Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation

Biophysical Journal

Volumn 101, Issue 7, 2011, Pages 1569-1579

  Geisel, Nico ^a   Gerland, Ulrich ^b  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; KINETICS; METABOLISM; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; THERMODYNAMICS;

DNA; GENE EXPRESSION REGULATION; KINETICS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; THERMODYNAMICS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 80053345824     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.08.041     Document Type: Article

References (42)

1. O.G. Berg, R.B. Winter, and P.H. von Hippel Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory Biochemistry 20 1981 6929 6948
2. R.F. Bruinsma Physics of protein-DNA interaction Physica A 313 2002 211 237
3. S.E. Halford, and J.F. Marko How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32 2004 3040 3052 (Pubitemid 39022995)
4. M. Slutsky, and L.A. Mirny Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential Biophys. J. 87 2004 4021 4035 (Pubitemid 39602906)
5. M. Coppey, and O. Bénichou M. Moreau Kinetics of target site localization of a protein on DNA: a stochastic approach Biophys. J. 87 2004 1640 1649 (Pubitemid 39167021)
6. M.A. Lomholt, T. Ambjörnsson, and R. Metzler Optimal target search on a fast-folding polymer chain with volume exchange Phys. Rev. Lett. 95 2005 260603
7. T. Hu, A.Y. Grosberg, and B.I. Shklovskii How proteins search for their specific sites on DNA: the role of DNA conformation Biophys. J. 90 2006 2731 2744
8. P.H. von Hippel, and O.G. Berg On the specificity of DNA-protein interactions Proc. Natl. Acad. Sci. USA 83 1986 1608 1612 (Pubitemid 16018613)
9. G.D. Stormo, and D.S. Fields Specificity, free energy and information content in protein-DNA interactions Trends Biochem. Sci. 23 1998 109 113 (Pubitemid 28175261)
10. U. Gerland, J.D. Moroz, and T. Hwa Physical constraints and functional characteristics of transcription factor-DNA interaction Proc. Natl. Acad. Sci. USA 99 2002 12015 12020
11. J. Elf, G.-W. Li, and X.S. Xie Probing transcription factor dynamics at the single-molecule level in a living cell Science 316 2007 1191 1194 (Pubitemid 46877481)
12. E. Richet, D. Vidal-Ingigliardi, and O. Raibaud A new mechanism for coactivation of transcription initiation: repositioning of an activator triggered by the binding of a second activator Cell 66 1991 1185 1195 (Pubitemid 121001408)
13. P. Gerlach, and L. Søgaard-Andersen E. Bremer The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12 J. Bacteriol. 173 1991 5419 5430
14. M.P. Jennings, and I.R. Beacham Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis Mol. Microbiol. 9 1993 155 164 (Pubitemid 23217746)
15. S. Scott, S. Busby, and I. Beacham Transcriptional co-activation at the ansB promoters: involvement of the activating regions of CRP and FNR when bound in tandem Mol. Microbiol. 18 1995 521 531 (Pubitemid 26009109)
16. H. Pedersen, and J. Dall P. Valentin-Hansen Gene-regulatory modules in Escherichia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter Mol. Microbiol. 17 1995 843 853
17. I. Brikun, and K. Suziedelis D.E. Berg Analysis of CRP-CytR interactions at the Escherichia coli udp promoter J. Bacteriol. 178 1996 1614 1622 (Pubitemid 26085609)
18. E. Richet Synergistic transcription activation: a dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP EMBO J. 19 2000 5222 5232
19. J.T. Wade, and T.A. Belyaeva S.J. Busby A simple mechanism for co-dependence on two activators at an Escherichia coli promoter EMBO J. 20 2001 7160 7167 (Pubitemid 34062307)
20. M. Shin, and S. Kang H.E. Choy Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor EMBO J. 20 2001 5392 5399 (Pubitemid 32959459)
21. M.D. Kumar, and M.M. Gromiha PINT: protein-protein interactions thermodynamic database Nucleic Acids Res. 34 Database issue 2006 D195 D198
22. J.J. Kohler, and S.J. Metallo A. Schepartz DNA specificity enhanced by sequential binding of protein monomers Proc. Natl. Acad. Sci. USA 96 1999 11735 11739 (Pubitemid 29502801)
23. J.J. Kohler, and A. Schepartz Kinetic studies of FosJunDNA complex formation: DNA binding prior to dimerization Biochemistry 40 2001 130 142 (Pubitemid 32052684)
24. A.L. Koch The protein burden of Lac operon products J. Mol. Evol. 19 1983 455 462 (Pubitemid 14210954)
25. E. Dekel, and U. Alon Optimality and evolutionary tuning of the expression level of a protein Nature 436 2005 588 592 (Pubitemid 41112935)
26. G.I. Lang, A.W. Murray, and D. Botstein The cost of gene expression underlies a fitness trade-off in yeast Proc. Natl. Acad. Sci. USA 106 2009 5755 5760
27. R. Galletto, and I. Amitani S.C. Kowalczykowski Direct observation of individual RecA filaments assembling on single DNA molecules Nature 443 2006 875 878 (Pubitemid 44622700)
28. T.M. Lohman, and M.E. Ferrari Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities Annu. Rev. Biochem. 63 1994 527 570
29. M. Ptashne, and A. Gann Genes and Signals 1st Ed. 2001 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
30. L. Bintu, and N.E. Buchler R. Phillips Transcriptional regulation by the numbers: models Curr. Opin. Genet. Dev. 15 2005 116 124 (Pubitemid 40410659)
31. J.A. Miller, and J. Widom Collaborative competition mechanism for gene activation in vivo Mol. Cell. Biol. 23 2003 1623 1632 (Pubitemid 36246044)
32. E.F. Koslover, and A.J. Spakowitz Twist- and tension-mediated elastic coupling between DNA-binding proteins Phys. Rev. Lett. 102 2009 178102
33. Y. Wang, and L. Guo N.P. Ong Quantitative transcription factor binding kinetics at the single-molecule level Biophys. J. 96 2009 609 620
34. R.B. Winter, O.G. Berg, and P.H. von Hippel Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: kinetic measurements and conclusions Biochemistry 20 1981 6961 6977 (Pubitemid 12185949)
35. Y. Bilu, and N. Barkai The design of transcription-factor binding sites is affected by combinatorial regulation Genome Biol. 6 2005 R103
36. J.A. Lefstin, and K.R. Yamamoto Allosteric effects of DNA on transcriptional regulators Nature 392 1998 885 888 (Pubitemid 28232051)
37. N.E. Buchler, U. Gerland, and T. Hwa On schemes of combinatorial transcription logic Proc. Natl. Acad. Sci. USA 100 2003 5136 5141 (Pubitemid 36542671)
38. N.E. Buchler, U. Gerland, and T. Hwa Nonlinear protein degradation and the function of genetic circuits Proc. Natl. Acad. Sci. USA 102 2005 9559 9564 (Pubitemid 40981720)
39. S. Gama-Castro, and H. Salgado J. Collado-Vides RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) Nucleic Acids Res. 39 Database issue 2011 D98 D105
40. E. Richet On the role of the multiple regulatory elements involved in the activation of the Escherichia coli malEp promoter J. Mol. Biol. 264 1996 852 862 (Pubitemid 27019478)
41. N. Majdalani, and M. Heck S. Gottesman Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli J. Bacteriol. 187 2005 6770 6778 (Pubitemid 41356251)
42. L. Bintu, and N.E. Buchler R. Phillips Transcriptional regulation by the numbers: applications Curr. Opin. Genet. Dev. 15 2005 125 135 (Pubitemid 40410660)