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Volume 146, Issue 12

The genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1 Free

Abstract

The physical and genetic maps of the strains GM and PSU-1, which represent two genomic divergent groups on the basis of macrorestriction and ribotyping analysis, were compared. To achieve this comparison, the GM maps were constructed and the PSU-1 maps, already established, were improved. All the recognition sites of the restriction enzymes I, I-I, I, I and I were located in both chromosomes and the position of 26 genetic markers, including two operons and 14 new putative oenococcal genes, were allocated to the restriction fragments generated by the five enzymes. The comparative analysis of GM and PSU-1 genomes revealed extensive conservation of loci order. As for the differences encountered in the locations of restriction sites, they seem to be a reflection of the differences in restriction fragment sizes, explainable by insertion/deletion events and point mutations. No evidence for major genomic rearrangements was found. The genomic conservation between the two strains is in agreement and suggests homogeneity within the species, which was not unexpected in view of the restricted ecological niche of . Further comparisons of physical maps, both of strains and related species, will certainly help to assess whether is really an homogeneous species and physical mapping is suitable for taxonomic purposes, both at the supra- and intraspecific levels.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): comparative genome analysis , genomic maps and Oenococcus oeni
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2000-12-01
2024-04-19
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References

  1. Altschul S. F., Madden T. L., Schaffer A. A., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
     [Google Scholar]
  2. Brito L. 1996 Molecular analysis in Leuconsotoc oenos PhD thesis Technical University of Lisbon;
     [Google Scholar]
  3. Cole S. T., Saint Girons I. 1994; Bacterial genomics. . FEMS Microbiol Rev 14:139–160 [CrossRef]
     [Google Scholar]
  4. Dicks L. M. T., Vuuren H. J. J., Dellaglio F. 1990; Taxonomy of Leuconostoc species, particularly Leuconostoc oenos, as revealed by numerical analysis of total soluble cell protein patterns, DNA base compositions and DNA-DNA hybridizations. Int J Syst Bacteriol 40:83–91 [CrossRef]
     [Google Scholar]
  5. Dicks L. M. T., Dellaglio F., Collins M. D. 1995; Proposal to reclassify Leuconostoc oenos as Oenococcus oeni [corrig.] gen. nov., comb. nov. Int J Syst Bacteriol 45:395–397 [CrossRef]
     [Google Scholar]
  6. Duwat P., Ehrlich S. D., Gruss A. 1992; A general method for cloning recA genes of gram-positive bacteria by polymerase chain reaction. J Bacteriol 174:5171–5175
     [Google Scholar]
  7. Duwat P., Cochu A., Erlich S. D., Gruss A. 1997; Characterization of Lactococcus lactis UV-sensitive mutants obtained by ISS1 transposition. J Bacteriol 17:4473–4479
     [Google Scholar]
  8. Garmyn D., Monnet C., Martineau B., Guzzo J., Cavin J.-F., Diviès C. 1996; Cloning and sequencing of the gene encoding α-acetolactate decarboxylase from Leuconostoc oenos. FEMS Microbiol Lett 145:445–450
     [Google Scholar]
  9. Garvie E. 1986; Genus Leuconostoc. In Bergey’s Manual of Systematic Bacteriology pp. 1071–1075Edited by Sneath P. H. A. , Mair N. S., Sharpe M. E., Holt J. G. Baltimore, MD: Williams & Wilkins;
     [Google Scholar]
  10. Heath J. D., Perkins J. D., Sharma B., Weinstock G. M. 1992; NotI cleavage map of Escherichia coli K12 strain MG1655. J Bacteriol 174:5171–5175
     [Google Scholar]
  11. Johansen E., Kibenich A. 1992; Isolation and characterization of IS1165, an insertion sequence of Leuconostoc mesenteroides subsp. cremoris and other lactic acid bacteria. . Plasmid 27:200–206 [CrossRef]
     [Google Scholar]
  12. Karlyshev A. V., Henderson J., Ketley J. M., Wren B. W. 1998; An improved physical and genetic map of Campylobacter jejuni NCTC 11168 (UA580). . Microbiology 144:503–508 [CrossRef]
     [Google Scholar]
