Quantitative Biology

, Volume 3, Issue 2, pp 69–80 | Cite as

A quantitative understanding of lac repressor’s binding specificity and flexibility

  • Zheng Zuo
  • Yiming Chang
  • Gary D. Stormo
Research Article


Lac repressor, the first discovered transcriptional regulator, has been shown to confer multiple modes of binding to its operator sites depending on the central spacer length. Other homolog members in the LacI/GalR family (PurR and YcjW) cannot bind their operator sites with similar structural flexibility. To decipher the underlying mechanism for this unique property, we used Spec-seq approach combined with site-directed mutagenesis to quantify the DNA binding specificity of multiple hybrids of lacI and PurR. We find that lac repressor’s recognition di-residues YQ and its hinge helix loop regions are both critical for its structural flexibility. Also, specificity profiling of the whole lac operator suggests that a simple additive model from single variants suffice to predict other multivariant sites’ energy reasonably well, and the genome occupancy model based on this specificity data correlates well with in vivo lac repressor binding profile.


lac repressor binding flexibility Spec-seq ionic strength 

Supplementary material

40484_2015_44_MOESM1_ESM.pdf (1.1 mb)
Supplementary material, approximately 1.05 MB.
40484_2015_44_MOESM2_ESM.xls (1.5 mb)
Supplementary material, approximately 1.50 MB.


  1. 1.
    Jacob, F. and Monod, J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3, 318–356CrossRefPubMedGoogle Scholar
  2. 2.
    Lewis, M. (2005) The lac repressor. C. R. Biol., 328, 521–548CrossRefPubMedGoogle Scholar
  3. 3.
    Gilbert, W. and Maxam, A. (1973) The nucleotide sequence of the lac operator. Proc. Natl. Acad. Sci. USA, 70, 3581–3584PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Zuo, Z. and Stormo, G. D. (2014) High-resolution specificity from DNA sequencing highlights alternative modes of lac repressor binding. Genetics, 198, 1329–1343CrossRefPubMedGoogle Scholar
  5. 5.
    Mossing, M. C. and Record, M. T. Jr. (1985) Thermodynamic origins of specificity in the lac repressor-operator interaction: Adaptability in the recognition of mutant operator sites. J. Mol. Biol., 186, 295–305CrossRefPubMedGoogle Scholar
  6. 6.
    Frank, D. E., Saecker, R. M., Bond, J. P., Capp, M.W., Tsodikov, O. V., Melcher, S. E., Levandoski, M. M. and Record, M. T. Jr. (1997) Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a nonspecific site. J. Mol. Biol., 267, 1186–1206CrossRefPubMedGoogle Scholar
  7. 7.
    Hart, D. J., Speight, R. E., Cooper, M. A., Sutherland, J. D. and Blackburn, J. M. (1999) The salt dependence of DNA recognition by NF-κB p50: a detailed kinetic analysis of the effects on affinity and specificity. Nucleic Acids Res., 27, 1063–1069PubMedCentralCrossRefPubMedGoogle Scholar
  8. 8.
    Benos, P. V., Bulyk, M. L. and Stormo, G. D. (2002) Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic Acids Res., 30, 4442–4451PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Stormo, G. D. (2013) Modeling the specificity of protein-DNA interactions. Quant. Biol., 1, 115–130PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    Maerkl, S. J. and Quake, S. R. (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science, 315, 233–237CrossRefPubMedGoogle Scholar
  11. 11.
    Novichkov, P. S., Laikova, O. N., Novichkova, E. S., Gelfand, M. S., Arkin, A. P., Dubchak, I. and Rodionov, D. A. (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res., 38, D111–D118PubMedCentralCrossRefPubMedGoogle Scholar
  12. 12.
    Daber, R. and Lewis, M. (2009) Towards evolving a better repressor. Protein Eng. Des. Sel., 22, 673–683PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Record, M. T. Jr, deHaseth, P. L. and Lohman, T. M. (1977) Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry, 16, 4791–4796CrossRefPubMedGoogle Scholar
  14. 14.
    von Hippel, P. H. (2014) Increased subtlety of transcription factor binding increases complexity of genome regulation. Proc. Natl. Acad. Sci. USA, 111, 17344–17345CrossRefGoogle Scholar
  15. 15.
    Schumacher, M. A., Choi, K. Y., Zalkin, H. and Brennan, R. G. (1994) Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science, 266, 763–770CrossRefPubMedGoogle Scholar
  16. 16.
    Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G. and Lu, P. (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science, 271, 1247–1254CrossRefPubMedGoogle Scholar
  17. 17.
    Romanuka, J., Folkers, G. E., Biris, N., Tishchenko, E., Wienk, H., Bonvin, A. M., Kaptein, R. and Boelens, R. (2009) Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J. Mol. Biol., 390, 478–489CrossRefPubMedGoogle Scholar
  18. 18.
    Milk, L., Daber, R. and Lewis, M. (2010) Functional rules for lac repressor-operator associations and implications for protein-DNA interactions. Protein Sci., 19, 1162–1172PubMedCentralCrossRefPubMedGoogle Scholar
  19. 19.
    Kalodimos, C. G., Boelens, R. and Kaptein, R. (2004) Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. Chem. Rev., 104, 3567–3586CrossRefPubMedGoogle Scholar
  20. 20.
    Riggs, A. D., Suzuki, H. and Bourgeois, S. (1970) Lac repressoroperator interaction: I. Equilibrium studies. J. Mol. Biol., 48, 67–83CrossRefPubMedGoogle Scholar
  21. 21.
    von Hippel, P. H. (2004) Completing the view of transcriptional regulation. Science, 305, 350–352CrossRefGoogle Scholar
  22. 22.
    Cournac, A. and Plumbridge, J. (2013) DNA looping in prokaryotes: experimental and theoretical approaches. J. Bacteriol., 195, 1109–1119PubMedCentralCrossRefPubMedGoogle Scholar
  23. 23.
    Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muñiz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., García-Sotelo, J. S., López-Fuentes, A., et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res., 39, D98–D105PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag GmbH 2015

Authors and Affiliations

  1. 1.Department of Genetics and Center for Genomic Sciences and Systems Biology, School of MedicineWashington UniversitySt. LouisUSA

Personalised recommendations