ClpV, a unique Hsp100/Clp member of pathogenic proteobacteria

References

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.25, 3389–3402.10.1093/nar/25.17.3389Search in Google Scholar

Badger, J.L., Young, B.M., Darwin, A.J., and Miller, V.L. (2000). Yersinia enterocolitica ClpB affects levels of invasin and motility. J. Bacteriol.182, 5563–5571.10.1128/JB.182.19.5563-5571.2000Search in Google Scholar

Beinker, P., Schlee, S., Groemping, Y., Seidel, R., and Reinstein, J. (2002). The N-terminus of ClpB from Thermus thermophilus is not essential for the chaperone activity. J. Biol. Chem.277, 47160–47166.10.1074/jbc.M207853200Search in Google Scholar

Bladergroen, M.R., Badelt, K., and Spaink, H.P. (2003). Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion. Mol. Plant Microbe Interact.16, 53–64.10.1094/MPMI.2003.16.1.53Search in Google Scholar

Clarke, A.K. and Eriksson, M.J. (2000). The truncated form of the bacterial heat shock protein ClpB/HSP100 contributes to development of thermotolerance in the cyanobacterium Synechococcus sp. strain PCC 7942. J. Bacteriol.182, 7092–7096.Search in Google Scholar

Das, S. and Chaudhuri, K. (2003). Identification of a unique IAHP (IcmF associated homologous proteins) cluster in Vibrio cholerae and other proteobacteria through in silico analysis. In Silico Biol.3, 287–300.Search in Google Scholar

Das, S., Chakrabortty, A., Banerjee, R., Roychoudhury, S., and Chaudhuri, K. (2000). Comparison of global transcription responses allows identification of Vibrio cholerae genes differentially expressed following infection. FEMS Microbiol. Lett.190, 87–91.10.1111/j.1574-6968.2000.tb09267.xSearch in Google Scholar

Das, S., Chakrabortty, A., Banerjee, R., and Chaudhuri, K. (2002). Involvement of in vivo induced icmF gene of Vibrio cholerae in motility, adherence to epithelial cells, and conjugation frequency. Biochem. Biophys. Res. Commun.295, 922–928.10.1016/S0006-291X(02)00782-9Search in Google Scholar

Dougan, D.A., Reid, B.G., Horwich, A.L., and Bukau, B. (2002). ClpS, a substrate modulator of the ClpAP machine. Mol. Cell9, 673–683.10.1016/S1097-2765(02)00485-9Search in Google Scholar

Dougan, D.A., Weber-Ban, E.U., and Bukau, B. (2003). Targeted delivery of an ssrA tagged substrate by the adaptor protein SspB to its cognate AAA+ protein ClpX. Mol. Cell12, 373–380.10.1016/j.molcel.2003.08.012Search in Google Scholar

Folkesson, A., Lofdahl, S., and Normark, S. (2002). The Salmonella enterica subspecies I specific centisome 7 genomic island encodes novel protein families present in bacteria living in close contact with eukaryotic cells. Res. Microbiol.153, 537–545.10.1016/S0923-2508(02)01348-7Search in Google Scholar

Glover, J.R. and Lindquist, S. (1998). Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell94, 73–82.10.1016/S0092-8674(00)81223-4Search in Google Scholar

Goloubinoff, P., Mogk, A., Peres Ben Zvi, A., Tomoyasu, T., and Bukau, B. (1999). Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc. Natl. Acad. Sci. USA96, 13732–13737.10.1073/pnas.96.24.13732Search in Google Scholar

Gonzalez, M., Rasulova, F., Maurizi, M.R., and Woodgate, R. (2000). Subunit-specific degradation of the UmuD/D′ heterodimer by the ClpXP protease: the role of trans recognition in UmuD′ stability. EMBO J.19, 5251–5258.10.1093/emboj/19.19.5251Search in Google Scholar

Hong, S.W. and Vierling, E. (2000). Mutants of Arabidopsis thaliana defective in the acquisition of tolerance to high temperature stress. Proc. Natl. Acad. Sci. USA97, 4392–4397.10.1073/pnas.97.8.4392Search in Google Scholar

Ishikawa, T., Beuron, F., Kessel, M., Wickner, S., Maurizi, M.R., and Steven, A.C. (2001). Translocation pathway of protein substrates in ClpAP protease. Proc. Natl. Acad. Sci. USA98, 4328–4333.10.1073/pnas.081543698Search in Google Scholar

Kedzierska, S., Akoev, V., Barnett, M.E., and Zolkiewski, M. (2003). Structure and function of the middle domain of ClpB from Escherichia coli. Biochemistry42, 14242–14248.10.1021/bi035573dSearch in Google Scholar

Kelley, L.A., MacCallum, R.M., and Sternberg, M.J. (2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol.299, 499–520.Search in Google Scholar

Kim, K.I., Cheong, G.W., Park, S.C., Ha, J.S., Woo, K.M., Choi, S.J., and Chung, C.H. (2000). Heptameric ring structure of the heat-shock protein ClpB, a protein-activated ATPase in Escherichia coli. J. Mol. Biol.303, 655–666.10.1006/jmbi.2000.4165Search in Google Scholar

Kim, Y.I., Levchenko, I., Fraczkowska, K., Woodruff, R.V., Sauer, R.T., and Baker, T.A. (2001). Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nat. Struct. Biol.8, 230–233.10.1038/84967Search in Google Scholar

Krzewska, J., Langer, T., and Liberek, K. (2001). Mitochondrial Hsp78, a member of the Clp/Hsp100 family in Saccharomyces cerevisiae, cooperates with Hsp70 in protein refolding. FEBS Lett.489, 92–96.10.1016/S0014-5793(00)02423-6Search in Google Scholar

Lee, S., Sowa, M.E., Watanabe, Y., Sigler, P.B., Chiu, W., Yoshida, M., and Tsai, F.T. (2003). The structure of ClpB. A molecular chaperone that rescues proteins from an aggregated state. Cell115, 229–240.10.1016/S0092-8674(03)00807-9Search in Google Scholar

Levchenko, I., Seidel, M., Sauer, R.T., and Baker, T.A. (2000). A specificity-enhancing factor for the ClpXP degradation machine. Science289, 2354–2356.10.1126/science.289.5488.2354Search in Google Scholar PubMed

Li, J. and Sha, B. (2002). Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity. J. Mol. Biol.318, 1127–1137.Search in Google Scholar

Lum, R., Tkach, J.M., Vierling, E., and Glover, J.R. (2004). Evidence for an unfolding/threading mechanism for protein disaggregation by Saccharomyces cerevisiae Hsp104.J. Biol. Chem.279, 29139–29146.10.1074/jbc.M403777200Search in Google Scholar

Lupas, A., Van Dyke, M., and Stock, J. (1991). Predicting coiled coils from protein sequences. Science252, 1162–1164.10.1126/science.252.5009.1162Search in Google Scholar

McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Du, F., et al. (2001). Complete genome sequence of Salmonella enterica serovar. typhimurium LT2. Nature413, 852–856.Search in Google Scholar

Mogk, A., Schlieker, C., Strub, C., Rist, W., Weibezahn, J., and Bukau, B. (2003). Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP-hydrolysis and chaperone activity. J. Biol. Chem.278, 15–24.10.1074/jbc.M209686200Search in Google Scholar

Motohashi, K., Watanabe, Y., Yohda, M., and Yoshida, M. (1999). Heat-inactivated proteins are rescued by the DnaK. J-GrpE set and ClpB chaperones. Proc. Natl. Acad. Sci. USA96, 7184–7189.10.1073/pnas.96.13.7184Search in Google Scholar

Neher, S.B., Sauer, R.T., and Baker, T.A. (2003). Distinct peptide signals in the UmuD and UmuD′ subunits of UmuD/D′ mediate tethering and substrate processing by the ClpXP protease. Proc. Natl. Acad. Sci. USA100, 13219–13224.10.1073/pnas.2235804100Search in Google Scholar

Neuwald, A.F., Aravind, L., Spouge, J.L., and Koonin, E.V. (1999). AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res.9, 27–43.10.1101/gr.9.1.27Search in Google Scholar

Ogura, T. and Wilkinson, A.J. (2001). AAA+ superfamily ATPases: common structure diverse function. Genes Cells6, 575–597.10.1046/j.1365-2443.2001.00447.xSearch in Google Scholar

Parsell, D.A., Sanchez, Y., Stitzel, J.D., and Lindquist, S. (1991). Hsp104 is a highly conserved protein with two essential nucleotide-binding sites. Nature353, 270–273.10.1038/353270a0Search in Google Scholar

Patel, S. and Latterich, M. (1998). The AAA team: related ATPases with diverse functions. Trends Cell Biol.8, 65–71.10.1016/S0962-8924(97)01212-9Search in Google Scholar

Perna, N.T., Plunkett, G. III, Burland, V., Mau, B., Glasner, J.D., Rose, D.J., Mayhew, G.F., Evans, P.S., Gregor, J., Kirkpatrick, H.A., et al. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature409, 529–533.10.1038/35054089Search in Google Scholar PubMed

Perriere, G. and Gouy, M. (1996). WWW-query: an on-line retrieval system for biological sequence banks. Biochimie78, 364–369.10.1016/0300-9084(96)84768-7Search in Google Scholar

Queitsch, C., Hong, S.W., Vierling, E., and Lindquist, S. (2000). Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell12, 479–492.10.1105/tpc.12.4.479Search in Google Scholar

Rao, P.S., Yamada, Y., Tan, Y.P., and Leung, K.Y. (2004). Use of proteomics to identify novel virulence determinants that are required for Edwardsiella tarda pathogenesis. Mol. Microbiol.53, 573–586.Search in Google Scholar

Sauer, R.T., Bolon, D.N., Burton, B.M., Burton, R.E., Flynn, J.M., Grant, R.A., Hersch, G.L., Joshi, S.A., Kenniston, J.A., Levchenko, I., et al. (2004). Sculpting the proteome with AAA+ proteases and disassembly machines. Cell119, 9–18.10.1016/j.cell.2004.09.020Search in Google Scholar

Schirmer, E.C., Glover, J.R., Singer, M.A., and Lindquist, S. (1996). HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem. Sci.21, 289–296.10.1016/S0968-0004(96)10038-4Search in Google Scholar

Schirmer, E.C., Homann, O.R., Kowal, A.S., and Lindquist, S. (2004). Dominant gain-of-function mutations in Hsp104p reveal crucial roles for the middle region. Mol. Biol. Cell15, 2061–2072.10.1091/mbc.e02-08-0502Search in Google Scholar PubMed PubMed Central

Schlieker, C., Weibezahn, J., Patzelt, H., Tessarz, P., Strub, C., Zeth, K., Erbse, A., Schneider-Mergener, J., Chin, J.W., Schultz, P.G., et al. (2004). Substrate recognition by the AAA+ chaperone ClpB. Nat. Struct. Mol. Biol.11, 607–615.10.1038/nsmb787Search in Google Scholar PubMed

Schmitt, M., Neupert, W., and Langer, T. (1996). The molecular chaperone Hsp78 confers compartment-specific thermotolerance to mitochondria. J. Cell Biol.134, 1375–1386.10.1083/jcb.134.6.1375Search in Google Scholar PubMed PubMed Central

Schouler, C., Koffmann, F., Amory, C., Leroy-Setrin, S., and Moulin-Schouleur, M. (2004). Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup. Microbiology150, 2973–2984.10.1099/mic.0.27261-0Search in Google Scholar PubMed

Segal, G. and Shuman, H.A. (1999). Legionella pneumophila utilizes the same genes to multiply within Acanthamoebacastellanii and human macrophages. Infect. Immun.67, 2117–2124.10.1128/IAI.67.5.2117-2124.1999Search in Google Scholar PubMed PubMed Central

Siddiqui, S.M., Sauer, R.T., and Baker, T.A. (2004). Role of the processing pore of the ClpX AAA+ ATPase in the recognition and engagement of specific protein substrates. Genes Dev.18, 369–374.10.1101/gad.1170304Search in Google Scholar PubMed PubMed Central

Singh, S.K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J., Steven, A.C., and Maurizi, M.R. (2001). Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J. Biol. Chem.276, 29420–29429.10.1074/jbc.M103489200Search in Google Scholar

Song, H.K., Hartmann, C., Ramachandran, R., Bochtler, M., Behrendt, R., Moroder, L., and Huber, R. (2000). Mutational studies on HslU and its docking mode with HslV. Proc. Natl. Acad. Sci. USA97, 14103–14108.10.1073/pnas.250491797Search in Google Scholar

Squires, C.L., Pedersen, S., Ross, B.M., and Squires, C. (1991). ClpB is the Escherichia coli heat shock protein F84.1. J. Bacteriol.173, 4254–4262.10.1128/jb.173.14.4254-4262.1991Search in Google Scholar

Turgay, K., Hahn, J., Burghoorn, J., and Dubnau, D. (1998). Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J.17, 6730–6738.Search in Google Scholar

Wah, D.A., Levchenko, I., Rieckhof, G.E., Bolon, D.N., Baker, T.A., and Sauer, R.T. (2003). Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol. Cell12, 355–363.10.1016/S1097-2765(03)00272-7Search in Google Scholar

Weibezahn, J., Schlieker, C., Bukau, B., and Mogk, A. (2003). Characterization of a trap mutant of the AAA+ chaperone ClpB. J. Biol. Chem.278, 32608–32617.10.1074/jbc.M303653200Search in Google Scholar PubMed

Weibezahn, J., Tessarz, P., Schlieker, C., Zahn, R., Maglica, Z., Lee, S., Zentgraf, H., Weber Ban, E.U., Dougan, D.A., Tsai, F.T., et al. (2004). Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB. Cell119, 653–665.10.1016/j.cell.2004.11.027Search in Google Scholar PubMed

Wojtyra, U.A., Thibault, G., Tuite, A., and Houry, W.A. (2003). The N-terminal zinc binding domain of ClpX is a dimerization domain that modulates the chaperone function. J. Biol. Chem.278, 48981–48990.10.1074/jbc.M307825200Search in Google Scholar PubMed

Yamada-Inagawa, T., Okuno, T., Karata, K., Yamanaka, K., and Ogura, T. (2003). Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis. J. Biol. Chem.278, 50182–50187.10.1074/jbc.M308327200Search in Google Scholar PubMed

Yeo, H.J. and Waksman, G. (2004). Unveiling molecular scaf-folds of the type IV secretion system. J. Bacteriol.186, 1919–1926.10.1128/JB.186.7.1919-1926.2004Search in Google Scholar PubMed PubMed Central

Zhou, Y., Gottesman, S., Hoskins, J.R., Maurizi, M.R., and Wickner, S. (2001). The RssB response regulator directly targets sigma(S) for degradation by ClpXP. Genes Dev.15, 627–637.10.1101/gad.864401Search in Google Scholar PubMed PubMed Central

Zolkiewski, M. (1999). ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. A novel multi-chaperone system from Escherichia coli. J. Biol. Chem.274, 28083–28086.10.1074/jbc.274.40.28083Search in Google Scholar PubMed

Zusman, T., Feldman, M., Halperin, E., and Segal, G. (2004). Characterization of the icmH and icmF genes required for Legionella pneumophila intracellular growth, genes that are present in many bacteria associated with eukaryotic cells. Infect. Immun.72, 3398–3409.10.1128/IAI.72.6.3398-3409.2004Search in Google Scholar PubMed PubMed Central