In vivo tests of thermodynamic models of transcription repressor function

Biophysical Chemistry

Volumn 159, Issue 1, 2011, Pages 142-151

  Tungtur, Sudheer ^a   Skinner, Harlyn ^b   Zhan, Hongli ^a,c   Swint Kruse, Liskin ^a   Beckett, Dorothy ^b  

^a UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^b Bldg 142   (United States)

^c GREENWOOD GENETIC CENTER   (United States)

Author keywords

BirA; Equilibrium; GalR; LacI; Protein DNA affinity; Repression

Indexed keywords

BIOTIN; CELL PROTEIN; PROTEIN BIRA; PROTEIN GA1R; TISSUE FACTOR PATHWAY INHIBITOR; UNCLASSIFIED DRUG;

BINDING AFFINITY; CONCENTRATION (PARAMETERS); CONFERENCE PAPER; CORRELATION ANALYSIS; DIMERIZATION; DNA BINDING; HOMOLOGOUS RECOMBINATION; IN VIVO STUDY; LACTOSE OPERON; LIGAND BINDING; MOLECULAR MODEL; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; SIMULATION; THERMODYNAMICS;

BINDING SITES; CARBON-NITROGEN LIGASES; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; LAC OPERON; LAC REPRESSORS; MODELS, GENETIC; MUTAGENESIS; PROTEIN BINDING; REPRESSOR PROTEINS; THERMODYNAMICS;

EID: 80052320249     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.06.005     Document Type: Conference Paper

References (56)

1. L. Swint-Kruse, and K.S. Matthews Allostery in the LacI/GalR family: variations on a theme Curr. Opin. Microbiol. 12 2009 129 137
2. M.J. Weickert, and S. Adhya A family of bacterial regulators homologous to Gal and Lac repressors J. Biol. Chem. 267 1992 15869 15874
3. C.E. Bell, and M. Lewis A closer view of the conformation of the Lac repressor bound to operator Nat. Struct. Biol. 7 2000 209 214 (Pubitemid 30140766)
4. M.A. Schumacher, K.Y. Choi, H. Zalkin, and R.G. Brennan Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices Science 266 1994 763 770
5. A. Majumdar, and S. Adhya Demonstration of two operator elements in gal: in vitro repressor binding studies Proc. Natl. Acad. Sci. U. S. A. 81 1984 6100 6104 (Pubitemid 15219600)
6. M.A. Schumacher, G.S. Allen, M. Diel, G. Seidel, W. Hillen, and R.G. Brennan Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P Cell 118 2004 731 741 (Pubitemid 39221732)
7. S. Alberti, S. Oehler, B. von Wilcken-Bergmann, H. Krämer, and B. Müller-Hill Dimer-to-tetramer assembly of lac repressor involves a leucine heptad repeat New Biol. 3 1991 57 62
8. K.S. Matthews DNA Looping Microbiol. Rev. 56 1992 123 136
9. S. Meinhardt, and L. Swint-Kruse Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives Proteins 73 2008 941 957
10. M.C. Mossing, and M.T. Record Jr. Upstream operators enhance repression of the lac promoter Science 233 1986 889 892 (Pubitemid 16011898)
11. S. Oehler, E.R. Eismann, H. Kramer, and B. Müller-Hill The three operators of the lac operon cooperate in repression EMBO J. 9 1990 973 979
12. S. Lin, and A.D. Riggs The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes Cell 4 1975 107 111
13. 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)
14. B. Richey, D.S. Cayley, M.C. Mossing, C. Kolka, C.F. Anderson, T.C. Farrar, and M.T. Record Variability of the intracellular ionic environment of Escherichia coli. Differences between in vitro and in vivo effects of ion concentrations on protein-DNA interactions and gene expression J. Biol. Chem. 262 1987 7157 7164
15. M.C. Mossing, and M.T. Record Jr. Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites J. Mol. Biol. 186 1985 295 305 (Pubitemid 16175729)
16. P.A. Whitson, J.S. Olson, and K.S. Matthews Thermodynamic analysis of the lactose repressor-operator DNA interaction Biochemistry 25 1986 3852 3858 (Pubitemid 16042512)
17. R. Daber, K. Sharp, and M. Lewis One is Not Enough J. Mol. Biol. 392 2009 1133 1144
18. R. Daber, M.A. Sochor, and M. Lewis Thermodynamic Analysis of Mutant lac Repressors J. Mol. Biol. 409 2011 76 87
19. D.F. Barker, and A.M. Campbell Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli J. Mol. Biol. 146 1981 469 492 (Pubitemid 11100438)
20. D.A. Rodionov, A.A. Mironov, and M.S. Gelfand Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea Genome Res. 12 2002 1507 1516 (Pubitemid 35175088)
21. M.D. Lane, K.L. Rominger, D.L. Young, and F. Lynen The enzymatic synthesis of holotranscarboxylase from apotranscarboxylase and (+)-biotin. II. Investigation of the reaction mechanism J. Biol. Chem. 239 1964 2865 2871
22. O. Prakash, and M.A. Eisenberg Biotinyl 5′-adenylate: corepressor role n the regulation of the biotin genes of Escherichia coli K-12 Proc. Natl. Acad. Sci. U. S. A. 76 1979 5592 5595
23. J.E. Cronan Jr. Expression of the biotin biosynthetic operon of Escherichia coli is regulated by the rate of protein biotination J. Biol. Chem. 263 1988 10332 10336
24. E.D. Streaker, and D. Beckett The biotin regulatory system: kinetic control of a transcriptional switch Biochemistry 45 2006 6417 6425 (Pubitemid 43787807)
25. H. Zhao, and D. Beckett Kinetic partitioning between alternative protein-protein interactions controls a transcriptional switch J. Mol. Biol. 380 2008 223 236
26. D.R. Wycuff, and K.S. Matthews Generation of an Ara-C-araBAD promoter-regulated T7 expression system Anal. Biochem. 277 2000 67 73 (Pubitemid 30041761)
27. L. Swint-Kruse, and K.S. Matthews Thermodynamics, protein modification, and molecular dynamics in characterizing lactose repressor protein: strategies for complex analyses of protein structure-function Methods Enzymol. 379 2004 188 209 (Pubitemid 38313473)
28. H. Zhan, L. Swint-Kruse, and K.S. Matthews Extrinsic interactions dominate helical propensity in coupled binding and folding of the lactose repressor protein hinge helix Biochemistry 45 2006 5896 5906
29. H. Zhan, M. Taraban, J. Trewhella, and L. Swint-Kruse Subdividing repressor function: DNA binding affinity, selectivity, and allostery can be altered by amino acid substitution of nonconserved residues in a LacI/GalR homologue Biochemistry 47 2008 8058 8069