  13. Labarre C., Diviès C., Guzzo J. 1996; Genetic organization of the mle locus and identification of mleR-like gene from Leuconostoc oenos. Appl Environ Microbiol 62:4493–4498
     [Google Scholar]
  14. Ladefoged S. A., Christiansen G. 1992; Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis. J Bacteriol 174:2199–2207
     [Google Scholar]
  15. Liu S.-L., Hessel A., Sanderson K. E. 1993; Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli and other bacteria. Proc Natl Acad Sci USA 90:6874–6878 [CrossRef]
     [Google Scholar]
  16. Liu S.-L., Schryvers A. B., Sanderson K. E., Johnston R. N. 1999; Bacterial phylogenetic clusters revealed by genome structure. J Bacteriol 181:6747–6755
     [Google Scholar]
  17. Marshall P., Lemieux C. 1992; 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 20:6401–6407 [CrossRef]
     [Google Scholar]
  18. Martı́nez-Murcia A. J., Harland N. M., Collins M. D. 1993; Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: assessment of congruence of small- and large-subunit rRNA derived trees. J Appl Bacteriol 74:532–541
     [Google Scholar]
  19. Morse R., Collins M. D., O’Hanlon K., Wallbanks S., Richarson P. T. 1996; Analysis of the β′ subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium. Int J Syst Bacteriol 46:1004–1009 [CrossRef]
     [Google Scholar]
  20. Peynaud E., Domercq S. 1968; Etude de quatre cents souches de conques heterolactiques isolés de vins. Ann Inst Pasteur 19:159–169
     [Google Scholar]
  21. Philipp W. J., Nair S., Guglielmi G., Lagranderie M., Gicquel B., Cole S. T. 1996; Physical mapping of Mycobacterium bovis BCG Pasteur reveals differences from the genome map of Mycobacterium tuberculosis H37Rv and from M. bovis. Microbiology 142:3135–3145 [CrossRef]
     [Google Scholar]
  22. St. Jean A., Charlebois R. L. 1996; Comparative genomic analysis of the Haloferax volcani DS2 and Halobacterium salinarium GRB contig maps reveals extensive rearrangement. J Bacteriol 178:3860–3868
     [Google Scholar]
  23. Sá-Nogueira I., Nogueira T. V., Soares S., de Lencastre H. 1997; The Bacillus subtilis l-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. Microbiology 143:957–969 [CrossRef]
     [Google Scholar]
  24. Sesma F., Gardiol D., Holgado A. P. R., de Mendoza D. 1990; Cloning of the citrate permease gene of Lactococcus lactis subsp. lactis biovar diacetylactis and expression in Escherichia coli. Appl Environ Microbiol 56:2099–2103
     [Google Scholar]
  25. Tenreiro R., Santos R., Brito L., Paveia H., Vieira G., Santos M. A. 1993; Bacteriophages induced by mitomycin C treatment of Leuconostoc oenos strains from Portuguese wines. Lett Appl Microbiol 16:207–209 [CrossRef]
     [Google Scholar]
  26. Tenreiro R., Santos M. A., Paveia H., Vieira G. 1994; Inter-strain relationships among wine leuconostocs and their divergence from other Leuconostoc species, as revealed by low frequency restriction fragment analysis of genomic DNA. J Appl Bacteriol 77:271–280 [CrossRef]
     [Google Scholar]
  27. Yamamoto S., Harayama S. 1995; PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109
     [Google Scholar]
  28. Zavaleta A. I., Martı́nez-Murcia A. J., Rodrı́guez-Valera F. 1996; 16S–23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. . Microbiology 142:2105–2114 [CrossRef]
     [Google Scholar]
  29. Zavaleta A. I., Martı́nez-Murcia A. J., Rodrı́guez-Valera F. 1997; Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analysis. Appl Environ Microbiol 63:1261–1267
     [Google Scholar]
  30. Zé-Zé L., Tenreiro R., Brito L., Santos M. A., Paveia H. 1998; Physical map of the genome of Oenococcus oeni PSU-1 and localization of genetic markers. Microbiology 144:1145–1156 [CrossRef]
     [Google Scholar]
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The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a ‘divergent’ strain, PSU-1
Microbiology 146, 3195 (2000); https://doi.org/10.1099/00221287-146-12-3195
/content/journal/micro/10.1099/00221287-146-12-3195
/content/journal/micro/10.1099/00221287-146-12-3195
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