| [1] | Nixon BT, Ronson CW, Ausubel FM (1986) Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC. Proc Natl Acad Sci U S A 83: 7850–7854.
|
| [2] | Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3: 165–170.
|
| [3] | Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal transduction. Annu Rev Biochem 69: 183–215.
|
| [4] | Mascher T, Helmann JD, Unden G (2006) Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol Mol Biol Rev 70: 910–938.
|
| [5] | Bourret RB (2010) Receiver domain structure and function in response regulator proteins. Curr Opin Microbiol 13: 142–149.
|
| [6] | Gao R, Stock AM (2010) Molecular strategies for phosphorylation-mediated regulation of response regulator activity. Curr Opin Microbiol 13: 160–167.
|
| [7] | Galperin MY (2010) Diversity of structure and function of response regulator output domains. Curr Opin Microbiol 13: 150–159.
|
| [8] | Galperin MY (2006) Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 188: 4169–4182.
|
| [9] | Martinez-Hackert E, Stock AM (1997) The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor. Structure 5: 109–124.
|
| [10] | Baikalov I, Schroder I, Kaczor-Grzeskowiak M, Grzeskowiak K, Gunsalus RP, et al. (1996) Structure of the Escherichia coli response regulator NarL. Biochemistry 35: 11053–11061.
|
| [11] | Pelton JG, Kustu S, Wemmer DE (1999) Solution structure of the DNA-binding domain of NtrC with three alanine substitutions. J Mol Biol 292: 1095–1110.
|
| [12] | Csonka LN (1989) Physiological and genetic responses of bacteria to osmotic stress. Microbiol Rev 53: 121–147.
|
| [13] | Wood JM, Bremer E, Csonka LN, Kraemer R, Poolman B, et al. (2001) Osmosensing and osmoregulatory compatible solute accumulation by bacteria. Comp Biochem Physiol A Mol Integr Physiol 130: 437–460.
|
| [14] | Altendorf K, Siebers A, Epstein W (1992) The KDP ATPase of Escherichia coli. Ann N Y Acad Sci 671: 228–243.
|
| [15] | Epstein W (2003) The roles and regulation of potassium in bacteria. Prog Nucleic Acid Res Mol Biol 75: 293–320.
|
| [16] | Walderhaug MO, Polarek JW, Voelkner P, Daniel JM, Hesse JE, et al. (1992) KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators. J Bacteriol 174: 2152–2159.
|
| [17] | Heermann R, Jung K (2010) The complexity of the ‘simple’ two-component system KdpD/KdpE in Escherichia coli. FEMS Microbiol Lett 304: 97–106.
|
| [18] | Zimmann P, Puppe W, Altendorf K (1995) Membrane topology analysis of the sensor kinase KdpD of Escherichia coli. J Biol Chem 270: 28282–28288.
|
| [19] | Laimins LA, Rhoads DB, Epstein W (1981) Osmotic control of kdp operon expression in Escherichia coli. Proc Natl Acad Sci U S A 78: 464–468.
|
| [20] | Asha H, Gowrishankar J (1993) Regulation of kdp operon expression in Escherichia coli: evidence against turgor as signal for transcriptional control. J Bacteriol 175: 4528–4537.
|
| [21] | Stallkamp I, Dowhan W, Altendorf K, Jung K (1999) Negatively charged phospholipids influence the activity of the sensor kinase KdpD of Escherichia coli. Arch Microbiol 172: 295–302.
|
| [22] | Ohwada T, Sagisaka S (1987) An immediate and steep increase in ATP concentration in response to reduced turgor pressure in Escherichia coli B. Arch Biochem Biophys 259: 157–163.
|
| [23] | Nakashima K, Sugiura A, Kanamaru K, Mizuno T (1993) Signal transduction between the two regulatory components involved in the regulation of the kdpABC operon in Escherichia coli: phosphorylation-dependent functioning of the positive regulator, KdpE. Mol Microbiol 7: 109–116.
|
| [24] | Sugiura A, Nakashima K, Tanaka K, Mizuno T (1992) Clarification of the structural and functional features of the osmoregulated kdp operon of Escherichia coli. Mol Microbiol 6: 1769–1776.
|
| [25] | Toro-Roman A, Wu T, Stock AM (2005) A common dimerization interface in bacterial response regulators KdpE and TorR. Protein Sci 14: 3077–3088.
|
| [26] | Fiedler U, Weiss V (1995) A common switch in activation of the response regulators NtrC and PhoB: phosphorylation induces dimerization of the receiver modules. EMBO J 14: 3696–3705.
|
| [27] | Yoshida T, Qin L, Egger LA, Inouye M (2006) Transcription regulation of ompF and ompC by a single transcription factor, OmpR. J Biol Chem 281: 17114–17123.
|
| [28] | Rhee JE, Sheng W, Morgan LK, Nolet R, Liao X, et al. (2008) Amino acids important for DNA recognition by the response regulator OmpR. J Biol Chem 283: 8664–8677.
|
| [29] | Heermann R, Altendorf K, Jung K (2003) The N-terminal input domain of the sensor kinase KdpD of Escherichia coli stabilizes the interaction between the cognate response regulator KdpE and the corresponding DNA-binding site. J Biol Chem 278: 51277–51284.
