title: Systematic prediction of control proteins and their DNA binding sites.
abstract: We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as restriction endonuclease genes in many type II restriction-modification systems. More than 290 C protein homologs were identified and DNA-binding sites for approximately 70% of new and previously known C proteins were predicted by a combination of phylogenetic footprinting and motif searches in DNA upstream of C protein genes. Additional analysis revealed that a large proportion of C protein genes are translated from leaderless RNA, which may contribute to time-delayed nature of genetic switches operated by these proteins. Analysis of genetic contexts of newly identified C protein genes revealed that they are not exclusively associated with restriction-modification genes; numerous instances of associations with genes originating from mobile genetic elements were observed. These instances might be vestiges of ancient horizontal transfers and indicate that during evolution ancestral restriction-modification system genes were the sites of mobile elements insertions.
authors.affiliation: Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Valeriy
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: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000235:genetics; D023281:Genomics; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000145:classification / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific