SEARCH

SEARCH BY CITATION

References

  • [1]
    Salmond, G.P.C. (1994) Secretion of extracellular virulence factors by plant pathogenic bacteria. Annu. Rev. Phytopathol. 32, 181200.
  • [2]
    Bauer, D.W., Bogdanove, A.J., Beer, S.V., Collmer, A. (1994) Erwinia chrysanthemi hrp genes and their involvement in soft rot pathogenesis and elicitation of the hypersensitive response. Mol. Plant–Microbe Interact. 7, 573581.
  • [3]
    Herlache, T.C. A.T. Hotchkiss Jr Burr, T.J., Collmer, A. (1997) Characterization of the Agrobacterium vitis pehA gene and comparison of the encoded polygalacturonase with the homologous enzymes from Erwinia carotovora and Ralstonia solanacearum. Appl. Environ. Microbiol. 63, 338346.
  • [4]
    Marie, C., Broughton, W.J., Deakin, W.J. (2001) Rhizobium type III secretion systems: legume charmers or alarmers. Curr. Opin. Plant Biol. 4, 336342.
  • [5]
    Preston, G.M. (2004) Plant perceptions of plant growth-promoting Pseudomonas. Philos. Trans. Royal Soc. B 359, 907918.
  • [6]
    Rezzonico, F., Defago, G., Moenne-Loccoz, Y. (2004) Comparison of ATPase-encoding type III secretion system hrcN genes in biocontrol fluorescent pseudomonads and in phytopathogenic Proteobacteria. Appl. Environ. Microbiol. 70, 51195131.
  • [7]
    Wilhelm, S., Tommassen, J., Jaeger, K.-E. (1999) A novel lipolytic enzyme located in the outer membrane of Pseudomonas aeruginosa. J. Bacteriol. 181, 69776986.
  • [8]
    Ochsner, U.A., Snyder, A., Vasil, A.I., Vasil, M.L. (2002) Effects of the twin-arginine translocase on secretion of virulence factors, stress response, and pathogenesis. Proc. Natl. Acad. Sci. USA 99, 83128317.
  • [9]
    Rojas, C.M., Ham, J.H., Deng, W.L., Doyle, J.J., Collmer, A. (2002) HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings. Proc. Natl. Acad. Sci. USA 99, 1314213147.
  • [10]
    Simpson, A., Al, E. (2000) The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151159.
  • [11]
    Plotnikova, J.M., Rahme, L.G., Ausubel, F.M. (2000) Pathogenesis of the human opportunistic pathogen Pseudomonas aeruginosa PA14 in Arabidopsis. Plant Physiol. 124, 17661774.
  • [12]
    Walker, T.S., Bais, H.P., Deziel, E., Schweizer, H.P., Rahme, L.G., Fall, R., Vivanco, J.M. (2004) Pseudomonas aeruginosa -plant root interactions. Pathogenicity, biofilm formation, and root exudation. Plant Physiol. 134, 320331.
  • [13]
    Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Goldman, B.S., Cao, Y., Askenazi, M., Halling, C., Mullin, L., Houmiel, K., Gordon, J., Vaudin, M., Iartchouk, O., Epp, A., Liu, F., Wollam, C., Allinger, M., Doughty, D., Scott, C., Lappas, C., Markelz, B., Flanagan, C., Crowell, C., Gurson, J., Lomo, C., Sear, C., Strub, G., Cielo, C., Slater, S. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294, 23232328.
  • [14]
    Wood, D.W., Setubal, J.C., Kaul, R., Monks, D.E., Kitajima, J.P., Okura, V.K., Zhou, Y., Chen, L., Wood, G.E., Almeida, N.F.J., Woo, L., Chen, Y., Paulsen, I.T., Eisen, J.A., Karp, P.D., Bovee, D.S., Chapman, P., Clendenning, J., Deatherage, G., Gillet, W., Grant, C., Kutyavin, T., Levy, R., Li, M.J., McClelland, E., Palmieri, A., Raymond, C.K., Rouse, G., Saenphimmachak, C., Wu, Z., Romero, P., Gordon, D., Zhang, S., Yoo, H., Tao, Y., Biddle, P., Jung, M., Krespan, W., Perry, M., Gordon-Kamm, B., Liao, L., Kim, S., Hendrick, C., Zhao, Z.Y., Dolan, M., Chumley, F., Tingey, S.V., Tomb, J.F., Gordon, M.P., Olson, M.V., Nester, E.W. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 23172323.
  • [15]
    Gelvin, S.B. (2000) Agrobacterium and plant genes involved in T-DNA transfer and integration. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51, 223256.
  • [16]
    Tsolis, R.M. (2002) Comparative genome analysis of the alpha-proteobacteria: relationships between plant and animal pathogens and host specificity. Proc. Natl. Acad. Sci. USA 99, 1250312505.
  • [17]
    Bell, K.S., Sebaihia, M., Pritchard, L. (2004) Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. USA 101, 1110511110.
  • [18]
    Bell, K.S., Avrova, A.O., Holeva, M.C., Cardle, L., Morris, W., De Jong, W., Toth, I.K., Waugh, R., Bryan, G.J., Birch, P.R.J. (2002) Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli. Microbiology 148, 13671378.
  • [19]
    Toth, I.K., Bell, K.S., Holeva, M.C., Birch, P.R.J. (2003) Soft rot erwiniae: from genes to genomes. Mol. Plant Pathol. 4, 1730.
  • [20]
    Buell, C.R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I.T., Gwinn, M.L., Dodson, R.J., Deboy, R.T., Durkin, A.S., Kolonay, J.F., Madupu, R., Daugherty, S., Brinkac, L., Beanan, M.J., Haft, D.H., Nelson, W.C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Van Aken, S.E., Feldblyum, T.V., D'Ascenzo, M., Deng, W.-L., Ramos, A.R., Alfano, J.R., Cartinhour, S., Chatterjee, A.K., Delaney, T.P., Lazarowitz, S.G., Martin, G.B., Schneider, D.J., Tang, X., Bender, C.L., White, O., Fraser, C.M., Collmer, A. (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100, 1018110186.
  • [21]
    Preston, G. (2000) Pseudomonas syringae pv. tomato : the right pathogen, of the right plant, at the right time. Mol. Plant Pathol. 1, 263275.
  • [22]
    Stover, C.K., Pham, X.Q. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406, 959964.
  • [23]
    Ma, Q., Zhai, Y., Schneider, J.C., Ramseier, T.M., Saier, J., Milton, H. (2003) Protein secretion systems of Pseudomonas aeruginosa and Pseudomonas fluorescens. Biochim. Biophys. Acta – Biomembranes 1611, 223233.
  • [24]
    Lyczak, J.B., Cannon, C.L., Pier, G.B. (2000) Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist. Microbes Infect. 2, 10511060.
  • [25]
    da Silva, J. (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459463.
  • [26]
    Vorhölter, F.-J., Thias, T., Meyer, F., Bekel, T., Kaiser, O., Puhler, A., Niehaus, K. (2003) Comparison of two Xanthomonas campestris pv. campestris genomes revealed differences in their gene composition. J. Biotechnol. 106, 193202.
  • [27]
    Graham, J.H., Gottwald, T.R., Cubero, J., Achor, D.S. (2004) Xanthomonas axonopodis pv. citri: factors affecting successful eradication of citrus canker. Mol. Plant Pathol. 5, 115.
  • [28]
    Moreira, L.M., De Souza, R.F., Almeida, N.F., Setubal, J.C., Oliviera, J.C.F., Furlan, L.R., Ferro, J.A., da Silva, A.C.R. (2004) Comparative genomics analysis of citrus-associated bacteria. Annu. Rev. Phytopathol. 42, 163184.
  • [29]
    Van Sluys, M.A., De Oliveira, M.C., Monteiro-Vitorello, C.B., Miyaki, C.Y., Furlan, L.R., Camargo, L.E.A., da Silva, A.C.R., Moon, D.H., Takita, M.A., Lemos, E.G.M., Machado, M.A., Ferro, M.I.T., da Silva, F.R., Goldman, M.H.S., Goldman, G.H., Lemos, M.V.F., El-Dorry, H., Tsai, S.M., Carrer, H., Carraro, D.M., De Oliveira, R.C., Nunes, L.R., Siqueira, W.J., Coutinho, L.L., Kimura, E.T., Ferro, E.S., Harakava, R., Kuramae, E.E., Marino, C.L., Giglioti, E., Abreu, I.L., Alves, L.M.C., do Amaral, A.M., Baia, G.S., Blanco, S.R., Brito, M.S., Cannavan, F.S., Celestino, A.V., da Cunha, A.F., Fenille, R.C., Ferro, J.A., Formighieri, E.F., Kishi, L.T., Leoni, S.G., Oliveira, A.R. V.E. Rosa Jr Sassaki, F.T., Sena, J.A.D., De Souza, A.A., Truffi, D., Tsukumo, F., Yanai, G.M., Zaros, L.G., Civerolo, E.L., Simpson, A.J.G. N.F. Almeida Jr Setubal, J.C., Kitajima, J.P. (2003) Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185, 10181026.
  • [30]
    Koide, T., Zaini, P.A., Moreira, L.M., Vencio, R.Z.N., Matsukuma, A.Y., Durham, A.M., Teixeira, D.C., El-Dorry, H., Monteiro, P.B., da Silva, A.C.R., Verjovski-Almeida, S., da Silva, A.M., Gomes, S.L. (2004) DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J. Bacteriol. 186, 54425449.
  • [31]
    Meidanis, J., Braga, M.D., Verjovski-Almeida, S. (2002) Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa. Microbiol. Mol. Biol. Rev. 66, 272299.
  • [32]
    Salanoubat, M., Genin, S., Artiguenave, F., Gouzy, J., Mangenot, S., Arlat, M., Billault, A., Brottier, P., Camus, J.C., Cattolico, L., Chandler, M., Choisne, N., Claudel-Renard, C., Cunnac, S., Demange, N., Gaspin, C., Lavie, M., Moisan, A., Robert, C., Saurin, W., Schiex, T., Siguier, P., Thebault, P., Whalen, M., Wincker, P., Levy, M., Weissenbach, J., Boucher, C.A. (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415, 497502.
  • [33]
    Genin, S., Boucher, C.A. (2002) Ralstonia solanacearum: secrets of a major pathogen unveiled by analysis of its genome. Mol. Plant Pathol. 3, 111118.
  • [34]
    Genin, S., Boucher, C. (2004) Lessons learned from the genome analysis of Ralstonia solanacearum. Annu. Rev. Phytopathol. 42, 107134.
  • [35]
    Bitter, W. (2003) Secretins of Pseudomonas aeruginosa: large holes in the outer membrane. Arch. Microbiol. 179, 307314.
  • [36]
    Koraimann, G. (2003) Lytic transglycosylases in macromolecular transport systems of Gram-negative bacteria. Cell. Mol. Life Sci. 60, 23712388.
  • [37]
    Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277D280.
  • [38]
    M.H. Saier Jr (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64, 354411.
  • [39]
    De Keyzer, J., van der Does, C., Driessen, A.J. (2003) The bacterial translocase: a dynamic protein channel complex. Cell. Mol. Life Sci. 60, 20342052.
  • [40]
    Fisher, A.C., DeLisa, M.P. (2004) A little help from my friends: quality control of presecretory proteins in bacteria. J. Bacteriol. 186, 74677473.
  • [41]
    Sapriel, G., Wandersman, C., Delepelaire, P. (2003) The SecB chaperone is bifunctional in Serratia marcescens: SecB is involved in the Sec Pathway and required for HasA secretion by the ABC transporter. J. Bacteriol. 185, 8088.
  • [42]
    Wolff, N., Sapriel, G., Bodenreider, C., Chaffotte, A., Delepelaire, P. (2003) Antifolding activity of the SecB chaperone is essential for secretion of HasA, a quickly folding ABC pathway substrate. J. Biol. Chem. 278, 3824738253.
  • [43]
    Ullers, R.S., Luirink, J., Harms, N., Schwager, F., Georgopoulos, C., Genevaux, P. (2004) SecB is a bona fide generalized chaperone in Escherichia coli. Proc. Natl. Acad. Sci. USA 101, 75837588.
  • [44]
    Duong, F., Eichler, J., Price, A., Leonard, M.R., Wickner, W. (1997) Biogenesis of the gram-negative bacterial envelope. Cell 91, 567573.
  • [45]
    De Gier, J.-W., Luirink, J. (2003) The ribosome and YidC. EMBO Rep. 4, 939943.
  • [46]
    Dalbey, R.E., Kuhn, A. (2004) YidC family members are involved in the membrane insertion, lateral integration, folding, and assembly of membrane proteins. J. Cell Biol. 166, 769774.
  • [47]
    Luirink, J., Sinning, I. (2004) SRP-mediated protein targeting: structure and function revisited. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 1735.
  • [48]
    Samuelson, J.C., Chen, M., Jiang, F., Moller, I., Wiedmann, M., Kuhn, A., Phillips, G.J., Dalbey, R.E. (2000) YidC mediates membrane protein insertion in bacteria. Nature 406, 637641.
  • [49]
    Rawlings, N.D., Tolle, D.P., Barrett, A.J. (2004) MEROPS: the peptidase database. Nucleic Acids Res. 32, D160D164.
  • [50]
    Berks, B.C., Palmer, T., Sargent, F. (2003) The Tat protein translocation pathway and its role in microbial physiology. Adv. Microb. Physiol. 47, 187254.
  • [51]
    Voulhoux, R., Ball, G., Ize, B., Vasil, A.I., Lazdunski, A., Wu, L.-F., Filloux, A. (2001) Involvement of the twin-arginine translocation system in protein secretion via the type II pathway. EMBO J. 20, 67356741.
  • [52]
    Ding, Z., Christie, P.J. (2003) Agrobacterium tumefaciens Twin-Arginine-dependent translocation is important for virulence, flagellation, and chemotaxis but not Type IV secretion. J. Bacteriol. 185, 760771.
  • [53]
    Jack, R.L., Sargent, F., Berks, B.C., Sawers, G., Palmer, T. (2001) Constitutive expression of Escherichia coli tat genes indicates an important role for the twin-arginine translocase during aerobic and anaerobic growth. J. Bacteriol. 183, 18011804.
  • [54]
    Wexler, M., Sargent, F., Jack, R.L., Stanley, N.R., Bogsch, E.G., Robinson, C., Berks, B.C., Palmer, T. (2000) TatD is a cytoplasmic protein with DNase activity. J. Biol. Chem. 275, 1671716722.
  • [55]
    Sonnhammer, E.L., von Heijne, G., Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 175182.
  • [56]
    Palmer, T., Sargent, F., Berks, B.C. (2004) Light traffic: photo-crosslinking a novel transport system. Trends Biochem. Sci. 29, 5557.
  • [57]
    Davidson, A.L., Chen, J. (2004) ATP-binding cassette transporters in bacteria. Annu. Rev. Biochem. 73, 241268.
  • [58]
    Ren, Q., Kang, K.H., Paulsen, I.T. (2004) TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res. 32, D284D288.
  • [59]
    York, G.M., Walker, G.C. (1997) The Rhizobium meliloti exoK gene and the prsD/prsE/exsH genes are components of independent degradative pathways which contribute to production of low-molecular-weight succinoglycan. Mol. Microbiol. 25, 117134.
  • [60]
    da Silva, F.G., Shen, Y., Dardick, C., Burdman, S., Yadav, R.C., De Leon, A.L., Ronald, P.C. (2004) Bacterial genes involved in type I secretion and sulfation are required to elicit the rice Xa21-mediated innate immune response. Mol. Plant–Microbe Interact. 17, 593601.
  • [61]
    Schmitt, L., Tampe, R. (2000) Structure and mechanism of ABC transporters. Curr. Opin. Struct. Biol. 12, 754760.
  • [62]
    Omori, K., Idei, A. (2003) Gram-negative bacterial ATP-binding cassette protein exporter family and diverse secretory proteins. J. Biosci. Bioeng. 95, 112.
  • [63]
    Binet, R., Letoffe, S., Ghigo, J.M., Delepelaire, P., Wandersman, C. (1997) Protein secretion by Gram-negative bacterial ABC exporters – a review. Gene 192, 711.
  • [64]
    Russel, M. (1998) Macromolecular assembly and secretion across the bacterial cell envelope: type II protein secretion systems. J. Mol. Biol. 279, 485499.
  • [65]
    Filloux, A. (2004) The underlying mechanisms of type II protein secretion. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 163179.
  • [66]
    Nudleman, E., Kaiser, D. (2004) Pulling together with type IV pili. J. Mol. Microbiol. Biotechnol. 7, 5262.
  • [67]
    Peabody, C.R., Chung, Y.J., Yen, M.-R., Vidal-Ingigliardi, D., Pugsley, A.P. M.H. Saier Jr (2003) Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Microbiology 149, 30513072.
  • [68]
    Filloux, A., Michel, G., Bally, M. (1998) GSP-dependent protein secretion in gram-negative bacteria: the Xcp system of Pseudomonas aeruginosa. FMR Microbiol. Rev. 22, 177198.
  • [69]
    Possot, O.M., Letellier, L., Pugsley, A.P. (1997) Energy requirement for pullulanase secretion by the main terminal branch of the general secretory pathway. Mol. Microbiol. 24, 457464.
  • [70]
    Suh, Y., Benedik, M.J. (1997) Secretion of nuclease across the outer membrane of Serratia marcescens and its energy requirements. J. Bacteriol. 179, 677683.
  • [71]
    Lindeberg, M., Salmond, G.P.C., Collmer, A. (1996) Complementation of deletion mutations in a cloned functional cluster of Erwinia chrysanthemi out genes with Erwinia carotovora out homologs reveals OutC and OutD as candidate gatekeepers of species-specific secretion of proteins via the type II pathway. Mol. Microbiol. 20, 175190.
  • [72]
    Shevchik, V.E., Robert-Baudouy, J., Condemine, G. (1997) Specific interaction between OutD, an Erwinia chrysanthemi outer membrane protein of the general secretory pathway, and secreted proteins. EMBO J. 16, 30073016.
  • [73]
    Lindeberg, M., Collmer, A. (1992) Analysis of eight out genes in a cluster required for pectic enzyme secretion by Erwinia chrysanthemi: Sequence comparison with secretion genes from other gram-negative bacteria. J. Bacteriol. 174, 73857397.
  • [74]
    Shevchik, V., Condemine, G. (1998) Functional characterization of the Erwinia chrysanthemi OutS protein, an element of a type II secretion system. Microbiology 144, 32193228.
  • [75]
    Condemine, G., Shevchik, V.E. (2000) Overproduction of the secretin OutD suppresses the secretion defect of an Erwinia chrysanthemi outB mutant. Microbiology 146, 639647.
  • [76]
    He, S.Y., Nomura, K., Whittam, T.S. (2004) Type III protein secretion mechanism in mammalian and plant pathogens. Biochim. Biophys. Acta Mol. Cell Res. 1694, 181206.
  • [77]
    He, S.Y., Jin, Q. (2003) The Hrp pilus: learning from flagella. Curr. Opin. Microbiol. 6, 1519.
  • [78]
    Preston, G., Collmer, A. The type III secretion systems of plant-associated pseudomonads: genes and proteins on the move. Ramos, J.L., Ed. The Pseudomonads Vol. 2, 2004. Kluwer Academic Press, Dordrecht.
  • [79]
    Pallen, M.J., Beatson, S., Bailey, C. Bioinformatics, genomics and the evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FMR Microbiol. Rev. 2005
  • [80]
    Ghosh, P. (2004) Process of Protein Transport by the Type III Secretion System. Microbiol. Mol. Biol. Rev. 68, 771795.
  • [81]
    Young, B.M., Young, G.M. (2002) YplA is exported by the Ysc, Ysa, and flagellar type III secretion systems of Yersinia enterocolitica. J. Bacteriol. 184, 13241334.
  • [82]
    Lee, S.H., Galan, J.E. (2004) Salmonella type III secretion-associated chaperones confer secretion-pathway specificity. Mol. Microbiol. 51, 483495.
  • [83]
    Gophna, U., Ron, E.Z., Graur, D. (2003) Bacterial type III secretion systems are ancient and evolved by mutiple horizontal-transfer events. Gene 312, 151163.
  • [84]
    Blocker, A., Komoriya, K., Aizawa, S.-I. (2003) Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proc. Natl. Acad. Sci. USA 100, 30273030.
  • [85]
    Kubori, T., Matsushima, Y., Nakamura, D., Uralil, J., Lara-Tejero, M., Sukhan, A., Galán, J.E., Aizawa, S.-I. (1998) Supramolecular structure of the Salmonella typhimurium type III protein secretion system. Science 280, 602605.
  • [86]
    Sekiya, K., Ohishi, M., Ogino, T., Tamano, K., Sasakawa, C., Abe, A. (2001) Supermolecular structure of the enteropathogenic Escherichia coli type III secretion system and its direct interaction with the EspA-sheath-like structure. Proc. Natl. Acad. Sci. USA 98, 1163811643.