|
| [30] | Rossmann MG (1990) The molecular replacement method. Acta Crystallogr A 46(Pt 2): 73–82.
|
| [31] | Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132.
|
| [32] | Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240–255.
|
| [33] | Schuck P (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J 78: 1606–1619.
|
| [34] | Dam J, Velikovsky CA, Mariuzza RA, Urbanke C, Schuck P (2005) Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s). Biophys J 89: 619–634.
|
| [35] | Woodward RS, Lebowitz J (1980) A revised equation relating DNA buoyant density to guanine plus cytosine content. J Biochem Biophys Methods 2: 307–309.
|
| [36] | Kar SR, Lebowitz J, Blume S, Taylor KB, Hall LM (2001) SmtB-DNA and protein-protein interactions in the formation of the cyanobacterial metallothionein repression complex: Zn2+ does not dissociate the protein-DNA complex in vitro. Biochemistry 40: 13378–13389.
|
| [37] | Ghirlando R (2011) The analysis of macromolecular interactions by sedimentation equilibrium. Methods 54: 145–156.
|
| [38] | Vistica J, Dam J, Balbo A, Yikilmaz E, Mariuzza RA, et al. (2004) Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition. Anal Biochem 326: 234–256.
|
| [39] | Tsuzuki M, Aiba H, Mizuno T (1994) Gene activation by the Escherichia coli positive regulator, OmpR. Phosphorylation-independent mechanism of activation by an OmpR mutant. J Mol Biol 242: 607–613.
|
| [40] | Ellison DW, McCleary WR (2000) The unphosphorylated receiver domain of PhoB silences the activity of its output domain. J Bacteriol 182: 6592–6597.
|
| [41] | Friedland N, Mack TR, Yu M, Hung LW, Terwilliger TC, et al. (2007) Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 46: 6733–6743.
|
| [42] | Blanco AG, Sola M, Gomis-Ruth FX, Coll M (2002) Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 10: 701–713.
|
| [43] | Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29: 2860–2874.
|
| [44] | Garvie CW, Wolberger C (2001) Recognition of specific DNA sequences. Mol Cell 8: 937–946.
|
| [45] | Janin J, Rodier F, Chakrabarti P, Bahadur RP (2007) Macromolecular recognition in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 63: 1–8.
|
| [46] | Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248–1253.
|
| [47] | Rohs R, Jin X, West SM, Joshi R, Honig B, et al. (2010) Origins of specificity in protein-DNA recognition. Annu Rev Biochem 79: 233–269.
|
| [48] | Hizver J, Rozenberg H, Frolow F, Rabinovich D, Shakked Z (2001) DNA bending by an adenine–thymine tract and its role in gene regulation. Proc Natl Acad Sci U S A 98: 8490–8495.
|
| [49] | Makino K, Amemura M, Kawamoto T, Kimura S, Shinagawa H, et al. (1996) DNA binding of PhoB and its interaction with RNA polymerase. J Mol Biol 259: 15–26.
|
| [50] | Das AK, Pathak A, Sinha A, Datt M, Singh B, et al. (2010) A single-amino-acid substitution in the C terminus of PhoP determines DNA-binding specificity of the virulence-associated response regulator from Mycobacterium tuberculosis. J Mol Biol 398: 647–656.
|
| [51] | Brown PH, Schuck P (2006) Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys J 90: 4651–4661.
|
| [52] | Naue N, Fedorov R, Pich A, Manstein DJ, Curth U (2011) Site-directed mutagenesis of the chi subunit of DNA polymerase III and single-stranded DNA-binding protein of E. coli reveals key residues for their interaction. Nucleic Acids Res 39: 1398–1407.
|
| [53] | Dam J, Schuck P (2005) Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory. Biophys J 89: 651–666.
|
| [54] | Rippe K (1997) Analysis of protein-DNA binding at equilibrium. B I F Futura 12: 20–26.
|
| [55] | Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc 2: 1849–1861.
|
| [56] | Mack TR, Gao R, Stock AM (2009) Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB. J Mol Biol 389: 349–364.
|
| [57] | Tate S, Kato M, Nishimura Y, Arata Y, Mizuno T (1988) Location of DNA-binding segment of a positive regulator, OmpR, involved in activation of the ompF and ompC genes of Escherichia coli. FEBS Lett 242: 27–30.
|
| [58] | Kato M, Aiba H, Tate S, Nishimura Y, Mizuno T (1989) Location of phosphorylation site and DNA-binding site of a positive regulator, OmpR, involved in activation of the osmoregulatory genes of Escherichia coli. FEBS Lett 249: 168–172.
|
| [59] | Straume D, Johansen RF, Bjoras M, Nes IF, Diep DB (2009) DNA binding kinetics of two response regulators, PlnC and PlnD, from the bacteriocin regulon of Lactobacillus plantarum C11. BMC Biochem 10: 17.
|
| [60] | Lacal J, Guazzaroni ME, Gutierrez-del-Arroyo P, Busch A, Velez M, et al. (2008) Two levels of cooperativeness in the binding of TodT to the tod operon promoter. J Mol Biol 384: 1037–1047.
|
| [61] | Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190.
|
