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.
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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).
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).
Madan Babu, M., Teichmann, S.A. & Aravind, L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358, 614–633 (2006).
Matic, I., Taddei, F. & Radman, M. Survival versus maintenance of genetic stability: a conflict of priorities during stress. Res. Microbiol. 155, 337–341 (2004).
Teichmann, S.A. & Babu, M.M. Gene regulatory network growth by duplication. Nat. Genet. 36, 492–496 (2004).
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).
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).
Baumbach, J., Tauch, A. & Rahmann, S. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief. Bioinform. 10, 75–83 (2009).
Herrgard, M.J., Covert, M.W. & Palsson, B.O. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15, 70–77 (2004).
Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474 (1997).
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).
Baumbach, J. CoryneRegNet 4.0—a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8, 429 (2007).
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).
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).
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).
Jacques, P.E. et al. MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis . Bioinformatics 21, 2563–2565 (2005).
Munch, R. et al. PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266–269 (2003).
Munch, R. et al. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21, 4187–4189 (2005).
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).
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).
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).
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).
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).
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).
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).
Salgado, H. et al. RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli . Nucleic Acids Res. 27, 59–60 (1999).
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).
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).
Cerdeno-Tarraga, A.M. et al. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 31, 6516–6523 (2003).
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).
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).
Cole, S.T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998).
Philippi, S. & Kohler, J. Addressing the problems with life-science databases for traditional uses and systems biology. Nat. Rev. Genet. 7, 482–488 (2006).
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).
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).
Kel, A.E. et al. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31, 3576–3579 (2003).
Rahmann, S. et al. Exact and heuristic algorithms for weighted cluster editing. Comput. Syst. Bioinformatics Conf. 6, 391–401 (2007).
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).
Enright, A.J., Kunin, V. & Ouzounis, C.A. Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31, 4632–4638 (2003).
Paccanaro, A., Casbon, J.A. & Saqi, M.A. Spectral clustering of protein sequences. Nucleic Acids Res. 34, 1571–1580 (2006).
Frey, B.J. & Dueck, D. Clustering by passing messages between data points. Science 315, 972–976 (2007).
Dondrup, M. EMMA 2—a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50 (2009).
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).
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).
Baumbach, J., Rahmann, S. & Tauch, A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst. Biol. 3, 8 (2009).
Cline, M.S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366–2382 (2007).
Baumbach, J. & Apeltsin, L. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics 9, 184 (2008).
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).
Meyer, F. et al. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195 (2003).
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.
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)
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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
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