  • [87]
    Tamano, K., Aizawa, S., Katayama, E., Nonaka, T., Imajoh-Ohmi, S., Kuwae, A., Nagai, S., Sasakawa, C. (2000) Supramolecular structure of the Shigella type III secretion machinery: the needle part is changeable in length and essential for delivery of effectors. EMBO J. 19, 38763887.
  • [88]
    Jin, Q., He, S.-Y. (2001) Role of the Hrp Pilus in Type III Protein Secretion in Pseudomonas syringae. Science 294, 25562558.
  • [89]
    Roine, E., Wei, W., Yuan, J., Nurmiaho-Lassila, E.-L., Kalkkinen, N., Romantschuk, M., He, S.Y. (1997) Hrp pilus: an hrp-dependent bacterial surface appendage produced by Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 94, 34593464.
  • [90]
    Van Gijsegem, F., Vasse, J., Camus, J.C., Marenda, M., Boucher, C. (2000) Ralstonia solanacearum produces Hrp-dependent pili that are required for PopA secretion but not for attachment of bacteria to plant cells. Mol. Microbiol. 36, 249260.
  • [91]
    Buttner, D., Bonas, U. (2002) Getting across – bacterial type III effector proteins on their way to the plant cell. EMBO J. 21, 53135322.
  • [92]
    Aizawa, S.-I. (2001) Bacterial flagella and type III secretion systems. FMR Microbiol. Lett. 202, 157164.
  • [93]
    Hueck, C.J. (1998) Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol. Mol. Biol. Rev. 62, 379433.
  • [94]
    Koster, M., Bitter, W., De Cock, H., Allaoui, A., Cornelis, G.R., Tommassen, J. (1997) The outer membrane component, YscC, of the Yop secretion machinery of Yersinia enterocolitica forms a ring-shaped multimeric complex. Mol. Microbiol. 26, 789797.
  • [95]
    Charkowski, A.O., Huang, H.-C., Collmer, A. (1997) Altered localization of the HrpZ harpin in Pseudomonas syringae pv. syringae hrp mutants suggests that different components of the type III secretion pathway control secretion across the inner and outer membranes of gram-negative bacteria. J. Bacteriol. 179, 38663874.
  • [96]
    Minamino, T., Macnab, R.M. (1999) Components of the Salmonella flagellar export apparatus and classification of export substrates. J. Bacteriol. 181, 13881394.
  • [97]
    Wilharm, G., Lehmann, V., Krauss, K., Lehnert, B., Richter, S., Ruckdeschel, K., Heesemann, J., Trulzsch, K. (2004) Yersinia enterocolitica type III secretion depends on the proton motive force but not on the flagellar motor components MotA and MotB. Infect. Immun. 72, 40044009.
  • [98]
    Deng, W.-L., Huang, H.-C. (1998) Cellular locations of Pseudomonas syringae pv. syringae HrcC and HrcJ proteins, required for harpin secretion via the type III pathway. J. Bacteriol. 181, 22982301.
  • [99]
    Foultier, B., Troisfontaines, P., Muller, S., Opperdoes, F.R., Cornelis, G.R. (2002) Characterization of the ysa pathogenicity locus in the chromosome of Yersinia enterocolitica and phylogeny analysis of type III secretion systems. J. Mol. Evol. 55, 3751.
  • [100]
    Arnold, D.L., Pitman, A., Jackson, R.W. (2003) Pathogenicity and other genomic islands in plant pathogenic bacteria. Mol. Plant Pathol. 4, 407420.
  • [101]
    Jin, Q., Hu, W., Brown, I., McGhee, G., Hart, P., Jones, A.L., He, S.Y. (2001) Visualization of secreted Hrp and Avr proteins along the Hrp pilus during type III secretion in Erwinia amylovora and Pseudomonas syringae. Mol. Microbiol. 40, 11291139.
  • [102]
    Li, C.-M., Brown, I., Mansfield, J., Stevens, C., Boureau, T., Romantschuk, M., Taira, S. (2002) The Hrp pilus of Pseudomonas syringae elongates from its tip and acts as a conduit for translocation of the effector protein HrpZ. EMBO J. 21, 19091915.
  • [103]
    Wei, W., Plovanich-Jones, A., Deng, W.-L., Ling, J.Q., Collmer, A., Huang, H.-C., He, S.Y. (2000) The gene coding for the Hrp pilus structural protein is required for type III secretion of Hrp and Avr proteins in Pseudomonas syringae pv. tomato. Proc. Natl. Acad. Sci. USA 97, 22472252.
  • [104]
    He, S.Y., Huang, H.-C., Collmer, A. (1993) Pseudomonas syringae pv. syringae harpinPss: a protein that is secreted via the Hrp pathway and elicits the hypersensitive response in plants. Cell 73, 12551266.
  • [105]
    Yuan, J., He, S.Y. (1996) The Pseudomonas syringae Hrp regulation and secretion system controls the production and secretion of multiple extracellular proteins. J. Bacteriol. 178, 63996402.
  • [106]
    Charkowski, A., Alfano, J.R., Preston, G.M., Yuan, J., He, S.Y., Collmer, A. (1998) The Pseudomonas syringae pv. tomato HrpW protein has domains similar to harpins and pectate lyases and can elicit the plant hypersensitive response and bind pectate. J. Bacteriol. 180, 52115217.
  • [107]
    Kim, J.-G., Jeon, E., Oh, J., Moon, J.S., Hwang, I. (2004) Mutational analysis of Xanthomonas harpin HpaG identifies a key functional region that elicits the hypersensitive response in nonhost plants. J. Bacteriol. 186, 62396247.
  • [108]
    Cascales, E., Christie, P.J. (2003) The versatile bacterial type IV secretion systems. Nat. Rev. Microbiol. 1, 137149.
  • [109]
    Ding, Z., Atmakuri, K., Christie, P.J. (2003) The outs and in of bacterial type IV secretion substrates. Trends Microbiol. 11, 527535.
  • [110]
    Burns, D.L. (2003) Type IV transporters of pathogenic bacteria. Curr. Opin. Microbiol. 6, 2934.
  • [111]
    Christie, P.J. (2004) Type IV secretion: the Agrobacterium VirB/D4 and related conjugation systems. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 219234.
  • [112]
    Engledow, A.S., Medrano, E.G., Mahenthiralingam, E., LiPuma, J.J., Gonzalez, C.F. (2004) Involvement of a plasmid-encoded Type IV secretion system in the plant tissue watersoaking phenotype of Burkholderia cenocepacia. J. Bacteriol. 186, 60156024.
  • [113]
    Jakubowski, S.J., Krishnamoorthy, V., Cascales, E., Christie, P.J. (2004) Agrobacterium tumefaciens VirB6 domains direct the ordered export of a DNA substrate through a Type IV secretion system. J. Mol. Biol. 341, 961977.
  • [114]
    Cascales, E., Christie, P.J. (2004) Definition of a bacterial Type IV secretion pathway for a DNA substrate. Science 304, 11701173.
  • [115]
    Stavrinides, J., Guttman, D.S. (2004) Nucleotide sequence and evolution of the five-plasmid complement of the phytopathogen Pseudomonas syringae pv. maculicola ES4326. J. Bacteriol. 186, 51015115.
  • [116]
    Hubber, A., Vergunst, A.C., Sullivan, J.T., Hooykaas, P.J.J., Ronson, C.W. (2004) Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system. Mol. Microbiol. 54, 561574.
  • [117]
    Desvaux, M., Parham, N.J., Henderson, I.R. (2004) The autotransporter secretion system. Res. Microbiol. 155, 5360.
  • [118]
    Jacob-Dubuisson, F., Fernandez, R., Coutte, L. (2004) Protein secretion through autotransporter and two-partner pathways. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 235257.
  • [119]
    Thanassi, D.G. (2002) Ushers and secretins: channels for the secretion of folded proteins across the bacterial outer membrane. J. Mol. Microbiol. Biotechnol. 4, 1120.
  • [120]
    Sauer, F.G., Remaut, H., Hultgren, S.J., Waksman, G. (2004) Fiber assembly by the chaperone-usher pathway. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 259267.
  • [121]
    Li, H., Qian, L., Chen, Z., Thibault, D., Liu, G., Liu, G., Thanassi, D.G. (2004) The outer membrane usher forms a twin-pore secretion complex. J. Mol. Biol. 344, 13971407.
  • [122]
    Sukharev, S., Anishkin, A. (2004) Mechanosensitive channels: what can we learn from ‘simple’ model systems. Trends Neurosci. 27, 345351.
  • [123]
    Berrier, C., Garrigues, A., Richarme, G., Ghazi, A. (2000) Elongation factor Tu and DnaK are transferred from the cytoplasm to the periplasm of Escherichia coli during osmotic downshock presumably via the mechanosensitive channel MscL. J. Bacteriol. 182, 248251.
  • [124]
    Wang, I.-N., Smith, D.L., Young, R. (2000) HOLINS: The protein clocks of bacteriophage infections. Annu. Rev. Microbiol. 54, 799825.
  • [125]
    Grundling, A., Manson, M.D., Young, R. (2001) Holins kill without warning. Proc. Natl. Acad. Sci. USA 98, 93489352.
  • [126]
    Canchaya, C., Proux, C., Fournous, G., Bruttin, A., Brussow, H. (2003) Prophage genomics. Microbiol. Mol. Biol. Rev. 67, 238276.
  • [127]
    Brillard, J., Boyer-Giglio, M.-H., Boemare, N., Givaudan, A. (2003) Holin locus characterisation from lysogenic Xenorhabdus nematophila and its involvement in Escherichia coli SheA haemolytic phenotype. FMR Microbiol. Lett. 218, 107113.
  • [128]
    Hurst, M.R.H., Glare, T.R., Jackson, T.A. (2004) Cloning Serratia entomophila antifeeding genes – a putative defective prophage active against the grass grub Costelytra zealandica. J. Bacteriol. 186, 51165128.
  • [129]
    Wai, S.N., Lindmark, B., Soderblom, T., Takade, A., Westermark, M., Oscarsson, J., Jass, J., Richter-Dahlfors, A., Mizunoe, Y., Uhlin, B.E. (2003) Vesicle-mediated export and assembly of pore-forming oligomers of the enterobacterial ClyA cytotoxin. Cell 115, 2535.
  • [130]
    Kadurugamuwa, J.L., Beveridge, T.J. (1995) Virulence factors are released from Pseudomonas aeruginosa in association with membrane vesicles during normal growth and exposure to gentamicin: a novel mechanism of enzyme secretion. J. Bacteriol. 177, 39984008.
  • [131]
    Chou, K.C. (2001) Prediction of signal peptides using scaled window. Peptides 22, 19731979.
  • [132]
    von Heijne, G. (1986) A new method for predicting signal sequence cleavage sites. Nucleic Acids Res. 14, 46834690.
  • [133]
    Nielsen, H., Englebrecht, J., Brunak, S., von Heijne, G. (1997) A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst. 8, 581599.
  • [134]
    Nielsen, M.N., Krogh, A. (1998) Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 122130.
  • [135]
    Menne, K.M., Hermjakob, H., Apweiler, R. A comparison of signal sequence prediction methods using a test set of signals. Bioinformatics. 2000. 741–742
  • [136]
    Cai, Y.D., Lin, S.L., Chou, K.C. (2003) Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides 24, 159161.
  • [137]
    Yu, C.S., Lin, C.J., Hwang, J.K. (2004) Predicting subcellular localisation of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 13, 14021406.
  • [138]
    Gardy, J.L., Spencer, D.H., Wang, K., Ester, M., Tusnady, G.E., Simon, I., Hua, S., Defays, K., Lambert, C., Nakai, K., Brinkman, F.S. (2003) PSORT-B: improving protein subcellular localisation prediction for gram-negative bacteria. Nucleic Acids Res. 31, 36133617.
  • [139]
    Kall, L., Krogh, A., Sonnhammer, E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338, 10271036.
  • [140]
    Bendtsen, J.D., Nielsen, M.N., von Heijne, G., Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783795.
  • [141]
    D'Ascenzo, M.D., Collmer, A., Martin, G.B. (2004) PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucleic Acids Res. 32, 31243135.
  • [142]
    Chaudhuri, R.R., Kahn, A.M., Pallen, M.J. (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res. 32, D296D299.
  • [143]
    Stanley, N.R., Palmer, D.A., Berks, B.C. (2000) The twin arginine consensus motif of Tat signal peptides is involved in Sec-independent protein targeting in Escherichia coli. J. Biol. Chem. 275, 1159111596.
  • [144]
    Jack, R.L., Grant, B., Dubini, A., Hatzixanthis, K., Palmer, T., Sargent, F. (2004) Coordinating assembly and export of complex bacterial proteins. EMBO J. 23, 39623972.
  • [145]
    Dilks, K., Rose, R.W., Hartmann, E., Pohlschroder, M. (2003) Prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey. J. Bacteriol. 185, 14781483.
  • [146]
    Jongbloed, J.D., Antelmann, H., Hecker, M., Nijland, R., Bron, S., Airaksinen, U., Pries, F., Quax, W.J., Van Dijl, J.M., Braun, P.G. (2002) Selective contribution of the twin-arginine translocation pathway to protein secretion in Bacillus subtilis. J. Biol. Chem. 277, 4406844078.
  • [147]
    Gerard, F., Pradel, N., Ye, C., Ize, B., Yi, L., Xu, J., Dalbey, R.E., Wu, L.F. (2004) Putative membrane assembly of EtpM-colicin V chimeras. Biochimie 86, 283286.
  • [148]
    Rosqvist, R., Hakansson, S., Forsberg, A., Wolf-Watz, H. (1995) Functional conservation of the secretion and translocation machinery for virulence proteins of yersiniae, salmonellae and shigellae. EMBO J. 14, 41874195.
  • [149]
    Anderson, D.M., Fouts, D.E., Collmer, A., Schneewind, O. (1999) Reciprocal secretion of proteins by the bacterial type III machines of plant and animal pathogens suggests universal recognition of mRNA targeting signals. Proc. Natl. Acad. Sci. USA 96, 1283912843.
  • [150]
    Ham, J.H., Bauer, D.W., Fouts, D.E., Collmer, A. (1998) A cloned Erwinia chrysanthemi Hrp (type III protein secretion) system functions in Escherichia coli to deliver Pseudomonas syringae Avr signals to plant cells and to secrete Avr proteins in culture. Proc. Natl. Acad. Sci. USA 95, 1020610211.
  • [151]
    Guttman, D.S. (2004) Plants as models for the study of human pathogenesis. Biotechnol. Adv. 22, 363382.
  • [152]
    Alfano, J.R., Collmer, A. (2004) Type III secretion system effector proteins: double agents in bacterial disease and plant defense. Annu. Rev. Phytopathol. 42, 385414.
  • [153]
    Espinosa, A., Alfano, J.R. (2004) Disabling surveillance: bacterial type III secretion system effectors that suppress innate immunity. Cell Microbiol. 6, 10271040.
  • [154]
    Guttman, D.S., Greenberg, J.T. (2001) Functional analysis of the type III effectors AvrRpt2 and AvrRpm1 of Pseudomonas syringae with the use of a single-copy integration system. Mol. Plant–Microbe Interact. 14, 145155.
  • [155]
    Mudgett, M.B., Staskawicz, B.J. (1999) Characterization of the Pseudomonas syringae pv. tomato AvrRpt2 protein: demonstration of secretion and processing during bacterial pathogenesis. Mol. Microbiol. 32, 927941.
  • [156]
    Wehling, M.D., Guo, M., Fu, Z.Q., Alfano, J.R. (2004) The Pseudomonas syringae HopPtoV protein is secreted in culture and translocated into plant cells via the Type III protein secretion system in a manner dependent on the ShcV Type III chaperone. J. Bacteriol. 186, 36213630.
  • [157]
    Lloyd, S.A., Forsberg, A., Wolf-Watz, H., Francis, M.S. (2001) Targeting exported substrates to the Yersinia TTSS: different functions for different signals. Trends Microbiol. 9, 367371.
  • [158]
    Ramamurthi, K.S., Schneewind, O. (2002) Type III protein secretion in Yersinia species. Annu. Rev. Cell Dev. Biol. 18, 107133.
  • [159]
    Ramamurthi, K.S., Schneewind, O. (2003) Substrate recognition by the Yersinia type III protein secretion machinery. Mol. Microbiol. 50, 10951102.
  • [160]
    Anderson, D.M., Schneewind, O. (1997) A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica. Science 278, 11401143.
  • [161]
    Ramamurthi, K.S., Schneewind, O. (2002) Yersinia enterocolitica type III secretion: mutational analysis of the YopQ secretion signal. J. Bacteriol. 184, 33213328.
  • [162]
    Ramamurthi, K.S., Schneewind, O. (2003) Yersinia yopQ mRNA encodes a bipartite type III secretion signal in the first 15 codons. Mol. Microbiol. 50, 11891198.
  • [163]
    Lloyd, S.A., Norman, M., Rosqvist, R., Wolf-Watz, H. (2001) Yersinia YopE is targeted for type III secretion by N-terminal, not mRNA, signals. Mol. Microbiol. 39, 520532.
  • [164]
    Karlinsey, J.E., Lonner, J., Brown, K.L., Hughes, K.T. (2000) Translation/secretion coupling by type III secretion systems. Cell 102, 487497.
  • [165]
    Guttman, D.S., Vinatzer, B.A., Sarkar, S.F., Ranall, M.V., Kettler, G., Greenberg, J.T. (2002) A functional screen for the type III (Hrp) secretome of the plant pathogen Pseudomonas syringae. Science 295, 17221726.
  • [166]
    Petnicki-Ocwieja, T., Schneider, D.J., Tam, V.C., Chancey, S.T., Shan, L., Jamir, Y., Schechter, L.M., Buell, C.R., Tang, X., Collmer, A., Alfano, J.R. (2002) Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 99, 76527657.
  • [167]
    Collmer, A., Lindeberg, M., Petnicki-Ocwieja, T., Schneider, D.J., Alfano, J.R. (2002) Genomic mining type III secretion system effectors in Pseudomonas syringae yields new picks for all TTSS prospectors. Trends Microbiol. 10, 462469.
  • [168]
    Greenberg, J.T., Vinatzer, B.A. (2003) Identifying type III effectors of plant pathogens and analyzing their interaction with plant cells. Curr. Opin. Microbiol. 6, 2028.
  • [169]
    Van Dijk, K., Fouts, D.E., Rehm, A.H., Hill, A.R., Collmer, A., Alfano, J.R. (1999) The Avr (effector) proteins HrmA (HopPsyA) and AvrPto are secreted in culture from Pseudomonas syringae pathovars via the Hrp (Type III) protein secretion system in a temperature- and pH-sensitive manner. J. Bacteriol. 181, 47904797.
  • [170]
    Buttner, D., Gurlebeck, D., Noel, L.D., Bonas, U. (2004) HpaB from Xanthomonas campestris pv. vesicatoria acts as an exit control protein in type III-dependent protein secretion. Mol. Microbiol. 54, 755768.
  • [171]
    Chapon, V., Czjzek, M., El Hassouni, M., Py, B., Juy, M., Barras, F. (2001) Type II protein secretion in gram-negative pathogenic bacteria: the study of the structure/secretion relationships of the cellulase cel5 (formerly EGZ) from Erwinia chrysanthemi. J. Mol. Biol. 310, 10551066.
  • [172]
    Bouley, J., Condemine, G., Shevchik, V.E. (2001) The PDZ domain of OutC and the N-terminal region of OutD determine the secretion specificity of the type II out pathway of Erwinia chrysanthemi. J. Mol. Biol. 308, 205219.
  • [173]
    Marits, R., Koiv, V., Laasik, E., Mae, A. (1999) Isolation of an extracellular protease gene of Erwinia carotovora subsp. carotovora strain SCC3193 by transposon mutagenesis and the role of protease in phytopathogenicity. Microbiology 145, 19591966.
  • [174]
    Letoffe, S., Delepelaire, P., Wandersman, C. (1990) Protease secretion by Erwinia chrysanthemi: the specific secretion functions are analogous to those of Escherichia coli alpha-hemolysin. EMBO J. 9, 13751382.
  • [175]
    Duong, F., Bonnet, E., Geli, V., Lazdunski, A., Murgier, M., Filloux, A. (2001) The AprX protein of Pseudomonas aeruginosa: a new substrate for the Apr type I secretion system. Gene 262, 147153.
  • [176]
    Ahn, J.H., Pan, J.G., Rhee, J.S. (1999) Identification of the tliDEF ABC transporter specific for lipase in Pseudomonas fluorescens SIK W1. J. Bacteriol. 181, 18471852.
  • [177]
    Rojas, C.M., Ham, J.H., Schecter, L.M., Kim, J.F., Beer, S.V., Collmer, A. (2004) The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system. Mol. Plant–Microbe Interact. 17, 644653.
  • [178]
    Delepelaire, P. (2004) Type I secretion in gram-negative bacteria. Biochim. Biophys. Acta – Mol. Cell Res. 1694, 149161.
  • [179]
    Ginalski, K., Kinch, L., Rychlewski, L., Grishin, N.V. (2004) BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases. Trends Biochem. 29, 392395.
  • [180]
    Kim, H.K., Jung, Y.-J., Choi, W.-C., Ryu, H.S., Oh, T.-K., Lee, J.-K. (2004) Sequence-based approach to finding functional lipases from microbial genome databases. FMR Microbiol. Lett. 235, 349355.
  • [181]
    Oliver, D.C., Huang, G., Fernandez, R.C. (2003) Identification of secretion determinants of the Bordetella pertussis BrkA autotransporter. J. Bacteriol. 185, 489495.
  • [182]
    Henderson, I.R., Navarro-Garcia, F., Nataro, J.P. (1998) The great escape: structure and function of the autotransporter proteins. Trends Microbiol. 6, 370378.
  • [183]
    Poulsen, K., Kilian, M. IgA1-specific endopeptidase. Barret, A.J., Rawlings, N.D., Woessner, J.F., Eds. Handbook of proteolytic enzymes. 2004. Elsevier, London
  • [184]
    Montecucco, C., De Bernard, M. (2003) Molecular and cellular mechanisms of action of the vacuolating cytotoxin (VacA) and neutrophil-activating protein (HP-NAP) virulence factors of Helicobacter pylori. Microbes Infect. 5, 715721.
  • [185]
    Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., Studholme, D.J., Yeats, C., Eddy, S.R. (2004) The Pfam protein families database. Nucleic Acid Res. 32, D138D141.
  • [186]
    Fouts, D.E., Abramovitch, R.B., Alfano, J.R., Baldo, A.M., Buell, C.R., Cartinhour, S., Chatterjee, A.K., D'Ascenzo, M., Gwinn, M.L., Lazarowitz, S.G., Lin, N.-C., Martin, G.B., Rehm, A.H., Schneider, D.J., Van Dijk, K., Tang, X., Collmer, A. (2002) Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. USA 99, 22752280.
  • [187]
    Innes, R.W., Bent, A.F., Kunkel, B.N., Bisgrove, S.R., Staskawicz, B.J. (1993) Molecular analysis of avirulence gene avrRpt2 and identification of a putative regulatory sequence common to all known Pseudomonas syringae avirulence genes. J. Bacteriol. 175, 48594869.
  • [188]
    Shen, H., Keen, N.T. (1993) Characterization of the promoter of avirulence gene D from Pseudomonas syringae pv. tomato. J. Bacteriol. 175, 59165924.
  • [189]
    Xiao, Y., Hutcheson, S. A single promoter sequence recognized by a newly identified alternate sigma factor directs expression of pathogenicity and host range determinants in Pseudomonas syringae. J. Bacteriol. >176 1994. 3089–3091 (Author's correction 3176:6158).
  • [190]
    Missiakas, D., Raina, S. (1998) The extracytoplasmic function sigma factors: role and regulation. Mol. Microbiol. 28, 10591066.
  • [191]
    Hughes, J.D., Estep, P.W., Tavazoie, S., Church, G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 12051214.
  • [192]
    Bailey, T., Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 4854.
  • [193]
    Buttner, D., Noel, L., Thieme, F., Bonas, U. (2003) Genomic approaches in Xanthomonas campestris pv. vesicatoria allow fishing for virulence genes. J. Biotechnol. 106, 203214.
  • [194]
    Mukaihara, T., Tamura, N., Murata, Y., Iwabuchi, M. (2004) Genetic screening of Hrp type III-related pathogenicity genes controlled by the HrpB transcriptional activator in Ralstonia solanacearum. Mol. Microbiol. 54, 863875.
  • [195]
    Roitsch, T., Jin, S., Nester, E.W. (1994) The binding site of the transcriptional activator VirG from Agrobacterium comprises both conserved and specific nonconserved sequences. FEBS Lett. 338, 127132.
  • [196]
    Smirnova, A.V., Ullrich, M.S. (2004) Topological and deletion analysis of CorS, a Pseudomonas syringae sensor kinase. Microbiology 150, 27152726.
  • [197]
    Das, A., Xie, Y.-H. (1998) Construction of transposon Tn3phoA: its application in defining the membrane topology of the Agrobacterium tumefaciens DNA transfer proteins. Mol. Microbiol. 27, 405414.
  • [198]
    Marchesini, M.I., Ugalde, J.E., Czibener, C., Comerci, D.J., Ugalde, R.A. (2004) N-terminal-capturing screening system for the isolation of Brucella abortus genes encoding surface exposed and secreted proteins. Microb. Pathogen. 37, 95105.
  • [199]
    Becker, F., Schnorr, K., Wilting, R., Tolstrup, N., Bendtsen, J.D., Olsen, P.B. (2004) Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries. J. Microbiol. Methods 57, 123133.
  • [200]
    Schechter, L.M., Roberts, K.A., Jamir, Y., Alfano, J.R., Collmer, A. (2004) Pseudomonas syringae type III secretion system targeting signals and novel effectors studied with a Cya translocation reporter. J. Bacteriol. 186, 543555.
  • [201]
    Casper Lindley, C., Dahlbeck, D., Clark, E.T., Staskawicz, B.J. (2002) Direct biochemical evidence for type III secretion-dependent translocation of the AvrBs2 effector protein into plant cells. Proc. Natl. Acad. Sci. USA 99, 83368341.
  • [202]
    Charpentier, X., Oswald, E. (2004) Identification of the secretion and translocation domain of the enteropathogenic and enterohemorrhagic Escherichia coli effector Cif, using TEM-1 β-lactamase as a new fluorescence-based reporter. J. Bacteriol. 186, 54865495.
  • [203]
    Schrammeijer, B., Dulk-Ras, A.d., Vergunst, A.C., Jurado Jacome, E., Hooykaas, P.J.J. (2003) Analysis of Vir protein translocation from Agrobacterium tumefaciens using Saccharomyces cerevisiae as a model: evidence for transport of a novel effector protein VirE3. Nucleic Acids Res. 31, 860868.
  • [204]
    Vergunst, A.C., Schrammeijer, B., den Dulk-Ras, A., De Vlaam, C.M.T., Regensburg-Tuink, T.J.G., Hooykaas, P.J.J. (2000) VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 290, 979982.
  • [205]
    Bailey, J., Manoil, C. (2002) Genome-wide internal tagging of bacterial exported proteins. Nat. Biotechnol. 20, 839842.
  • [206]
    Gaietta, G., Deerinck, T.J., Adams, S.R., Bouwer, J., Tour, O., Laird, D.W., Sosinsky, G.E., Tsien, R.Y., Ellisman, M.H. (2002) Multicolor and electron microscopic imaging of connexin trafficking. Science 296, 503507.
  • [207]
    Cambronne, E.D., Sorg, J.A., Schneewind, O. (2004) Binding of SycH chaperone to YscM1 and YscM2 activates effector yop expression in Yersinia enterocolitica. J. Bacteriol. 186, 829841.
  • [208]
    Szurek, B., Rossier, O., Hause, G., Bonas, U. (2002) Type III-dependent translocation of the Xanthomonas AvrBs3 protein into the plant cell. Mol. Microbiol. 46, 1323.
  • [209]
    Kazemi-Pour, N., Condemine, G., Hugouvieux-Cotte-Pattat, N. (2004) The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics 4, 31773186.
  • [210]
    Tjalsma, H., Antelmann, H., Jongbloed, J.D.H., Braun, P.G., Darmon, E., Dorenbos, R., Dubois, J.-Y.F., Westers, H., Zanen, G., Quax, W.J., Kuipers, O.P., Bron, S., Hecker, M., Van Dijl, J.M. (2004) Proteomics of protein secretion by Bacillus subtilis: separating the secrets of the secretome. Microbiol. Mol. Biol. Rev. 68, 207233.
  • [211]
    Wehmhoner, D., Haussler, S., Tummler, B., Jansch, L., Bredenbruch, F., Wehland, J., Steinmetz, I. (2003) Inter- and intraclonal diversity of the Pseudomonas aeruginosa proteome manifests within the secretome. J. Bacteriol. 185, 58075814.
  • [212]
    Dentler, W.L. (1995) Nonradioactive methods for labeling and identifying membrane surface proteins. Methods Cell Biol. 47, 407411.
  • [213]
    Pizza, M., Scarlato, V., Masignani, V., Giuliani, M.M., Aricó, B., Comanducci, M., Jennings, G.T., Baldi, L., Bartolini, E., Capecchi, B., Galeotti, C.L., Luzzi, E., Manetti, R., Marchetti, E., Mora, M., Nuti, S., Ratti, G., Santini, L., Savino, S., Scarselli, M., Storni, E., Zuo, P., Broeker, M., Hundt, E., Knapp, B., Blair, E., Mason, T., Tettelin, H.e., Hood, D.W., Jeffries, A.C., Saunders, N.J., Granoff, D.M., Venter, J.C., Moxon, E.R., Grandi, G., Rappuoli, R. (2000) Identification of vaccine candidates against serogroup B Meningococcus by whole-genome sequencing. Science 287, 18161820.
  • [214]
    Atmakuri, K., Ding, Z., Christie, P.J. (2003) VirE2, a Type IV secretion substrate, interacts with the VirD4 transfer protein at cell poles of Agrobacterium tumefaciens. Mol. Microbiol. 49, 16991713.
  • [215]
    Szpirer, C.Y., Faelen, M., Couturier, M. (2000) Interaction between the RP4 coupling protein TraG and the pBHR1 mobilization protein Mob. Mol. Microbiol. 37, 12831292.
  • [216]
    Schroder, G., Krause, S., Zechner, E.L., Traxler, B., Yeo, H.J., Lurz, R., Waksman, G., Lanka, E. (2002) TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system inner membrane gate for exported substrates. J. Bacteriol. 184, 27672779.
  • [217]
    Alegria, M.C., Docena, C., Khater, L., Ramos, C.H.I., da Silva, A.C.R., Farah, C.S. (2004) New protein–protein interactions identified for the regulatory and structural components and substrates of the type III secretion system of the phytopathogen Xanthomonas axonopodis Pathovar citri. J. Bacteriol. 186, 61866197.
  • [218]
    Jamir, Y., Guo, M., Oh, H.-S., Petnicki-Ocwieja, T., Chen, S., Tang, X., Dickman, M.B., Collmer, A., Alfano, J. (2004) R. Identification of Pseudomonas syringae type III effectors that can suppress programmed cell death in plants and yeast. Plant J. 37, 554565.
  • [219]
    Hotson, A., Mudgett, M.B. (2004) Cysteine proteases in phytopathogenic bacteria: identification of plant targets and activation of innate immunity. Curr. Opin. Plant Biol. 7, 384390.
  • [220]
    Abramovitch, R.B., Martin, G.B. (2004) Strategies used by bacterial pathogens to suppress plant defenses. Curr. Opin. Plant Biol. 7, 356364.
  • [221]
    Chang, J.H., Goel, A.K., Grant, S.R., Dangl, J.L. (2004) Wake of the flood: ascribing functions to the wave of type III effector proteins of phytopathogenic bacteria. Curr. Opin. Microbiol. 7, 1118.
  • [222]
    Noirot, P., Noirot-Gros, M.-F. (2004) Protein interaction networks in bacteria. Curr. Opin. Microbiol. 7, 505512.
  • [223]
    Creasey, E.A., Delahay, R.M., Daniell, S.J., Frankel, G. (2003) Yeast two-hybrid system survey of interactions between LEE-encoded proteins of enteropathogenic Escherichia coli. Microbiology 149, 20932106.
  • [224]
    Swietnicki, W., O'Brien, S., Holman, K., Cherry, S., Brueggemann, E., Tropea, J.E., Hines, H.B., Waugh, D.S., Ulrich, R.G. (2004) Novel protein–protein interactions of the Yersinia pestis type III secretion system elucidated with a matrix analysis by surface plasmon resonance and mass spectrometry. J. Biol. Chem. 279, 3869338700.
  • [225]
    Marlovits, T.C., Kubori, T., Sukhan, A., Thomas, D.R., Galan, J.E., Unger, V.M. (2004) Structural insights into the assembly of the type III secretion needle complex. Science 306, 10401042.
  • [226]
    Kumar, R.B., Das, A. (2002) Polar location and functional domains of the Agrobacterium tumefaciens DNA transfer protein VirD4. Mol. Microbiol. 43, 15231532.
  • [227]
    Hienonen, E., Rantakari, A., Romantschuk, M., Taira, S. (2004) The bacterial type III secretion system-associated pilin HrpA has an unusually long mRNA half-life. FEBS Lett. 2004, 217220.
  • [228]
    Viala, J., Chaput, C., Boneca, I.G., Cardona, A., Girardin, S.E., Moran, A.P., Athman, R., Memet, S., Huerre, M.R., Coyle, A.J., DiStefano, P.S., Sansonetti, P.J., Labigne, A., Bertin, J., Philpott, D.J., Fererro, R.L. (2004) Nod1 responds to peptidoglycan delivered by the Helicobacter pylori pathogenicity island. Nature Immunol. 5, 11661174.
  • [229]
    Oshima, K., Shiomi, T., Kuboyama, T., Sawayanagi, H., Nishigawa, S., Kakizawa, S., Miyata, S., Ugaki, M., Namba, S. (2001) Isolation and characterisation of derivative lines of the onion yellows phytoplasma that do not cause stunting or phloem hyperplasia. Phytopathology 91, 10241029.
  • [230]
    Rice, P., Longden, I., Bleasby, A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276277.
  • [231]
    Fariselli, P., Finocchiaro, G., Casadio, R. (2003) SREPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19, 24982499.
  • [232]
    Hua, S., Sun, Z. (2001) Support vector machine approach for protein subcellular localisation prediction. Bioinformatics 17, 721728.