Abstract
The restriction-modification system is a toxin–antitoxin mechanism of bacterial cells to resist phage attacks. High efficiency comes at a price of high maintenance costs: (1) a host cell dies whenever it loses restriction-modification genes and (2) whenever a plasmid with restriction-modification genes enters a naïve cell, modification enzyme (methylase) has to be expressed prior to the synthesis of the restriction enzyme (restrictase) or the cell dies. These phenomena imply a sophisticated regulatory mechanism. During the evolution several such mechanisms were developed, of which one relies on a special C(control)-protein, a short autoregulatory protein containing an HTH-domain. Given the extreme diversity among restriction-modification systems, one could expect that C-proteins had evolved into several groups that might differ in autoregulatory binding sites architecture. However, only a few C-proteins (and the corresponding binding sites) were known before this study. Bioinformatics studies applied to C-proteins and their binding sites were limited to groups of well-known C-proteins and lacked systematic analysis. In this work, the authors use bioinformatics techniques to discover 201 C-protein genes with predicted autoregulatory binding sites. The systematic analysis of the predicted sites allowed for the discovery of 10 structural classes of binding sites.
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References
Bertani, G., Weigle, J.J. (1953) Host controlled variation in bacterial viruses. J Bacteriol 65, 113–121.
Lurlia, S.E., and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J Bacteriol 64, 557–569.
Bickle, T.A., and Krueger, D.H. (1993) Biology of DNA restriction. Microbiol Rev 57, 434–450.
King, G., and Murray, N.E. (1994) Restriction enzymes in cells, not eppendorfs. Trends Microbiol 2, 465–469.
Knowle, D., Lintner, R., Touma, Y.M., and Blumenthal, R.M. (2005) Nature of promoter activated by C. PvuII, an unusual regulatory protein conserved among restriction-modification systems. J Bacteriol 187, 488–497.
Sawaya, M.R., Zhu, Z., Mersha, F. et al. (2005) Crystal structure of the restriction modification system control element C.Bcll and mapping of its binding site. Structure 13, 1837–1847.
McGeehan, J.E., Streeter, S.D., Papapanagiotou, I. et al. (2005) High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila. J Mol Biol 346, 689–701.
Bart, A., Dankert, J., and van der Ende, A. (1999) Operator sequences for the regulatory proteins of restriction modification systems. Mol Microbiol 31, 1277–1278.
Bogdanova, E., Djordjevic, M., Papapanagiotou, I. et al. (2008) Transcription regulation of type II restriction-modification system AhdI. Nucleic Acids Res 36, 1429–1442.
Semenova, E., Minakhin, L., Bogdanova, E. et al. (2005) Transcription regulation of the EcoRV restriction modification system. Nucleic Acids Res 33, 6942–6951.
Zheleznaya, L.A., Kainov, D.E., Yunusova, A.K. et al. (2003) Regulatory C protein of the EcoRV modification–restriction system. Biochemistry (Moscow) 68, 125–132.
Cesnaviciene, E., Mitkaite, G., Stankevicius, K. et al. (2003) Esp1396I restriction-modification system: structural organization and mode of regulation. Nucleic Acids Res 31, 743–749.
Rimseliene, R, Vaisvila, R, and Janulaitis, A. (1995) The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system. Gene 157, 217–219.
Anton, B.P., Heiter, D.F., Benner, J.S. et al. (1997) Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint. Gene 187, 19–27.
Bart, A., Dankert, J., and van der Ende, A. (1999) Operator sequences for the regulatory proteins of restriction-modification systems. Mol Microbiol 31, 1275–1281.
Mruk, I., Rajesh, P., and Blumenthal, R.M. (2007) Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. Nucleic Acids Res 35, 6935–6952.
Sorokin, V., Severinov, K., and Gelfand, M.S. (2009) Systematic prediction of control proteins and their DNA binding sites. Nucleic Acid Res 37, 441–451.
Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J. et al. (2000) Genbank. Nucleic Acids Res 28, 15–18.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.
Felsenstein, J. (1989) PHYLIP – Phylogeny inference package (version 3.2). Cladistics 5, 164–166.
Stavrovskaia, E.D., Makeev, V.I., Mironov, A.A. (2006) ClusterTree-RS: the binary tree algorithm for identification of co-regulated genes by clustering regulatory signals. Mol Biol (Moscow) 40, 524–532.
Wasserman, W.W., and Fickett, J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 278, 167–181.
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Sorokin, V., Severinov, K., Gelfand, M.S. (2010). Large-Scale Identification and Analysis of C-Proteins. In: Ladunga, I. (eds) Computational Biology of Transcription Factor Binding. Methods in Molecular Biology, vol 674. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-854-6_17
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DOI: https://doi.org/10.1007/978-1-60761-854-6_17
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