Artículos de revistas
Comparative Genomics Analyses Of Citrus-associated Bacteria
Registro en:
Annual Review Of Phytopathology. , v. 42, n. , p. 163 - 184, 2004.
664286
10.1146/annurev.phyto.42.040803.140310
2-s2.0-4744374207
Autor
Moreira L.M.
De Souza R.F.
Almeida Jr. N.F.
Setubal J.C.
Oliveira J.C.R.
Furlan L.R.
Ferro J.A.
Da Silva A.C.R.
Institución
Resumen
Xylella fastidiosa 9a5c (XF-9a5c) and Xanthomonas axonopodis pv. citri (XAC) are bacteria that infect citrus plants. Sequencing of the genomes of these strains is complete and comparative analyses are now under way with the genomes of other bacteria of the same genera. In this review, we present an overview of this comparative genomic work. We also present a detailed genomic comparison between XF-9a5a and XAC. Based on this analysis, genes and operons were identified that might be relevant for adaptation to citrus. XAC has two copies of a type II secretion system, a large number of cell wall-degrading enzymes and sugar transporters, a complete energy metabolism, a whole set of avirulence genes associated with a type III secretion system, and a complete flagellar and chemotatic system. By contrast, XF-9a5c possesses more genes involved with type IV pili biosynthesis than does XAC, contains genes encoding for production of colicins, and has 4 copies of Type I restriction/modification system while XAC has only one. 42
163 184 Alm, R.A., Mattick, J.S., Genes involved in the biogenesis and function of type-4 fimbriae in Pseudomonas aeruginosa (1997) Gene, 192, pp. 89-98 Anraku, Y., Gennis, R.B., The aerobic respiratory chain of Escherichia coli (1987) Trends Biochem. Sci., 12, pp. 262-266 Banks, D., Albibi, R., Chen, J., Lamikanra, O., Jarret, R.L., Smith, B.J., Specific detection of Xylella fastidiosa Pierce's disease strains (1999) Curr. Microbiol., 39, pp. 85-88 Barber, C.E., Tang, J.L., Feng, J.X., Pan, M.Q., Wilson, T.J., A novel regulatory system required for pathogenicity of Xanthomonas campestris is mediated by a small diffusible signal molecule (1997) Mol. Microbiol., 24, pp. 555-566 Barry, T., Colleran, G.G.M., Dunican, L.K., Gannon, F., The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria (1991) PCR Methods Appl., 1, pp. 233-236 Bhattacharyya, A., Stilwagen, S., Ivanova, N., D'Souza, M., Bernal, A., Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains (2002) Proc. Natl. Acad. Sci. USA, 99, pp. 12403-12408 Bhattacharyya, A., Stilwagen, S., Reznik, G., Feil, H., Feil, W.S., Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights (2002) Genome Res., 12, pp. 1556-1563 Bonas, U., Schulte, R., Fenselau, S., Minsavage, G.V., Staskawicz, B.J., Stall, R.E., Isolation of a gene cluster from Xanthomonas campestris pv. vesicatoria that determines pathogenicity and the hypersensitive response on pepper and tomato (1991) Mol. Plant Microbe Interact., 4, pp. 81-88 Capage, M.A., Doherty, D.H., Betlach, M.R., Vanderslice, R.W., (1987), Int. Patent No. WO87/05938Chang, C.J., Garnier, M., Zreik, L., Rossetti, V., Bové, J.M., Culture and serological detection of the xylem-limited bacterium causing citrus variegated chlorosis and its identification as a strain of Xylella fastidiosa (1993) Curr. Microbiol., 27, pp. 137-142 Chang, C.J., Schaad, N.W., Electrophoretic protein profiles of total cell envelopes of xylem-limited plant pathogenic rickettsia-like bacteria (RLB) (1982) Phytopathology, 72, pp. 935-936 Chou, F.L., Chou, H.C., Lin, Y.S., Yang, B.Y., Lin, N.T., The Xanthomonas campestris gumD gene required for synthesis of xanthan gum is involved in normal pigmentation and virulence in causing black rot (1997) Biochem. Biophys. Res. Commun., 233, pp. 265-269 Da Costa, P.I., Franco, C.F., Miranda, V.S., Teixeira, D.C., Hartung, J.S., Strains of Xylella fastidiosa rapidly distinguished by arbitrarily primed-PCR (2000) Curr. Microbiol., 40, pp. 279-282 Da Silva, A.C.R., Ferro, J.A., Reinach, F.C., Farah, C.S., Furlan, L.R., Comparison of the genomes of two Xanthomonas pathogens with differing host specificities (2002) Nature, 417, pp. 459-463 Da Silva, F.R., Vettore, A.L., Kemper, E.L., Leite, A., Arruda, P., Fastidian gum: The Xylella fastidiosa exopolysaccharide possibly involved in bacterial pathogenicity (2001) FEMS Microbiol. Lett., 203, pp. 165-171 Dow, J.M., Daniels, M.J., Xylella genomics and bacterial pathogenicity to plants (2000) Yeast, 17, pp. 263-271 Duan, Y.P., Castaneda, A., Zhao, G., Erdos, G., Gabriel, D.W., Expression of a single, host-specific, bacterial pathogenicity gene in plant cells elicits division, enlargement and cell death (1999) Mol. Plant Microbe Interact., 12, pp. 556-560 Earhart, C.F., (1996) Uptake and Metabolism of Iron and Molybdenum, pp. 1075-1090. , See Ref. 39a Fath, M.J., Mahanty, H.K., Kolter, R., Characterization of a purF operon mutation which affects colicin V production (1989) J. Bacteriol., 171, pp. 3158-3161 Galan, J.E., Collmer, A., Type III secretion machines: Bacterial devices for protein delivery into host cells (1999) Science, 284, pp. 1322-1328 Goel, A.K., Rajagopal, L., Nagesh, N., Sonti, R.V., Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in Xanthomonas oryzae pv. oryzae (2002) J. Bacterial., 184, pp. 3539-3548 Goel, A.K., Rajagopal, L., Sonti, R.V., Pigment and virulence deficiencies associated with mutations in the aroE gene of Xanthomonas oryzae pv. oryzae (2001) Appl. Environ. Microbiol., 67, pp. 245-250 Gottwald, T.R., Graham, J.H., Bacterial diseases (2000) Compendium of Citrus Diseases, , ed. LW Timmer, SM Garnsey, JH Graham. St. Paul: APS Press Harding, N.E., Cleary, J.M., Ielpi, L., Genetics and biochemistry of xanthan gum production by Xanthomonas campestris (1995) Food Biotechnology Microorganisms, pp. 495-514. , ed. YH Hui, G Khachatourians, New York: VCH Publ Hendson, M., Purcell, A.H., Chen, D., Smart, C., Guilhabert, M., Kirkpatrick, B., Genetic diversity of Pierce's disease strains and other pathotypes of Xylella fastidiosa (2001) Appl. Environ. Microbiol., 67, pp. 895-903 Hugouvieux-Cotte-Pattat, N., Condemine, G., Nasser, W., Reverchon, S., Regulation of pectinolysis in Erwinia chrysanthemi (1996) Annu. Rev. Microbiol., 50, pp. 213-257 Ingledew, W.J., Poole, R.K., The respiratory chains of Escherichia coli (1984) Microbiol. Rev., 48, pp. 222-271 Kamper, S.M., French, W.J., DeKloet, S.R., Genetic relationships of some fastidious xylem-limited bacteria (1985) Int. J. Syst. Bacteriol., 35, pp. 185-188 Katzen, F., Becker, A., Zorreguieta, A., Puhler, A., Ielpi, L., Promoter analysis of the Xanthomonas campestris pv. campestris gum operon directing biosynthesis of the xanthan polysaccharide (1996) J. Bacteriol., 178, pp. 4313-4318 Katzen, F., Ferreiro, D.U., Oddo, C.G., Ielmini, M.V., Becker, A., Xanthomonas campestris pv. campestris gum mutants: Effects on xanthan biosynthesis and plant virulence (1998) J. Bacteriol., 180, pp. 1607-1617 Lazdunski, C.J., Bouveret, E., Rigal, A., Journet, L., Lloubes, R., Benedetti, H., Colicin import into Escherichia coli cells (1998) J. Bacteriol., 180, pp. 4993-5002 Lee, R.F., Beretta, M.J.G., Hartung, J.H., Hooker, M.E., Derrick, K.S., Citrus variegated chlorosis: Confirmation of a Xylella fastidiosa as the causal agent (1993) Summa Phytopathol., 19, pp. 123-125 Loh, J., Garcia, M., Stacey, G., NodV and NodW, a second flavonoid recognition system regulating nod gene expression in Bradyrhizobium japonicum (1997) J. Bacteriol., 179, pp. 3013-3020 Lopes, J.R.S., Beretta, M.J.G., Harakava, R., Almeida, R.P.P., Krugner, R., Garcia Jr., A., Confirmação da transmissão por cigarrinhas do agente causal da clorose variada dos citros, Xylella fastidiosa (1996) Fitopatol. Bras., 1, p. 343 MacFarlane, S.A., Merrick, M., The nucleotide sequence of the nitrogen regulation gene ntrB and the glnA-ntrBC intergenic region of Klebsiella pneumoniae (1985) Nucleic Acids Res., 13, pp. 7591-7606 Martinez-Argudo, I., Martin-Nieto, J., Salinas, P., Maldonado, R., Drummond, M., Contreras, A., Two-hybrid analysis of domain interactions involving NtrB and NtrC two-component regulators (2001) Mol. Microbiol., 40, pp. 169-178 Mehta, A., Rosato, Y.B., Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences (2001) Int. J. Syst. Evol. Microbiol., 51, pp. 311-318 Meidanis, J., Braga, M.D., Verjovski-Almeida, S., Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa (2002) Microbiol. Mol. Biol. Rev., 66, pp. 272-299 Moreira, L.M., Da Silva, A.C.R., (2002) Analise Comparativa Entre Os Genomas Dos Fitopatogenos Xylella Fastidiosa e Xanthomonas Axonopodis Pv Citri, , MSc. thesis. Univ. Sao Paulo, Chem. Inst Neidhardt, F.C., Curtiss, R.I., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikopp, W.S., Umbarger, H.E., (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology, , Washington, DC: ASM Press Newman, K., Almeida, R.P.P., Purcell, A.H., Lindow, S.E., Cell-cell signaling controls Xylella fastidiosa interactions with both insects and plants (2004) Proc. Natl. Acad. Sci.USA, 101, pp. 1737-1742 Nierman, W.C., Feldblyum, T.V., Laub, M.T., Paulsen, I.T., Nelson, K.E., Complete genome sequence of Caulobacter crescentus (2001) Proc. Natl. Acad. Sci. USA, 98, pp. 4136-4141 Nunes, L.R., Rosato, Y.B., Muto, N.H., Yanai, G.M., Da Silva, V.S., Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements (2003) Genome Res., 13, pp. 570-578 Pickard, D., Wain, J., Baker, S., Line, A., Chohan, S., Composition, acquisition, and distribution of the Vi exopolysaccharide- encoding Salmonella enterica pathogenicity island SPI-7 (2003) J. Bacteriol., 185, pp. 5055-5065 Poole, R.K., Ingledew, W.J., Pathways of electrons to oxygen (1987) Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology, pp. 170-200. , ed. FC Neidhardt, JL Ingraham, KB Low, B Magasanik, M Schaechter & HE Umbarger, Washington, DC: ASM Press Pooler, M.R., Hartung, J.S., Genetic relationships among strains of Xylella fastidiosa from RAPD-PCR data (1995) Curr. Microbiol., 31, pp. 134-137 Poplawsky, A.R., Chun, W., pigB determines a diffusible factor needed for extracellular polysaccharide slime and xanthomonadin production in Xanthomonas campestris pv. campestris (1997) J. Bacteriol., 179, pp. 439-444 Poplawsky, A.R., Chun, W., Xanthomonas campestris pv. campestris requires a functional pigB for epiphytic survival and host infection (1998) Mol. Plant Microbe Interact., 11, pp. 466-475 Poplawsky, A.R., Urban, S.C., Chun, W., Biological role of xanthomonadin pigments in Xanthomonas campestris pv. campestris (2000) Appl. Environ. Microbiol., 66, pp. 5123-5127 Redaschi, N., Bickle, T.A., (1996) DNA Restriction and Modification Systems, pp. 773-781. , See Ref. 39a Reizer, J., Bachem, S., Reizer, A., Arnaud, M., Saier Jr., M.H., Stulke, J., Novel phosphotransferase system genes revealed by genome analysis - The complete complement of PTS proteins encoded within the genome of Bacillus subtilis (1999) Microbiology, 145, pp. 3419-3429 Rossetti, V., Garnier, M., Bove, J.M., Beretta, M.J.G., Teixeira, A.R.R., Présence de bactéries dans le xylème d'orangers atteints de chlorose variéguée, une nouvelle maladie des agrumes au Brésil (1990) C. R. Acad. Paris, 310, pp. 345-349 Rudolph, K., Infection of the plant by Xanthomonas (1993) Xanthomonas, pp. 193-264. , ed. JG Swings, EL Civerolo, London: Chapman & Hall Russel, M., Macromolecular assembly and secretion across the bacterial cell envelope: Type II protein secretion systems (1998) J. Mol. Biol., 279, pp. 485-499 Scarpari, L.M., Lambais, M.R., Silva, D.S., Carraro, D.M., Carrer, H., Expression of putative pathogenicity-related genes in Xylella fastidiosa grown at low and high cell density conditions in vitro (2003) FEMS Microbiol. Lett., 222, pp. 83-92 Simpson, A.J., Reinach, F.C., Arruda, P., Abreu, F.A., Acencio, M., The genome sequence of the plant pathogen Xylella fastidiosa (2000) Nature, 406, pp. 151-157 Slater, H., Alvarez-Morales, A., Barber, C.E., Daniels, M.J., Dow, J.M., A two-component system involving an HD-GYP domain protein links cell-cell signalling to pathogenicity gene expression in Xanthomonas campestris (2000) Mol. Microbiol., 38, pp. 986-1003 Stock, J.B., Surette, M.G., (1996) Chemotaxis, pp. 1103-1129. , See Ref. 39a Strom, M.S., Lory, S., Structure-function and biogenesis of the type IV pili (1993) Annu. Rev. Microbiol., 47, pp. 565-596 Tang, J.L., Feng, J.X., Li, Q.Q., Wen, H.X., Zhou, D.L., Cloning and characterization of the rpfC gene of Xanthomonas oryzae pv. oryzae: Involvement in exopolysaccharide production and virulence to rice (1996) Mol. Plant Microbe Interact., 9, pp. 664-666 Tang, J.L., Liu, Y.N., Barber, C.E., Dow, J.M., Wootton, J.C., Daniels, M.J., Genetic and molecular analysis of a cluster of rpf genes involved in positive regulation of synthesis of extracellular enzymes and polysaccharide in Xanthomonas campestris pathovar campestris (1991) Mol. Gen. Genet., 226, pp. 409-417 Van Sluys, M.A., De Oliveira, M.C., Monteiro-Vitorello, C.B., Miyaki, C.Y., Furlan, L.R., Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa (2003) J. Bacteriol., 185, pp. 1018-1026 Van Sluys, M.A., Monteiro-Vitorello, C.B., Camargo, L.E., Menck, C.F., Da Silva, A.C., Comparative genomic analysis of plant-associated bacteria (2002) Annu. Rev. Phytopathol., 40, pp. 169-189 Vojnov, A.A., Slater, H., Daniels, M.J., Dow, J.M., Expression of the gum operon directing xanthan biosynthesis in Xanthomonas campestris and its regulation in planta (2001) Mol. Plant Microbe Interact., 14, pp. 768-774 Whitehead, N.A., Barnard, A.M., Slater, H., Simpson, N.J., Salmond, G.P., Quorum-sensing in Gram-negative bacteria (2001) FEMS Microbiol. Rev., 25, pp. 365-404 Wiggerich, H.G., Klauke, B., Koplin, R., Priefer, U.B., Puhler, A., Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not (1997) J. Bacteriol., 179, pp. 7103-7110 Wylie, J.L., Worobec, E.A., The OprB porin plays a central role in carbohydrate uptake in Pseudomonas aeruginosa (1995) J. Bacteriol., 177, pp. 3021-3026