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The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.

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Ball NJ, McGeehan JE, Streeter SD, Thresh SJ, Kneale GG
OpenAccess logo Nucleic Acids Res 40 10532-42 (2012)
Cited: 13 times
EuropePMC logo PMID: 22941636

Abstract

Controller (C) proteins regulate the expression of restriction-modification (RM) genes in a wide variety of RM systems. However, the RM system Esp1396I is of particular interest as the C protein regulates both the restriction endonuclease (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned genetic switch depends on differential binding affinities for the promoters controlling the R and M genes, which in turn depends on differential DNA sequence recognition and the ability to recognize dual symmetries. We report here the crystal structure of the C protein bound to the M promoter, and compare the binding affinities for each operator sequence by surface plasmon resonance. Comparison of the structure of the transcriptional repression complex at the M promoter with that of the transcriptional activation complex at the R promoter shows how subtle changes in protein-DNA interactions, underpinned by small conformational changes in the protein, can explain the molecular basis of differential regulation of gene expression.

Articles - 3ufd mentioned but not cited (4)

  1. The structural basis of differential DNA sequence recognition by restriction-modification controller proteins. Ball NJ, McGeehan JE, Streeter SD, Thresh SJ, Kneale GG. Nucleic Acids Res 40 10532-10542 (2012)
  2. iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots. Zhu X, Liu L, He J, Fang T, Xiong Y, Mitchell JC. BMC Bioinformatics 21 289 (2020)
  3. Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein. Sedhom J, Kinser J, Solomon LA. NAR Genom Bioinform 4 lqac101 (2022)
  4. Structural and mutagenic analysis of the RM controller protein C.Esp1396I. Martin RN, McGeehan JE, Kneale G. PLoS One 9 e98365 (2014)


Articles citing this publication (9)

  1. Highlights of the DNA cutters: a short history of the restriction enzymes. Loenen WA, Dryden DT, Raleigh EA, Wilson GG, Murray NE. Nucleic Acids Res 42 3-19 (2014)
  2. Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system. Morozova N, Sabantsev A, Bogdanova E, Fedorova Y, Maikova A, Vedyaykin A, Rodic A, Djordjevic M, Khodorkovskii M, Severinov K. Nucleic Acids Res 44 790-800 (2016)
  3. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS. Nucleic Acids Res 47 9448-9463 (2019)
  4. Understanding key features of bacterial restriction-modification systems through quantitative modeling. Rodic A, Blagojevic B, Zdobnov E, Djordjevic M, Djordjevic M. BMC Syst Biol 11 377 (2017)
  5. The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. Ciges-Tomas JR, Alite C, Humphrey S, Donderis J, Bowring J, Salvatella X, Penadés JR, Marina A. Nat Commun 10 3676 (2019)
  6. Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor. Negri A, Jąkalski M, Szczuka A, Pryszcz LP, Mruk I. Nucleic Acids Res 47 9542-9556 (2019)
  7. Induced DNA bending by unique dimerization of HigA antitoxin. Park JY, Kim HJ, Pathak C, Yoon HJ, Kim DH, Park SJ, Lee BJ. IUCrJ 7 748-760 (2020)
  8. Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. Liang J, Blumenthal RM. BMC Evol Biol 13 218 (2013)
  9. Kinetic Basis of the Bifunctionality of SsoII DNA Methyltransferase. Timofeyeva NA, Ryazanova AY, Norkin MV, Oretskaya TS, Fedorova OS, Kubareva EA. Molecules 23 E1192 (2018)


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