Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet

Nature Protocols volume 4, pages 992–1005 (2009)Cite this article

Abstract

CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. It provides web-based access to integrated data on gene regulatory interactions of corynebacteria relevant to human medicine and biotechnology, Escherichia coli and Mycobacterium tuberculosis. To facilitate the analysis and reconstruction of the corresponding networks, CoryneRegNet provides user-friendly interfaces for bioinformatics analysis and network visualization tools. This protocol describes four major workflows: (1) querying the regulatory network of a gene of interest, (2) prediction and interspecies transfer of gene regulatory interactions, (3) visualization and comparison of predicted or known networks and (4) integration of gene expression data analysis and visualization. This protocol guides the user through the most important features of CoryneRegNet and takes 45–60 min to complete.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Overview of the CoryneRegNet user interface.
Figure 2: Details page for the global iron-dependent repressor protein DtxR of Corynebacterium glutamicum.
Figure 3: Visualization of the gene regulatory network of DtxR with GraphVis.
Figure 4: Prediction of GlxR transcription factor binding sites—network transfer from Corynebacterium glutamicum to Corynebacterium jeikeium.

Similar content being viewed by others

References

  1. Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. & Teichmann, S.A. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283–291 (2004).

    Article  CAS  Google Scholar 

  2. Madan Babu, M. & Teichmann, S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli . Nucleic Acids Res. 31, 1234–1244 (2003).

    Article  CAS  Google Scholar 

  3. Madan Babu, M., Teichmann, S.A. & Aravind, L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358, 614–633 (2006).

    Article  CAS  Google Scholar 

  4. Matic, I., Taddei, F. & Radman, M. Survival versus maintenance of genetic stability: a conflict of priorities during stress. Res. Microbiol. 155, 337–341 (2004).

    Article  CAS  Google Scholar 

  5. Teichmann, S.A. & Babu, M.M. Gene regulatory network growth by duplication. Nat. Genet. 36, 492–496 (2004).

    Article  CAS  Google Scholar 

  6. Balaji, S., Babu, M.M. & Aravind, L. Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli . J. Mol. Biol. 372, 1108–1122 (2007).

    Article  CAS  Google Scholar 

  7. Balaji, S., Iyer, L.M., Babu, M.M. & Aravind, L. Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet. 24, 319–323 (2008).

    Article  CAS  Google Scholar 

  8. Baumbach, J., Tauch, A. & Rahmann, S. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief. Bioinform. 10, 75–83 (2009).

    Article  CAS  Google Scholar 

  9. Herrgard, M.J., Covert, M.W. & Palsson, B.O. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15, 70–77 (2004).

    Article  CAS  Google Scholar 

  10. Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474 (1997).

    Article  CAS  Google Scholar 

  11. Kalinowski, J. et al. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104, 5–25 (2003).

    Article  CAS  Google Scholar 

  12. Baumbach, J. CoryneRegNet 4.0—a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8, 429 (2007).

    Article  Google Scholar 

  13. Baumbach, J., Brinkrolf, K., Czaja, L.F., Rahmann, S. & Tauch, A. CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics 7, 24 (2006).

    Article  Google Scholar 

  14. Baumbach, J., Brinkrolf, K., Wittkop, T., Tauch, A. & Rahmann, S. CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes. J. Integr. Bioinform. 3, 24 (2006).

    Article  Google Scholar 

  15. Baumbach, J. et al. CoryneRegNet 3.0—an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli . J. Biotechnol. 129, 279–289 (2007).

    Article  CAS  Google Scholar 

  16. Jacques, P.E. et al. MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis . Bioinformatics 21, 2563–2565 (2005).

    Article  CAS  Google Scholar 

  17. Munch, R. et al. PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266–269 (2003).

    Article  CAS  Google Scholar 

  18. Munch, R. et al. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21, 4187–4189 (2005).

    Article  Google Scholar 

  19. Ishii, T., Yoshida, K., Terai, G., Fujita, Y. & Nakai, K. DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res. 29, 278–280 (2001).

    Article  CAS  Google Scholar 

  20. Makita, Y., Nakao, M., Ogasawara, N. & Nakai, K. DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32, D75–D77 (2004).

    Article  CAS  Google Scholar 

  21. Sierro, N., Makita, Y., de Hoon, M. & Nakai, K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 36, D93–D96 (2008).

    Article  CAS  Google Scholar 

  22. Gama-Castro, S. et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36, D120–D124 (2008).

    Article  CAS  Google Scholar 

  23. Huerta, A.M., Salgado, H., Thieffry, D. & Collado-Vides, J. RegulonDB: a database on transcriptional regulation in Escherichia coli . Nucleic Acids Res. 26, 55–59 (1998).

