A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization.
Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato.
Stevens
Patricia
P
Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen, 9759 AA Haren, The Netherlands.
van Elsas
Jan Dirk
JD
D015373:Bacterial Typing Techniques; D001459:Bangladesh; D001483:Base Sequence; D016172:DNA Fingerprinting; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D016521:Electrophoresis, Gel, Pulsed-Field; D005618:Fresh Water / Q000382:microbiology; D044404:Genomic Islands; D019015:Geologic Sediments / Q000382:microbiology; D008969:Molecular Sequence Data; D009426:Netherlands; D009693:Nucleic Acid Hybridization; D010935:Plant Diseases / Q000382:microbiology*; D010944:Plants / Q000382:microbiology; D016133:Polymerase Chain Reaction; D043368:Ralstonia solanacearum / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000382:microbiology*; D014774:Virulence; D014871:Water Microbiology
D004251:DNA Transposable Elements; D004269:DNA, Bacterial
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