Systematic prediction of control proteins and their DNA binding sites

Valeriy Sorokin, Konstantin Severinov, Mikhail S. Gelfand

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


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 ∼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.

Original languageEnglish (US)
Pages (from-to)441-451
Number of pages11
JournalNucleic acids research
Issue number2
StatePublished - 2009

All Science Journal Classification (ASJC) codes

  • Genetics

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