    Article  CAS  Google Scholar 

  24. Salgado, H. et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 32, D303–D306 (2004).

    Article  CAS  Google Scholar 

  25. Salgado, H. et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34, D394–D397 (2006).

    Article  CAS  Google Scholar 

  26. Salgado, H. et al. RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli . Nucleic Acids Res. 27, 59–60 (1999).

    Article  CAS  Google Scholar 

  27. Salgado, H. et al. RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 28, 65–67 (2000).

    Article  CAS  Google Scholar 

  28. Salgado, H. et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29, 72–74 (2001).

    Article  CAS  Google Scholar 

  29. Cerdeno-Tarraga, A.M. et al. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 31, 6516–6523 (2003).

    Article  CAS  Google Scholar 

  30. Tauch, A. et al. Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J. Bacteriol. 187, 4671–4682 (2005).

    Article  CAS  Google Scholar 

  31. Nishio, Y. et al. Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens . Genome Res. 13, 1572–1579 (2003).

    Article  CAS  Google Scholar 

  32. Cole, S.T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998).

    Article  CAS  Google Scholar 

  33. Philippi, S. & Kohler, J. Addressing the problems with life-science databases for traditional uses and systems biology. Nat. Rev. Genet. 7, 482–488 (2006).

    Article  CAS  Google Scholar 

  34. Rahmann, S., Müller, T. & Vingron, M. On the power of profiles for transcription factor binding site detection. Stat. Appl. Genet. Mol. Biol. 2, Article 7 (2003).

    Article  Google Scholar 

  35. Beckstette, M., Homann, R., Giegerich, R. & Kurtz, S. Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics 7, 389 (2006).

    Article  Google Scholar 

  36. Kel, A.E. et al. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31, 3576–3579 (2003).

    Article  CAS  Google Scholar 

  37. Rahmann, S. et al. Exact and heuristic algorithms for weighted cluster editing. Comput. Syst. Bioinformatics Conf. 6, 391–401 (2007).

    Article  Google Scholar 

  38. Wittkop, T., Baumbach, J., Lobo, F.P. & Rahmann, S. Large scale clustering of protein sequences with FORCE—a layout based heuristic for weighted cluster editing. BMC Bioinformatics 8, 396 (2007).

    Article  Google Scholar 

  39. Enright, A.J., Kunin, V. & Ouzounis, C.A. Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31, 4632–4638 (2003).

    Article  CAS  Google Scholar 

  40. Paccanaro, A., Casbon, J.A. & Saqi, M.A. Spectral clustering of protein sequences. Nucleic Acids Res. 34, 1571–1580 (2006).

    Article  CAS  Google Scholar 

  41. Frey, B.J. & Dueck, D. Clustering by passing messages between data points. Science 315, 972–976 (2007).

    Article  CAS  Google Scholar 

  42. Dondrup, M. EMMA 2—a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50 (2009).

    Article  Google Scholar 

  43. Brune, I. et al. The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum . BMC Genomics 7, 21 (2006).

    Article  Google Scholar 

  44. Baumbach, J., Wittkop, T., Weile, J., Kohl, T. & Rahmann, S. MoRAine—a web server for fast computational transcription factor binding motif re-annotation. J. Integr. Bioinform. 5 (2008).

  45. Baumbach, J., Rahmann, S. & Tauch, A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst. Biol. 3, 8 (2009).

    Article  Google Scholar 

  46. Cline, M.S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366–2382 (2007).

    Article  CAS  Google Scholar 

  47. Baumbach, J. & Apeltsin, L. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics 9, 184 (2008).

    Article  Google Scholar 

  48. Hartmann, M. et al. The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum . Arch. Microbiol. 182, 299–312 (2004).

    Article  CAS  Google Scholar 

  49. Meyer, F. et al. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

J.B. thanks the German Academic Exchange Service (DAAD) for funding his work at ICSI, Berkeley. T.W. is grateful for financial support of the International Graduate School for Bioinformatics and Genome Research (IGS, Bielefeld, Germany) and the Boehringer Ingelheim Fonds. C.K.K. thanks the IGS as well as the Arabidopsis Functional Genomics network (AFGN)—2010 Young Researcher Exchange Program for funding her work at UC Berkeley.

Author information

Authors and Affiliations

  1. Algorithms Group, International Computer Science Institute, Berkeley, California, USA

    Jan Baumbach & Tobias Wittkop

  2. International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Bielefeld, Germany

    Tobias Wittkop & Christiane Katja Kleindt

  3. Graduiertenkolleg Bioinformatik, Bielefeld University, Bielefeld, Germany

    Tobias Wittkop

  4. Department of Plant and Microbial Biology, University of California, Berkeley, California, USA

    Christiane Katja Kleindt

  5. Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany

    Andreas Tauch

Authors
  1. Jan Baumbach
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tobias Wittkop
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christiane Katja Kleindt
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andreas Tauch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jan Baumbach.

Supplementary information

Supplementary Data 1: Sample transcription factor binding sites (15 arbitrarily selected) for DtxR of Corynebacterium glutamicum as text file in FASTA format.

This text file contains 15 arbitrarily selected binding sites of DtxR in FASTA format. They are used as input for the TFBScan feature in Step 2D of the protocol. (TXT 0 kb)

Supplementary Data 2: Sample DtxR knock-out gene expression data for Corynebacterium glutamicum as tab-delimited flat-file.

This text file contains all significantly differentially expressed genes and M-values for a DtxR knock-out microarray experiment43. The gene IDs and M-values are stored tab-delimited, one line for each pair. This file is used in Step 2E of the protocol. (TXT 3 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Baumbach, J., Wittkop, T., Kleindt, C. et al. Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nat Protoc 4, 992–1005 (2009). https://doi.org/10.1038/nprot.2009.81

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2009.81

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing