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Large-Scale Identification and Analysis of C-Proteins

  • Valery Sorokin
  • Konstantin Severinov
  • Mikhail S. GelfandEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 674)

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.

Key words

Restriction-modification systems C-proteins DNA-binding proteins bioinformatics transcription regulation 

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Valery Sorokin
    • 1
  • Konstantin Severinov
    • 2
    • 3
  • Mikhail S. Gelfand
    • 4
    Email author
  1. 1.Faculty of Bioengineering and BioinformaticsM.V. Lomonosov Moscow State UniversityMoscowRussia
  2. 2.Waksman Institute, RutgersThe State University of New JerseyNew BrunswickUSA
  3. 3.Institute of Gene Biology and Institute of Molecular GeneticsRussian Academy of SciencesMoscowRussia
  4. 4.BioinformaticsInstitute for Information Transmission Problems RASMoscowRussia

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