Genome plasticity among related Lactococcus strains: Identification of genetic events associated with macrorestriction polymorphisms

Journal of Bacteriology

Volumn 182, Issue 9, 2000, Pages 2481-2491

  Le Bourgeois, Pascal ^a   Daveran Mingot, Marie Line ^a   Ritzenthaler, Paul ^a  

^a UPS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; CHROMOSOMAL LOCALIZATION; GENE ISOLATION; GENETIC POLYMORPHISM; LACTOCOCCUS; NONHUMAN; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; STRAIN DIFFERENCE;

BACTERIAL OUTER MEMBRANE PROTEINS; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CARRIER PROTEINS; CHROMOSOMES, BACTERIAL; CONJUGATION, GENETIC; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; F FACTOR; GENOME, BACTERIAL; LACTOCOCCUS LACTIS; LIPOPROTEINS; MEMBRANE TRANSPORT PROTEINS; OLIGOPEPTIDES; OPERON; PLASMIDS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RESTRICTION MAPPING;

LACTOCOCCUS; LACTOCOCCUS LACTIS SUBSP. CREMORIS; POSIBACTERIA; PROKARYOTA;

EID: 0033998798     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.9.2481-2491.2000     Document Type: Article

References (79)

1. Anderson, D. G., and L. L. McKay. 1983. Isolation of a recombinationdeficient mutant at Streptococcus lactis ML3. J. Bacteriol. 155:930-932.
2. Birkenbihl, R. P., and W. Vielmetter. 1989. Cosmid-derived map of E. coli strain BHB2600 in comparison to the map of strain W3110. Nucleic Acids Res. 17:5057-5069.
3. Bolotin, A., S. Mauger, K. Malarme, S. D. Ehrlich, and A. Sorokin. 1999. Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Antonie Leeuwenhoek 76:27-76.
4. Borecka, P., S. Rosypal, R. Pantucek, and J. Doskar. 1996. Localization of prophages of serological group B and F on restriction fragments defined in the restriction map of Staphylococcus aureus NCTC 8325. FEMS Microbiol. Lett. 143:203-210.
5. Canard, B., and S. T. Cole. 1940. Lysogenic phages of Clostridium perfringens: mapping of the chromosomal attachment sites. FEMS Microbiol. Lett. 66:323-326.
6. Canard, B., B. Saint-Joanis, and S. T. Cole. 1992. Genomic diversity and organization of virulence genes in the pathogenic anaerobe Clostridium perfringens. Mol. Microbiol. 6:1421-1429.
7. Carlson, C. R., A. Gronstad, and A. B. Kolsto. 1992. Physical maps of the genomes of three Bacillus cereus strains. J. Bacteriol. 174:3750-3756.
8. Carlson, C. R., T. Johansen, M.-M. Lecadet, and A. B. Kolsto. 1996. Genomic organization of the entomopathogenic bacterium Bacillus thuringiensis subsp. berliner 1715. Microbiology 142:1625-1634.
9. Casjens, S., M. Delange, H. L. Ley III, P. Rosa, and W. M. Huang. 1995. Linear chromosome of Lyme disease agent spirochetes: genetic diversity and conservation of gene order. J. Bacteriol. 177:2769-2780.
10. Cole, S. T., and I. Saint Girons. 1994. Bacterial genomics. FEMS Microbiol. Rev. 14:139-160.
11. Daveran-Mingot, M.-L., N. Campo, P. Ritzenthaler, and P. Le Bourgeois. 1998. A natural large chromosomal inversion in Lactococcus lactis is mediated by homologous recombination between two insertion sequences. J. Bacteriol. 180:4834-4842.
12. Davidson, B. E., N. Kordias, M. Dobos, and A. J. Millier. 1996. Genomic organization of lactic acid bacteria, p. 65-87. In G. Venema, J. H. J. Huis in't Veld, and J. Hugenholtz (ed.). Lactic acid bacteria: genetics, metabolism and applications. Kluwer Academic Publishers, Dordrecht, The Netherlands.
13. Davies, F. L., H. M. Underwood, and M. J. Gasson. 1981. The value of plasmid profile for strain identification in lactic streptococci and the relationship between Streptococcus lactis 712, ML3 and C2. J. Appl. Bacteriol. 51:325-337.
14. Delorme, C., J. J. Godon, S. D. Ehrlich, and P. Renault. 1994. Mosaic structure of large regions of the Lactococcus lactis subsp. cremoris chromosome. Microbiology 140:3053-3060.