30. J.R. Sadler, H. Sasmor, and J.L. Betz A perfectly symmetric lac operator binds the lac repressor very tightly Proc. Natl. Acad. Sci. U. S. A. 80 1983 6785 6789 (Pubitemid 14243232)
31. P.H. Brown, J.E. Cronan, M. Grotli, and D. Beckett The biotin repressor: modulation of allostery by corepressor analogs J. Mol. Biol. 337 2004 857 869 (Pubitemid 38368930)
32. J. Abbott, and D. Beckett Cooperative binding of the Escherichia coli repressor of biotin biosynthesis to the biotin operator sequence Biochemistry 32 1993 9649 9656 (Pubitemid 23296809)
33. M. Brenowitz, D.F. Senear, M.A. Shea, and G.K. Ackers Quantitative DNase footprint titration: a method for studying protein-DNA interactions Methods Enzymol. 130 1986 132 181
34. J.H. Miller Experiments in Molecular Genetics 1972 Cold Spring Harbor Laboratory Cold Spring Harbor, NY
35. J. Chen, and K.S. Matthews Subunit dissociation affects DNA binding in a dimeric lac repressor produced by C-terminal deletion Biochemistry 33 1994 8728 8735 (Pubitemid 24255066)
36. S. Semsey, K. Virnik, and S. Adhya Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA J. Mol. Biol. 358 2006 355 363
37. L. Swint-Kruse, C. Larson, B.M. Pettitt, and K.S. Matthews Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR Protein Sci. 11 2002 778 794 (Pubitemid 34241287)
38. H.E. Kubitschek, and J.A. Friske Determination of bacterial cell volume with the Coulter Counter J. Bacteriol. 168 1986 1466 1467 (Pubitemid 17226844)
39. H.X. Zhou, G. Rivas, and A.P. Minton Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences Annu. Rev. Biophys. 37 2008 375 397
40. G.J. Pielak, and A.C. Miklos Crowding and function reunite Proc. Natl Acad. Sci. 107 2010 17457 17458
41. A.H. Elcock Models of macromolecular crowding effects and the need for quantitative comparisons with experiment Curr. Opin. Struct. Biol. 20 2010 196 206
42. P.H. von Hippel, A. Revzin, C.A. Gross, and A.C. Wang Non-specific DNA binding of genome regulating proteins as a biological control mechanism: 1. The lac operon: equilibrium aspects Proc. Natl Acad. Sci. 71 12 1974 4808 4812
43. S.Y. Lin, and A.D. Riggs Lac repressor binding to non-operator DNA: detailed studies and a comparison of equilibrium and rate competition methods J. Mol. Biol. 72 1972 671 690
44. Y. Kao-Huang, A. Revzin, A.P. Butler, P. O'Conner, D.W. Noble, and P.H. von Hippel Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: measurement of DNA-bound Escherichia coli lac repressor in vivo Proc. Natl. Acad. Sci. U. S. A. 74 1977 4228 4232 (Pubitemid 8228387)
45. P.H. von Hippel, A. Revzin, C.A. Gross, and A.C. Wang Interaction of lac repressor with non specific DNA binding sites Protein Ligand Interact. Symp. 1974 270 280
46. E.D. Streaker, and D. Beckett Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding J. Mol. Biol. 325 2003 937 948 (Pubitemid 36263405)
47. Y. Xu, and D. Beckett Kinetics of biotinyl-5′-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex Biochemistry 33 1994 7354 7360 (Pubitemid 24208775)
48. Y. Xu, C.R. Johnson, and D. Beckett Thermodynamic analysis of small ligand binding to the Escherichia coli repressor of biotin biosynthesis Biochemistry 35 1996 5509 5517 (Pubitemid 26136528)
49. E. Eisenstein, and D. Beckett Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly Biochemistry 38 1999 13077 13084
50. H. Zhao, E. Streaker, W. Pan, and D. Beckett Protein-protein interactions dominate the assembly thermodynamics of a transcription repression complex Biochemistry 46 2007 13667 13676 (Pubitemid 350209962)
51. M.A. Eisenberg, O. Prakash, and S.C. Hsiung Purification and properties of the biotin repressor. A bifunctional protein J. Biol. Chem. 257 1982 15167 15173 (Pubitemid 13164869)
52. E.D. Streaker, A. Gupta, and D. Beckett The biotin repressor: thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding Biochemistry 41 2002 14263 14271 (Pubitemid 35403346)
53. D.F. Barker, and A.M. Campbell Use of bio-lac fusion strains to study regulation of biotin biosynthesis in Escherichia coli J. Bacteriol. 143 1980 789 800 (Pubitemid 10017650)
54. S.J. Li, and J.E. Cronan Jr. Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis J. Bacteriol. 175 1993 332 340 (Pubitemid 23031993)
55. A. Gershenson, and L.M. Gierasch Protein folding in the cell: challenges and progress Curr. Opin. Struct. Biol. 21 2011 32 41
56. S. Ghaemmaghami, and T.G. Oas Quantitative protein stability measurement in vivo Nat. Struct. Biol. 8 2001 879 882 (Pubitemid 32923608)