Abstract
Multiple efforts have been made to comprehend the regulatory machinery of model prokaryotic organisms, such as Escherichia coli and Bacillus subtilis. However, the lack of unification of published regulatory data reduces the potential of reconstructing whole genome transcriptional regulatory networks. The work hereby discussed, focuses on the retrieval and integration of relevant regulatory data from multiple resources, including databases, such as RegulonDB and DBTBS as well as available literature. This study presents state-of-art, reconciled transcriptional regulatory networks of the previously mentioned model organisms, as well as a topological and functional analysis.
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References
Fang, X., Sastry, A., Mih, N., Kim, D., Tan, J., Yurkovich, J.T., Lloyd, C.J., Gao, Y., Yang, L., Palsson, B.O.: Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proc. Natl. Acad. Sci. U. S. A. 114, 10286–10291 (2017). https://doi.org/10.1073/pnas.1702581114
Arrieta-Ortiz, M.L., Hafemeister, C., Bate, A.R., Chu, T., Greenfield, A., Shuster, B., Barry, S.N., Gallitto, M., Liu, B., Kacmarczyk, T., Santoriello, F., Chen, J., Rodrigues, C.D., Sato, T., Rudner, D.Z., Driks, A., Bonneau, R., Eichenberger, P.: An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Mol. Syst. Biol. 11, 839–839 (2015). https://doi.org/10.15252/msb.20156236
Covert, M.W., Palsson, B.Ø.: Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058–28064 (2002). https://doi.org/10.1074/jbc.M201691200
Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñiz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Moral-Chávez, V. Del, Rinaldi, F., Collado-Vides, J.: RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 44, D133–D143 (2016). https://doi.org/10.1093/nar/gkv1156
Novichkov, P.S., Kazakov, A.E., Ravcheev, D.A., Leyn, S.A., Kovaleva, G.Y., Sutormin, R.A., Kazanov, M.D., Riehl, W., Arkin, A.P., Dubchak, I., Rodionov, D.A.: RegPrecise 3.0 – a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 14, 745 (2013). https://doi.org/10.1186/1471-2164-14-745
Faria, J.P., Overbeek, R., **a, F., Rocha, M., Rocha, I., Henry, C.S.: Genome-scale bacterial transcriptional regulatory networks: Reconstruction and integrated analysis with metabolic models. Brief. Bioinform. 15, 592–611 (2014). https://doi.org/10.1093/bib/bbs071
Kılıç, S., White, E.R., Sagitova, D.M., Cornish, J.P., Erill, I.: CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. Nucleic Acids Res. 42, D156–D160 (2014). https://doi.org/10.1093/nar/gkt1123
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). https://doi.org/10.1093/nar/gkm910
Faria, J.P., Overbeek, R., Taylor, R.C., Conrad, N., Vonstein, V., Goelzer, A., Fromion, V., Rocha, M., Rocha, I., Henry, C.S.: Reconstruction of the regulatory network for bacillus subtilis and reconciliation with gene expression data. Front. Microbiol. 7, 275 (2016). https://doi.org/10.3389/fmicb.2016.00275
Edgar, R.: Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207–210 (2002). https://doi.org/10.1093/nar/30.1.207
Zhu, B., Stülke, J.: SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. Nucleic Acids Res. 46, D743–D748 (2018). https://doi.org/10.1093/nar/gkx908
Federhen, S.: The NCBI taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012). https://doi.org/10.1093/nar/gkr1178
UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506–D515 (2019). https://doi.org/10.1093/nar/gky1049
Martínez-Antonio, A., Janga, S.C., Thieffry, D.: Functional organisation of Escherichia coli transcriptional regulatory network. J. Mol. Biol. 381, 238–247 (2008). https://doi.org/10.1016/j.jmb.2008.05.054
Lagomarsino, M.C., Jona, P., Bassetti, B., Isambert, H.: Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc. Natl. Acad. Sci. U. S. A. 104, 5516–5520 (2007). https://doi.org/10.1073/pnas.0609023104
Barabási, A.L.: Scale-free networks: a decade and beyond (2009). https://doi.org/10.1126/science.1173299
Burgess, R.R.: Sigma factors. Encycl. Genet. 1831–1834 (2001). https://doi.org/10.1006/RWGN.2001.1192
Youn, H., Kerby, R.L., Conrad, M., Roberts, G.P.: Study of highly constitutively active mutants suggests how cAMP activates cAMP receptor protein. J. Biol. Chem. 281, 1119–1127 (2006). https://doi.org/10.1074/jbc.M509421200
Alexeeva, S., Hellingwerf, K.J., Teixeira de Mattos, M.J.: Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J. Bacteriol. 185, 204–209 (2003). https://doi.org/10.1128/JB.185.1.204-209.2003
Lazazzera, B.A., Bates, D.M., Kiley, P.J.: The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Genes Dev. 7, 1993–2005 (1993). https://doi.org/10.1101/gad.7.10.1993
Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J., Hecker, M.: Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J. Bacteriol. 181, 6996–7004 (1999)
Perego, M., Spiegelman, G.B., Hoch, J.A.: Structure of the gene for the transition state regulator, abrB: regulator synthesis is controlled by the spo0A sporulation gene in Bacillus subtilis. Mol. Microbiol. 2, 689–699 (1988). https://doi.org/10.1111/j.1365-2958.1988.tb00079.x
Ratnayake-Lecamwasam, M., Serror, P., Wong, K.W., Sonenshein, A.L.: Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev. 15, 1093–1103 (2001). https://doi.org/10.1101/gad.874201
Acknowledgements
This study was performed under the scope of the project “BIODATA.PT – Portuguese Biological Data Network” (ref. LISBOA-01-0145-FEDER-022231), funded by FCT/MCTES, through national funds of PIDDAC, Fundo Europeu de Desenvolvimento Regional (FEDER), Programa Operacional de Competitividade e Internacionalização (POCI) and Programa Operacional Regional de Lisboa (Lisboa 2020). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 – Programa Operacional Regional do Norte. This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 686070.
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Lima, D., Cruz, F., Rocha, M., Dias, O. (2021). Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. In: Panuccio, G., Rocha, M., Fdez-Riverola, F., Mohamad, M., Casado-Vara, R. (eds) Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020). PACBB 2020. Advances in Intelligent Systems and Computing, vol 1240. Springer, Cham. https://doi.org/10.1007/978-3-030-54568-0_16
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