BMC Microbiology | |
Characterization of the PAS domain in the sensor-kinase BvgS: mechanical role in signal transmission | |
Rudy Antoine3  Françoise Jacob-Dubuisson3  Camille Locht3  Julien Herrou2  Alexandre Wohlkonig1  Elian Dupré3  | |
[1] VIB Department of Structural Biology, Free University of Brussels, Pleinlaan 2, Brussels 1050 Belgium;Present address: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA;Univ Lille Nord de France, 59019 Lille, France | |
关键词: Signaling; PAS domain; Virulence regulation; Bordetella; Two-component system; | |
Others : 1143372 DOI : 10.1186/1471-2180-13-172 |
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received in 2013-04-17, accepted in 2013-07-19, 发布年份 2013 | |
【 摘 要 】
Background
In bacteria, signal-transduction two-component systems are major players for adaptation to environmental stimuli. The perception of a chemical or physical signal by a sensor-kinase triggers its autophosphorylation. The phosphoryl group is then transferred to the cognate response regulator, which mediates the appropriate adaptive response. Virulence of the whooping cough agent Bordetella pertussis is controlled by the two-component system BvgAS. Atypically, the sensor-kinase BvgS is active without specific stimuli at 37°C in laboratory conditions and is inactivated by the addition of negative chemical modulators. The structure of BvgS is complex, with two tandem periplasmic Venus flytrap domains and a cytoplasmic PAS domain that precedes the kinase domain, which is followed by additional phosphotransfer domains. PAS domains are small, ubiquitous sensing or regulatory domains. The function of the PAS domain in BvgS remains unknown.
Results
We showed that recombinant BvgS PAS proteins form dimers that are stabilized by α helical regions flanking the PAS core. A structural model of the PAS domain dimer was built and probed by site-directed mutagenesis and by biochemical and functional analyses. Although we found no ligands for the PAS domain cavity, its integrity is required for signaling. We also showed that the structural stability of the PAS core and its proper coupling to its flanking N- and C-terminal α helices are crucial for BvgS activity.
Conclusions
We propose that a major function of the BvgS PAS domain is to maintain conformational signals arising from mechanical strain generated by the periplasmic domain. The tight structure of the PAS core and its connections with the upstream and downstream helices ensure signaling to the kinase domain, which determines BvgS activity. Many mild substitutions that map to the PAS domain keep BvgS active but make it unresponsive to negative modulators, supporting that modulation increases conformational strain in the protein.
【 授权许可】
2013 Dupré et al.; licensee BioMed Central Ltd.
【 预 览 】
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【 参考文献 】
- [1]Gao R, Stock AM: Biological insights from structures of two-component proteins. Annu Rev Microbiol 2009, 63:133-154.
- [2]Casino P, Rubio V, Marina A: The mechanism of signal transduction by two-component systems. Curr Opin Struct Biol 2010, 20:763-771.
- [3]Cotter PA, Jones AM: Phosphorelay control of virulence gene expression in Bordetella. Trends Microbiol 2003, 11:367-373.
- [4]Uhl MA, Miller JF: Integration of multiple domains in a two-component sensor protein: the Bordetella pertussis BvgAS phosphorelay. EMBO J 1996, 15:1028-1036.
- [5]Jacob-Dubuisson F, Wintjens R, Herrou J, Dupré E, Antone R: BvgS of pathogenic Bordetellae: a paradigm for sensor kinase with Venus Flytrap perception domains. In Two-component system in bacteria. Edited by Gros R, Beier D. Norfolk, UK: Caister Academic Press; 2012:57-83.
- [6]Herrou J, Bompard C, Wintjens R, Dupre E, Willery E, et al.: Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism. Proc Natl Acad Sci USA 2010, 107:17351-17355.
- [7]Taylor BL, Zhulin IB: PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 1999, 63:479-506.
- [8]Möglich A, Ayers RA, Moffat K: Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 2009, 17:1282-1294.
- [9]Henry JT, Crosson S: Ligand-binding PAS domains in a genomic, cellular, and structural context. Annu Rev Microbiol 2011, 65:261-286.
- [10]Little R, Salinas P, Slavny P, Clarke TA, Dixon R: Substitutions in the redox-sensing PAS domain of the NifL regulatory protein define an inter-subunit pathway for redox signal transmission. Mol Microbiol 2011, 82:222-235.
- [11]Slavny P, Little R, Salinas P, Clarke TA, Dixon R: Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein. Mol Microbiol 2010, 75:61-75.
- [12]Cheung J, Hendrickson WA: Crystal structures of C4-dicarboxylate ligand complexes with sensor domains of histidine kinases DcuS and DctB. J Biol Chem 2008, 283:30256-30265.
- [13]Sevvana M, Vijayan V, Zweckstetter M, Reinelt S, Madden DR, et al.: A ligand-induced switch in the periplasmic domain of sensor histidine kinase CitA. J Mol Biol 2008, 377:512-523.
- [14]Zhang Z, Hendrickson WA: Structural characterization of the predominant family of histidine kinase sensor domains. J Mol Biol 2010, 400:335-353.
- [15]Pappalardo L, Janausch IG, Vijayan V, Zientz E, Junker J, et al.: The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli. J Biol Chem 2003, 278:39185-39188.
- [16]Beier D, Deppisch H, Gross R: Conserved sequence motifs in the unorthodox BvgS two-component sensor protein of Bordetella pertussis. Mol Gen Genet 1996, 252:169-176.
- [17]Bock A, Gross R: The unorthodox histidine kinases BvgS and EvgS are responsive to the oxidation status of a quinone electron carrier. Eur J Biochem 2002, 269:3479-3484.