15. Dempsey, J. A. F., A. B. Wallace, and J. G. Cannon. 1995. The physical map of the chromosome of a serogroup A strain of Neisseria meningitidis shows complex rearrangements relative to the chromosome of the two mapped strains of the closely related species N. gonorrhoeae. J. Bacteriol. 177:6390-6400.
16. Fonstein, M., and R. Haselkorn. 1995. Physical mapping of bacterial genomes. J. Bacteriol. 177:3361-3369.
17. Gasson, M. J. 1983. Plasmid complements at Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J. Bacteriol. 154:1-9.
18. Gasson, M. J., S. R. Swindell, S. Maeda, and H. M. Dodd. 1992. Molecular rearrangement of lactose plasmid DNA associated with high-frequency transfer and cell aggregation in Laclococcus lactis 712. Mol. Microbiol. 6:3213-3223.
19. Gibbs, C. P., and T. F. Meyer. 1996. Genome plasticity in Neisseria gonorrhueae. FEMS Microbiol. Lett. 145:173-179.
20. Godon, J. J., K. Jury, C. A. Shearman, and M. J. Gasson. 1994. The Lactococcus lactis sex-factor aggregation gene cluA. Mol. Microbiol. 12:655-663.
21. Godon, J. J., C. J. Pillidge, K. Jury, and M. J. Gasson. 1996. Caractérisation d'un élément conjugatif original: le facteur sexuel de Lactococcus lactis 712. Lait 76:41-49.
22. Grothues, D., and B. Tümmler. 1991. New approaches in genome analysis by pulsed-field gel electrophoresis: application to the analysis of Pseudomonas species. Mol. Microbiol. 5:2763-2776.
23. Hackett, N. R., Y. Bobovnikova, and N. Heyrovska. 1994. Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium. J. Bacteriol. 176:7711-7718.
24. Hightower, R. C., D. W. Metge, and D. V. Santi. 1987. Plasmid migration using orthogonal-field-alternation gel electrophoresis. Nucleic Acids Res. 15:8387-8398.
25. Himmelreich, R., H. Plagens, H. Hilbert, B. Reiner, and R. Herrman. 1997. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma ginitalium. Nucleic Acids Res. 25:701-712.
26. Israelsen, H., and E. B. Hansen. 1993. Insertion of transposon Tn917 derivatives into the Lactococcus lactis subsp. lactis chromosome. Appl. Environ. Microbiol. 59:21-26.
27. Johansen, T., C. R. Carlson, and A. B. Kolsto. 1996. Variable numbers of rRNA gene operons in Bacillus cereus strains. FEMS Microbiol. Lett. 136: 325-328.
28. Juillard, V., D. Le Bars, E. R. S. Kunji, W. N. Konings, J. C. Gripon, and J. Richard. 1995. Oligopeptide are the main source of nitrogen for Lactococcus laclis during growth in milk. Appl. Environ. Microbiol. 61:3024-3030.
29. Kaiser, K., and N. E. Murray. 1979. Physical characterisation of the "Rac prophage" in E. coli K12. Mol. Gen. Genet. 175:159-174.
30. Krawiec, S., and M. Riley. 1990. Organization of the bacterial chromosome. Microbiol. Rev. 54:502-539.
31. Kunji, E. R. S., A. Hagting, C. J. de Vries, V. Juillard, A. J. Haandrikman, B. Poolman, and W. N. Konings. 1995. Transport of β-casein-derived peptides by the oligopeptide transport system is a crucial step in the proteolytic pathway of Lactococcus lactis. J. Biol. Chem. 270:1569-1574.
32. Leblond, P., G. Fischer, F. X, Francou, F. Berger, M. Guérineau, and B. Decaris. 1996. The unstable region of Streptomyces ambofaciens includes 210 kb terminal inverted repeats flanking the extremities of the linear chromosome. Mol. Microbiol. 19:261-271.
33. Leblond, P., M. Redenbach, and J. Cullum. 1993. Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2). J. Bacteriol. 175:3422-3429.
34. Le Bourgeois, P., M. Lautier, M. Mata, and P. Ritzenthaler. 1992. Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403. J. Bacteriol. 174:6752-6762.
35. Le Bourgeois, P., M. Lautier, L. van den Berghe, M. J. Gasson, and P. Ritzenthaler. 1995. Physical and genetic map of the Lactucoccus lactis subsp. cremoris MG1363 chromosome: comparison with that of Laclococcus lactis subsp. lactis IL1403 reveals a large genome inversion. J. Bacleriol. 177:2840-2850.
36. Le Bourgeois, P., M. Mata, and P. Ritzenthaler. 1989. Genome comparison of Lactococcus strains by pulsed-field gel electrophoresis. FEMS Microbiol. Lett. 59:65-70.
37. Le Bourgeois, P., M. Mata, and P. Ritzenthaler. 1991. Pulsed-field gel electrophoresis as a tool for studying the phylogeny and genetic history of lactococcal strains, p. 140-145. In G. M. Dunny, P. P. Cleary, and L. L. McKay (ed.), Genetics and molecular biology of streptococci, lactococci and enterococci. ASM Press, Washington, D.C.
38. Lindqvist, B. H., G. Deho, and R. Calendar. 1993. Mechanisms of genome propagation and helper exploitation by satellite phage P4. Microbiol Rev. 57:683-702.
39. Liu, S. L., and K. E. Sanderson. 1995. I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J. Bacteriol. 177:3355-3357.
40. Liu, S. L., and K. E. Sanderson. 1995. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnH. J. Bacteriol. 177:6585-6592.
41. Liu, S. L., and K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93:10303-10308.
42. Lopez-Garcia, P., A. St Jean, R. Amils, and R. L. Charlebois. 1995. Genomic stability in the archaeae Haloferas volcanii and Haloferax mediterranei. J. Bacteriol. 177:1405-1408.
43. Lucey, M., C. Daly, and G. F. Fitzgerald. 1993. Relationship between Laclococcus lactis subsp. lactis 952, an industrial lactococcal starter culture and strains 712, ML3 and C2. J. Appl. Bacteriol. 75:326-335.
44. Marshall, P, and C. Lemieux. 1991. Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast subunit rRNA-encoding gene of Chlamydomonas eugametos. Gene 104:1241-1245.
45. McKay, L. L., and K. A. Baldwin. 1973. Induction of prophage in Streptococcus lactis by ultraviolet irradiation. Appl. Microbiol. 25:682-684.
46. McKay, L. L., K. A. Baldwin, and J. D. Efstathiuu. 1976. Transductional evidence for plasmid linkage of lactose metabolism in Streptococcus lactis C2. Appl. Environ. Microbiol. 32:45-52.
47. Mills, D. A., C. K. Choi, G. M. Dunny, and L. L. McKay. 1994. Genetic analysis of regions of the Lactococcus lactis plasmid pRS01 involved in conjugative transfer. Appl. Environ. Microbiol. 60:4413-4420.
48. Nardi, M., P. Renault, and V. Monnet. 1997. Duplication of the pepF gene and shuffling of DNA fragments on the lactose plasmid of Lactococcus lactis. J. Bacteriol. 179:4164-4171.
49. Nikolskaya, T., M. Fonstein, and R. Haselkorn. 1995. Alignment of a 1.2Mb chromosomal region from three strains of Rhodobacter capsulatus reveals a significantly mosaic structure. Proc. Natl. Acad. Sci. USA 92:10609-10613.
50. Ojaimi, C., B. E. Davidson, I. Saint Girons, and I. G. Old. 1994. Conservation of gene arrangement and an unusual organization of rRNA genes in the linear chromosomes of the lyme disease spirochaetes Borrelia burgdorferi, B. garinii, and B. afzelii. Microbiology 140:2931-2940.
51. Okstad, O. A., I. Hegna, T. Lindback, A. L. Rishovd, and A. B. Kolsto. 1999. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology 145:621-631.
52. Perkins, J. D., J. Don Heath, B. R. Sharma, and G. M. Weinstock. 1993 XbaI and Bln1 genomic cleavage maps of Escherichia coli K-12 strain MG1655 and comparative analysis of other strains. J. Mol. Biol. 232:419-445.
53. Philipp, W. J., S. Nair, G. Guglielmi, M. Lagranderie, B. Gicquel, and S. T. Cole. 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.
54. Philipp, W. J., S. Poulet, K. Eiglmeier, L. Pascopella, V. Balasubramanian, B. Heym, S. Bergh, B. R. Bloom, W. R. Jacobs, and S. T. Cole. 1996. An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. Proc. Natl. Acad. Sci. USA 93:3132-3137.
55. Polzin, K. M., and M. Shimizu-Kadota. 1987. Identification of a new insertion element, similar to gram-negative IS26, on the lactose plasmid of Streptococcus lactis ML3. J. Bacteriol. 169:5481-5488.
56. Powell, I. B., M. G. Achen, A. J. Hillier, and B. E. Davidson. 1988. A simple and rapid method for genetic transformation of lactic streptococci by electroporation. Appl. Environ. Microbiol. 54:655-660.
57. Rauch, P. J. G., and W. M. de Vos. 1992. Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis. J. Bacteriol. 174:1280-1287.
