

Format: PDF Size: 993KB Download file

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Additional file 6:

Rodionov_AF6.pdf - Experimental validation of NagR regulon in S. oneidensis MR-1. (A) Electrophoretic mobility shift assays to assess NagR protein binding to their predicted DNA operators; (B) Differential regulation of NagR controlled genes determined by quantitative qPCR.

Format: PDF Size: 71KB Download file

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