title: Large-scale identification and analysis of C-proteins.
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.
authors.affiliation: Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia. gtr-sorokin@mail.ru
authors.forename: Valery
authors.initials: V
authors.lastname: Sorokin
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors