Genomic Diversity of Erwinia Carotovora Subsp. Carotovora and Its Correlation with Virulence

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2004 May 7

PMID 15128563

Citations 22

Authors

Mee-Ngan Yap

Jeri D Barak

Amy O Charkowski

Affiliations

Soon will be listed here.

Abstract

We used genetic and biochemical methods to examine the genomic diversity of the enterobacterial plant pathogen Erwinia carotovora subsp. carotovora. The results obtained with each method showed that E. carotovora subsp. carotovora strains isolated from one ecological niche, potato plants, are surprisingly diverse compared to related pathogens. A comparison of 23 partial mdh sequences revealed a maximum pairwise difference of 10.49% and an average pairwise difference of 2.13%, values which are much greater than the maximum variation (1.81%) and average variation (0.75%) previously reported for Escherichia coli. Pulsed-field gel electrophoresis analysis of I-CeuI-digested genomic DNA revealed seven rrn operons in all E. carotovora subsp. carotovora strains examined except strain WPP17, which had only six copies. We identified 26 I-CeuI restriction fragment length polymorphism patterns and observed significant polymorphism in fragment sizes ranging from 100 to 450 kb for all strains. We detected large plasmids in two strains, including the model strain E. carotovora subsp. carotovora 71. The two least virulent strains had an unusual chromosomal structure, suggesting that a particular pulsotype is correlated with virulence. To compare chromosomal organization of multiple enterobacterial genomes, several genes were mapped onto I-CeuI fragments. We identified portions of the genome that appear to be conserved across enterobacteria and portions that have undergone genome rearrangements. We found that the least virulent strain, WPP17, failed to oxidize cellobiose and was missing several hrp and hrc genes. The unexpected variability among isolates obtained from clonal hosts in one region and in one season suggests that factors other than the host plant, potato, drive the evolution of this common environmental bacterium and key plant pathogen.

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References

Hauben L, Moore E, Vauterin L, Steenackers M, Mergaert J, Verdonck L . Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol. 1998; 21(3):384-97. DOI: 10.1016/S0723-2020(98)80048-9. View

Reid S, Herbelin C, Bumbaugh A, Selander R, Whittam T . Parallel evolution of virulence in pathogenic Escherichia coli. Nature. 2000; 406(6791):64-7. DOI: 10.1038/35017546. View

Liu S, Schryvers A, Sanderson K, Johnston R . Bacterial phylogenetic clusters revealed by genome structure. J Bacteriol. 1999; 181(21):6747-55. PMC: 94140. DOI: 10.1128/JB.181.21.6747-6755.1999. View

Toth I, Avrova A, Hyman L . Rapid identification and differentiation of the soft rot erwinias by 16S-23S intergenic transcribed spacer-PCR and restriction fragment length polymorphism analyses. Appl Environ Microbiol. 2001; 67(9):4070-6. PMC: 93131. DOI: 10.1128/AEM.67.9.4070-4076.2001. View

Lopez-Solanilla E, Llama-Palacios A, Collmer A, Garcia-Olmedo F, Rodriguez-Palenzuela P . Relative effects on virulence of mutations in the sap, pel, and hrp loci of Erwinia chrysanthemi. Mol Plant Microbe Interact. 2001; 14(3):386-93. DOI: 10.1094/MPMI.2001.14.3.386. View

HELM R, Maloy S . Rapid approach to determine rrn arrangement in Salmonella serovars. Appl Environ Microbiol. 2001; 67(7):3295-8. PMC: 93015. DOI: 10.1128/AEM.67.7.3295-3298.2001. View

Deng W, Burland V, Plunkett 3rd G, Boutin A, Mayhew G, Liss P . Genome sequence of Yersinia pestis KIM. J Bacteriol. 2002; 184(16):4601-11. PMC: 135232. DOI: 10.1128/JB.184.16.4601-4611.2002. View

Sanderson K, Liu S . Chromosomal rearrangements in enteric bacteria. Electrophoresis. 1998; 19(4):569-72. DOI: 10.1002/elps.1150190417. View

Swaminathan B, Barrett T, Hunter S, Tauxe R . PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis. 2001; 7(3):382-9. PMC: 2631779. DOI: 10.3201/eid0703.010303. View

10.

Byun R, Elbourne L, Lan R, REEVES P . Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes. Infect Immun. 1999; 67(3):1116-24. PMC: 96437. DOI: 10.1128/IAI.67.3.1116-1124.1999. View

11.

Collmer A, Schoedel C, Roeder D, Ried J, Rissler J . Molecular cloning in Escherichia coli of Erwinia chrysanthemi genes encoding multiple forms of pectate lyase. J Bacteriol. 1985; 161(3):913-20. PMC: 214984. DOI: 10.1128/jb.161.3.913-920.1985. View

12.

Jock S, Kim W, Barny M, Geider K . Molecular characterization of natural Erwinia pyrifoliae strains deficient in hypersensitive response. Appl Environ Microbiol. 2003; 69(1):679-82. PMC: 152409. DOI: 10.1128/AEM.69.1.679-682.2003. View

13.

Liu S, Sanderson K . I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J Bacteriol. 1995; 177(11):3355-7. PMC: 177035. DOI: 10.1128/jb.177.11.3355-3357.1995. View

14.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

15.

Rantakari A, Virtaharju O, Vahamiko S, Taira S, Palva E, Saarilahti H . Type III secretion contributes to the pathogenesis of the soft-rot pathogen Erwinia carotovora: partial characterization of the hrp gene cluster. Mol Plant Microbe Interact. 2001; 14(8):962-8. DOI: 10.1094/MPMI.2001.14.8.962. View

16.

LINK A, Phillips D, Church G . Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol. 1997; 179(20):6228-37. PMC: 179534. DOI: 10.1128/jb.179.20.6228-6237.1997. View

17.

Ribot E, Fitzgerald C, Kubota K, Swaminathan B, Barrett T . Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni. J Clin Microbiol. 2001; 39(5):1889-94. PMC: 88044. DOI: 10.1128/JCM.39.5.1889-1894.2001. View

18.

Yang C, Gavilanes-Ruiz M, Okinaka Y, Vedel R, Berthuy I, Boccara M . hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol Plant Microbe Interact. 2002; 15(5):472-80. DOI: 10.1094/MPMI.2002.15.5.472. View

19.

Marshall P, Lemieux C . The I-CeuI endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene. Nucleic Acids Res. 1992; 20(23):6401-7. PMC: 334533. DOI: 10.1093/nar/20.23.6401. View

20.

Ginocchio C, Rahn K, Clarke R, Galan J . Naturally occurring deletions in the centisome 63 pathogenicity island of environmental isolates of Salmonella spp. Infect Immun. 1997; 65(4):1267-72. PMC: 175127. DOI: 10.1128/iai.65.4.1267-1272.1997. View