- [18]Huth JR, Bewley CA, Jackson BM, Hinnebusch AG, Clore GM, et al.: Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Protein Sci 1997, 6:2359-2364.
- [19]Herrou J, Debrie AS, Willery E, Renaud-Mongenie G, Locht C, et al.: Molecular evolution of the two-component system BvgAS involved in virulence regulation in Bordetella. PLoS One 2009, 4:e6996.
- [20]Antoine R, Alonso S, Raze D, Coutte L, Lesjean S, et al.: New virulence-activated and virulence-repressed genes identified by systematic gene inactivation and generation of transcriptional fusions in Bordetella pertussis. J Bacteriol 2000, 182:5902-5905.
- [21]Stibitz S, Black W, Falkow S: The construction of a cloning vector designed for gene replacement in Bordetella pertussis. Gene 1986, 50:133-140.
- [22]King-Scott J, Konarev PV, Panjikar S, Jordanova R, Svergun DI, et al.: Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis. Structure 2011, 19:56-69.
- [23]Pantoliano MW, Petrella EC, Kwasnoski JD, Lobanov VS, Myslik J, et al.: High-density miniaturized thermal shift assays as a general strategy for drug discovery. J Biomol Screen 2001, 6:429-440.
- [24]Imaizumi A, Suzuki Y, Ono S, Sato Y, Sato H: Heptakis (2,6-O-dimethyl)beta-cyclodextrin: a novel growth stimulant for Bordetella pertussis phase I. J Clin Microbiol 1983, 17:781-786.
- [25]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
- [26]Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779-815.
- [27]Krivov GG, Shapovalov MV MV, Dunbrack RL Jr: Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77(4):778-795.
- [28]Wiederstein M, Sippl MJ: ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucl Acids Res 2007, 35:W407-410. Web Server issue
- [29]Hao B, Isaza C, Arndt J, Soltis M, Chan MK: Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum. Biochemistry 2002, 41:12952-12958.
- [30]Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, et al.: Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol 2000, 301:415-431.
- [31]Gilles-Gonzalez MA, Gonzalez G: Signal transduction by heme-containing PAS-domain proteins. J Appl Physiol 2004, 96:774-783.
- [32]Melton AR, Weiss AA: Characterization of environmental regulators of Bordetella pertussis. Infect Immun 1993, 61:807-815.
- [33]Herrou J, Crosson S: Function, structure and mechanism of bacterial photosensory LOV proteins. Nat Rev Microbiol 2011, 9:713-723.
- [34]Malpica R, Franco B, Rodriguez C, Kwon O, Georgellis D: Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. Proc Natl Acad Sci USA 2004, 101:13318-13323.
- [35]Philip AF, Kumauchi M, Hoff WD: Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. Proc Natl Acad Sci USA 2010, 107:17986-17991.
- [36]Campbell AJ, Watts KJ, Johnson MS, Taylor BL: Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer. Mol Microbiol 2010, 77:575-586.
- [37]Kumauchi M, Kaledhonkar S, Philip AF, Wycoff J, Hara M, et al.: A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein. J Am Chem Soc 2010, 132:15820-15830.
- [38]Möglich A, Ayers RA, Moffat K: Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 2009, 385:1433-1444.
- [39]Beier D, Schwarz B, Fuchs TM, Gross R: In vivo characterization of the unorthodox BvgS two-component sensor protein of Bordetella pertussis. J Mol Biol 1995, 248:596-610.
- [40]Perraud AL, Kimmel B, Weiss V, Gross R: Specificity of the BvgAS and EvgAS phosphorelay is mediated by the C- terminal HPt domains of the sensor proteins. Mol Microbiol 1998, 27:875-887.
- [41]Perraud AL, Rippe K, Bantscheff M, Glocker M, Lucassen M, et al.: Dimerization of signalling modules of the EvgAS and BvgAS phosphorelay systems. Biochim Biophys Acta 2000, 1478:341-354.
- [42]Little R, Slavny P, Dixon R: Influence of PAS domain flanking regions on oligomerisation and redox signalling by NifL. PLoS One 2012, 7:e46651.
- [43]Key J, Hefti M, Purcell EB, Moffat K: Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry 2007, 46:3614-3623.
- [44]Kurokawa H, Lee DS, Watanabe M, Sagami I, Mikami B, et al.: A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor. J Biol Chem 2004, 279:20186-20193.
- [45]Evans MR, Card PB, Gardner KH: ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space. Proc Natl Acad Sci USA 2009, 106:2617-2622.
- [46]Park H, Suquet C, Satterlee JD, Kang C: Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry 2004, 43:2738-2746.
- [47]Miller JF, Johnson SA, Black WJ, Beattie DT, Mekalanos JJ, et al.: Constitutive sensory transduction mutations in the Bordetella pertussis bvgS gene. J Bacteriol 1992, 174:970-979.
- [48]Manetti R, Arico B, Rappuoli R, Scarlato V: Mutations in the linker region of BvgS abolish response to environmental signals for the regulation of the virulence factors in Bordetella pertussis. Gene 1994, 150:123-127.
- [49]Nakamura MM, Liew SY, Cummings CA, Brinig MM, Dieterich C, et al.: Growth phase- and nutrient limitation-associated transcript abundance regulation in Bordetella pertussis. Infect Immun 2006, 74:5537-5548.
- [50]Ezzell JW, Dobrogosz WJ, Kloos WE, Manclark CR: Phase-shift markers in the genus Bordetella: loss of cytochrome d-629 in phase IV variants. Microbios 1981, 31:171-181.