58. Redenbach, M., F. Flett, W. Piendl, I. Glocker, U. Rauland, O. Wafzig, R. Kliem, P. Leblond, and J. Cullum. 1993. The Streptomyces lividans 66 chromosome contains a 1 MB deletogenic region flanked by two amplifiable regions. Mol. Gen. Genet. 241:255-262.
59. Römling, U., J. Greipel, and B. Tümmler. 1995. Gradient of genomic diversity in the Pseudomonas aeruginosa chromosome. Mol. Microbiol. 17:323-332.
60. Römling, U., K. D. Schmidt, and B. Tümmler. 1997. Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats. J. Mol. Biol. 271:386-404.
61. Roussel, Y., F. Bourgoin, G. Guedon, M. Pebay, and B. Decaris. 1997. Analysis of the genetic polymorphism between three Streptococcus thermophilus strains by comparing their physical and genetic organization. Microbiology 143:1335-1343.
62. Roussel, Y., M. Pebay, G. Guedon, J. M. Simonet, and B. Decaris. 1994. Physical and genetic map of Streptococcus thermophilus A054. J. Bacteriol. 176:7413-7422.
63. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
64. Simske, J. S., and S. Scherer. 1989. Pulsed-field gel electrophoresis of circular DNA. Nucleic Acids Res. 17:4359-4365.
65. Smeltzer, M. S., M. E. Hart, and J. J. Iandolo. 1994. The effect of lysogeny on the genomic organization of Staphylococcus aureus. Gene 138:51-57.
66. Sneath, P. H. A., and R. R. Sokal. 1973. Numerical taxonomy: the principles and practice of numerical classification. W. H. Freeman & Co., San Francisco, Calif.
67. Tabata, K., and T. Hoshino. 1996. Mapping of 61 genes on the refined physical map of the chromosome of Thermus thermophilus HB27 and comparison of genome organization with that of T. thermophilus HB8. Microbiology 142:401-410.
68. Tanskanen, E. I., D. L. Tulloch, A. J. Hillier, and B. E. Davidson. 1990. Pulsed-field gel electrophoresis of Sma1 digest of lactococcal genomic DNA, a novel method of strain identification. Appl. Environ. Microbiol. 56:3105-3111.
69. Terzaghi, B. E., and W. E. Sandine. 1975. Improved medium for lactic streptococci and their bacteriophages. Appl. Microbiol. 29:807-81.1
70. Tigges, E., and F. C. Minion. 1944. Physical map of Mycoplasma gallisepticum. J. Bacteriol. 176:4157-4159.
71. Toda, T., and M. Itaya. 1995. I-Ceul recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmark for genome analysis. Microbiology 141:1937-1945.
72. Trautwetter, A., P. Ritzenthaler, T. Alatossava, and M. Mata-Gilsinger. 1986. Physical and genetic characterization of the genome of Lactobacillus laclis bacteriophage LL-H. J. Virol. 59:551-555.
73. Tulloch, D. L., L. R. Finch, A. J. Hillier, and B. E. Davidson. 1991. Physical map of the chromosome of Lactococcus lactis suhsp. laclis DL11 and localization of six putative rRNA operons. J. Bacteriol. 173:2768-2775.
74. Tynkkynen, S., G. Buist, E. R. S. Kunji, J. Kok, B. Poolman, G. Venema, and A. J. Haandrikman. 1993. Genetic and biochemical characterization of the oligopeptide transport system of Lactococcus lactis. J. Bacteriol. 175:7523-7532.
75. Walsh, P. M., and L. L. McKay. 1981. Recombinant plasmid associated with cell aggregation and high-frequency conjugation in Streptococcus lactis ML3. J. Bacteriol. 146:937-944.
76. Ward, A. C., A. J. Hillier, B. E. Davidson, and I. B. Powell. 1993. Stability analysis of the Lactococcus lactis DCR1 lactose plasmid using pulsed-field gel electrophoresis. Plasmid 29:70-73.
77. Waterbury, P. G., and M. J. Lane. 1987. Generation of lambda concatemers for use as pulsed-field electrophoresis size markers. Nucleic Acids Res. 15:3930.
78. Yu, W., K. Gillies, J. K. Kondo, J. R. Broadbent, and L. L. McKay. 1996. Loss of plasmid-mediated oligopeptide transport system in lactococci: another reason for slow milk coagulation. Plasmid 35:145-155.
79. Zuerner, R. L., J. L. Herrmann, and I. Saint Girons. 1993. Comparison of genetic maps for two Leptospira interrogans serovars provides evidence for two chromosomes and intraspecies heterogeneity. J. Bacteriol. 175:5445-5451.