The leucine-responsive regulatory protein (lrp) gene for characterization of the relationship among Xanthomonas species

International Journal of Systematic and Evolutionary Microbiology

Volumn 54, Issue 2, 2004, Pages 429-437

  Cubero, Jaime ^a   Graham, James H ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL DNA; BACTERIAL PROTEIN; LEUCINE RESPONSIVE REGULATORY PROTEIN; NUCLEOTIDE; PRIMER DNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BACTERIUM ISOLATION; BIOASSAY; CITRUS FRUIT; CONTROLLED STUDY; DATA ANALYSIS; DNA FINGERPRINTING; DNA HYBRIDIZATION; ENTEROBACTERIACEAE; GENE FUNCTION; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; GENUS; HOST; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SUBSPECIES; TAXONOMY; XANTHOMONAS; XANTHOMONAS CAMPESTRIS;

BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DNA-BINDING PROTEINS; LEUCINE; LEUCINE-RESPONSIVE REGULATORY PROTEIN; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; POLYMERASE CHAIN REACTION; TRANSCRIPTION FACTORS; XANTHOMONAS;

BACTERIA (MICROORGANISMS); CITRUS; ENTEROBACTERIACEAE; XANTHOMONAS; XANTHOMONAS AXONOPODIS; XANTHOMONAS AXONOPODIS PV. CITRI; XANTHOMONAS CAMPESTRIS;

EID: 1842475024     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.02784-0     Document Type: Article

References (52)

1. Bouzar, H., Jones, J. B., Stall, R. E., Louws, F. J., Schneider, M., Rademaker, J. L. W., de Bruijn, F. J. & Jackson, L. E. (1999). Multiphasic analysis of xanthomonads causing bacterial spot disease on tomato and pepper in the Caribbean and Central America: evidence for common lineages within and between countries. Phytopathology 89, 328-335.
2. Calvo, J. M. & Matthews, R. G. (1994). The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 58, 466-490.
3. Chen, S. & Calvo, J. M. (2002). Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers. J Mol Biol 318, 1031-1042.
4. Cubero, J. & Graham, J. H. (2002). Genetic relationships among worldwide strains of Xanthomonas causing canker in citrus species and design of new primers for their identification by PCR. Appl Environ Microbiol 68, 1257-1264.
5. da Silva, A. C. R., Ferro, J. A., Reinach, F. C. & 62 other authors (2002). Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459-463.
6. Dye, D. W. & Lelliott, R. A. (1974). Genus II. Xanthomonas. In Bergey's Manual of Determinative Bacteriology, 8th edn, pp. 243-249. Edited by R. E. Buchanan & N. E. Gibbons. Baltimore: Williams & Wilkins.
7. Egel, D. S., Graham, J. H. & Stall, R. E. (1991). Genomic relatedness of Xanthomonas campestris strains causing diseases of citrus. Appl Environ Microbiol 57, 2724-2730.
8. Friedberg, D., Platko, J. V., Tyler, B. & Calvo, J. M. (1995). The amino acid sequence of Lrp is highly conserved in four enteric microorganisms. J Bacteriol 177, 1624-1626.
9. Gabriel, D. W., Kingsley, M. T., Hunter, J. E. & Gottwald, T. (1989). Reinstatement of Xanthomonas citri (ex Hasse) and X. phaseoli (ex Smith) to species and reclassification of all X. campestris pv. citri strains. Int J Syst Bacteriol 39, 14-22.
10. Gonçalves, E. R. & Rosato, Y. B. (2002). Phylogenetic analysis of Xanthomonas species upon 16S-23S rDNA intergenic spacer sequences. Int J Syst Bacteriol 52, 355-361.
11. Graham, J. H. & Gottwald, T. R. (1990). Variation in aggressiveness of Xanthomonas campestris pv. citrumelo, associated with citrus bacterial spot in Florida citrus nurseries. Phytopathology 80, 190-196.
12. Graham, J. H., Hartung, J. S., Stall, R. E. & Chase, A. R. (1990). Pathological, restriction-fragment length polymorphism, and fatty acid profile relationships between Xanthomonas campestris from citrus and noncitrus hosts. Phytopathology 80, 829-836.
13. Graham, J. H., Gottwald, T. R., Riley, T. D. & Bruce, M. A. (1992). Susceptibility of citrus fruit to bacterial spot and citrus canker. Phytopathology 82, 452-457.
14. Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
15. Hauben, L., Vauterin, L., Swings, J. & Moore, E. R. B. (1997). Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47, 328-335.
16. Higgins, D. G. & Sharp, P. M. (1988). CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
17. Hulton, C. S. J., Higgins, C. F. & Sharp, P. M. (1991). ERIC sequences: A novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5, 825-834.
18. Jones, J. B., Stall, R. E. & Bouzar, H. (1998). Diversity among xanthomonads pathogenic on pepper and tomato. Annu Rev Phytopathol 36, 41-58.
19. Jones, J. B., Bouzar, H., Stall, R. E., Almira, E. C., Roberts, P. D., Bowen, B. W., Sudberry, J., Strickler, P. M. & Chun, J. (2000). Systematic analysis of xanthomonads (Xanthomonas spp.) associated with pepper and tomato lesions. Int J Syst Evol Microbiol 50, 1211-1219.
20. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
21. Khodakaramian, G. & Swings, J. (2002). AFLP fingerprinting of the strains of Xanthomonas axonopodis inducing citrus canker disease in southern Iran. Phytopathol Z 150, 227-231.
22. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: Molecular evolutionary genetic analysis software. Bioinformatics 17, 1244-1245.
23. Lawrence, J. G. (1999). Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 2, 519-523.
24. Leyns, F., De Cleene, M., Swings, J. G. & De Ley, J. (1984). The host range of the genus Xanthomonas. Bot Rev 50, 308-356.
25. Li, W.-H., Wu, C.-I. & Luo, C.-C. (1985). A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2, 150-174.
26. Louws, F. J., Fulbright, D. W., Stephens, C. T. & de Bruijn, F. J. (1994). Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl Environ Microbiol 60, 2286-2295.
27. Louws, F. J., Fulbright, D. W., Stephens, C. T. & de Bruijn, F. J. (1995). Differentiation of genomic structure by rep-PCR fingerprinting to rapidly classify Xanthomonas campestris pv. vesicatoria. Phytopathology 85, 528-536.
28. Louws, F. J., Rademaker, J. L. W. & de Bruijn, F. J. (1999). The three Ds of PCR-based genomic analysis of phytobacteria: Diversity, detection, and disease diagnosis. Annu Rev Phytopathol 37, 81-125.
29. Mohammadi, M., Mirzaee, M. R. & Rahimian, H. (2001). Physiological and biochemical characteristics of Iranian strains of Xanthomonas axonopodis pv. citri, the causal agent of citrus bacterial canker disease. Phytopathol Z 149, 65-75.
30. Newman, E. B., D'Ari, R. & Lin, R. T. (1992). The leucine-Lrp regulon in E. coli: A global response in search of a raison d'être. Cell 68, 617-619.
31. Opgenorth, D. C., Smart, C. D., Louws, F. J., de Bruijn, F. J. & Kirkpatrick B. C. (1996). Identification of Xanthomonas fragariae field isolates by rep-PCR genomic fingerprinting. Plant Dis 80, 868-873.
32. Platko, J. V. & Calvo, J. M. (1993). Mutations affecting the ability of Escherichia coli Lrp to bind DNA, activate transcription, or respond to leucine. J Bacteriol 175, 1110-1117.
33. Pooler, M. R., Ritchie, D. F. & Hartung, J. S. (1996). Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen. Appl Environ Microbiol 62, 3121-3127.
34. Rademaker, J. L. W., Hoste, B., Louws, F. J., Kersters, K., Swings, J., Vauterin, L., Vauterin, P. & de Bruijn, F. J. (2000). Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol 50, 665-677.
35. Saitou, N. & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
36. Salanoubat, M., Genin, S., Artiguenave, F. & 25 other authors (2002). Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415, 497-502.
37. Sambrook J. & Russell, D. (2000). Molecular Cloning. a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
38. Schaad, N. W., Vidaver, A. K., Lacy, G. H., Rudolph, K. & Jones, J. B. (2000). Evaluation of proposed amended names of several pseudomonads and xanthomonads and recommendations. Phytopathology 90, 208-213.
39. Schoulties, C. L., Civerolo, E. L., Miller, J. W., Stall, R. E., Krass, C. J., Poe, S. R. & Ducharme, E. P. (1987). Citrus canker in Florida. Plant Dis 71, 388-395.
40. Stover, C. K., Pham, X. Q., Erwin, A. L. & 28 other authors (2000). Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959-964.
41. Sun, X., Stall, R. E., Cubero, J. & 7 other authors (2000). Detection of a unique isolate of citrus canker bacterium from Key lime in Wellington and Lake Worth, Florida. In Proceedings of the International Citrus Canker Research Workshop, Fort Pierce, FL, USA, 20-22 June 2000 (http://www.doacs.state.fl.us/~pi/abstracts.pdf).
42. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
43. Van den Mooter, M. & Swings, J. (1990). Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol 40, 348-369.
44. Vauterin, L. & Swings, J. (1997). Are classification and phytopathological diversity compatible in Xanthomonas? J Ind Microbiol Biotechnol 19, 77-82.
45. Vauterin, L., Yang, P., Hoste, B., Vancanneyt, M., Civerolo, E. L., Swings, J. & Kersters, K. (1991). Differentiation of Xanthomonas campestris pv. citri strains by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins, fatty acid analysis, and DNA-DNA hybridization. Int J Syst Bacteriol 41, 535-542.
46. Vauterin, L., Hoste, B., Kersters, K. & Swings, J. (1995). Reclassification of Xanthomonas. Int J Syst Bacteriol 45, 472-489.
47. Vauterin, L., Rademaker, J. & Swings, J. (2000). Synopsis on the taxonomy of the genus Xanthomonas. Phytopathology 90, 677-682.
48. Vernière, C., Hartung, J. S., Pruvost, O. P., Civerolo, E. L., Alvarez, A. M., Maestri, P. & Luisetti, J. (1998). Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from Southwest Asia. Eur J Plant Pathol 104, 477-487.
49. Versalovic, J., Koeuth, T. & Lupski, J. R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19, 6823-6831.
50. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
51. Weiller, G. F. (1998). Phylogenetic profiles: A graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15, 326-335.
52. Young, J. M., Bull, C. T., De Boer, S. H., Firrao, G., Gordon, L., Saddler, G. E., Stead, D. E. & Takikawa, Y. (2001). Classification, nomenclature, and plant pathogenic bacteria - a clarification. Phytopathology 91, 617-620.