The complete genome sequence of the lactic acid bacterium lactococcus lactis ssp. lactis IL1403

Genome Research

Volumn 11, Issue 5, 2001, Pages 731-753

  Bolotin, Alexander ^a   Wincker, Patrick ^b   Mauger, Stéphane ^a   Jaillon, Olivier ^b   Malarme, Karine ^a   Weissenbach, Jean ^b   Ehrlich, S Dusko ^a   Sorokin, Alexei ^a  

^a CEMAGREF   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC METABOLISM; AT RICH SEQUENCE; BACTERIAL GENE; BACTERIUM COMPETENCE; BASE PAIRING; CHEESE; CHROMOSOME; CONTROLLED STUDY; ENTEROBACTERIACEAE; ESCHERICHIA; FERMENTATION; GENE INSERTION SEQUENCE; GENE SEQUENCE; GENE TRANSFER; GENETIC RECOMBINATION; GENETIC TRANSFORMATION; GENOME; GRAM NEGATIVE BACTERIUM; LABORATORY; LACTIC ACID BACTERIUM; LACTOCOCCUS LACTIS; LETTER; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROPHAGE; SALMONELLA; STREPTOCOCCUS;

AMINO ACIDS; BACTERIAL PROTEINS; BACTERIOPHAGES; BIOLOGICAL TRANSPORT, ACTIVE; CELL WALL; DNA TRANSPOSABLE ELEMENTS; ENDOPEPTIDASES; ENERGY METABOLISM; ENTEROBACTERIACEAE; GENE EXPRESSION REGULATION; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; LACTIC ACID; LACTOCOCCUS LACTIS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOTIDES; OPEN READING FRAMES; PROVIRUSES; RNA, BACTERIAL; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; TRANSFORMATION, GENETIC; VITAMINS;

BACTERIA (MICROORGANISMS); ENTERIC BACTERIA; ENTEROBACTERIACEAE; ESCHERICHIA; LACTOCOCCUS LACTIS; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA; SALMONELLA; STREPTOCOCCUS;

EID: 0035021812     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.GR-1697R     Document Type: Letter

References (52)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Bolhuis, A., Broekhuizen, C.P., Sorokin, A., van Roosmalen, M.L., Venema, G., Bron, S., Quax, W.J., and van Dijl, J.M. 1998. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. J. Biol. Chem. 273: 21217-21224.
3. Bolotin, A., Mauger, S., Malarme, K., Ehrlich, S.D., and Sorokin, A. 1999. Low-redundancy sequencing of the entire Lactococcus lactis IL1403 genome. Antonie Leeuwenhoek 76: 27-76.
4. Borodovsky, M. and McIninch, J. 1993. GENMARK: A parallel gene recognition for both DNA strands. Comput. Chem. 17: 123-133.
5. Buist, G., Karsens, H., Nauta, A., van Sinderen, D., Venema, G., and Kok, J. 1997. Autolysis of Lactococcus lactis caused by induced overproduction of its major autolysin, AcmA. Appl. Environ. Microbiol. 63: 2722-2728.
6. Chiaruttini, C. and Milet, M. 1993. Gene organization, primary structure and RNA processing analysis of a ribosomal RNA operon in Lactococcus lacris. J. Mol. Biol. 230: 57-76.
7. Chopin, A., Chopin, M.C., Moillo-Batt, A., and Langella, P. 1984. Two plasmid-determined restriction and modification systems in Streptococcus lactis. Plasmid 11: 260-263.
8. Chopin, A., Bolotin, A., Sorokin, A., Ehrlich, S.D., and Chopin, M.C. 2001. Analysis of six prophages in Lactococcus lactis IL1403: Different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 29: 644-651.
9. Christensen, J., Dudley, E., Pederson, J., and Steele, J. 1999. Peptidases and amino acid catabolism in lactic acid bacteria. Antonie Leeuwenhoek 76: 217-246.
10. Cocaign-Bousquet, M., Garrigues, C., Loubiere, P., and Lindley, N.D. 1996. Physiology of pyruvate metabolism in Lactococcus lactis. Antonie Leeuwenhoek 70: 253-267.
11. Cousineau, B., Smith, D., Lawrence-Cavanagh, S., Mueller, J.E., Yang, J., Mills, D., Manias, D., Dunny, G., Lambowitz, A.M., and Belfort, M. 1998. Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94: 451-462.
12. Dear, S. and Staden, R. 1991. A sequence assembly and editing program for efficient management of large projects. Nucl. Acids Res. 19: 3907-3911.
13. Dickely, F., Nilsson, D., Hansen, E.B., and Johansen, E. 1995. Isolation of Lactococcus lactis nonsense suppressors and construction of a food-grade cloning vector. Mol. Microbiol. 15: 839-847.
14. Dsouza, M., Larsen, N., and Overbeek, R. 1997. Searching for patterns in genomic data. Trends Genet. 13: 497-498.
15. Duwat, P., Cochu, A., Ehrlich, S.D., and Gruss, A. 1997. Characterization of Lactococcus lactis UV-sensitive mutants obtained by ISS1 transposition. J. Bacteriol. 179: 4473-4479.
16. Fernandez, S., Sorokin, A., and Alonso, J.C. 1998. Genetic recombination in Bacillus subtilis 168: Effects of recU and recS mutations on DNA repair and homologous recombination. J. Bacteriol. 180: 3405-3409.
17. Fox, P.F. 1989. Cheese: An overview. In Cheese: Chemistry, Physics and Microbiology (ed. P.F. Fox) pp. 1-36. Chapman & Hall, London.
18. Fraser, C.M. and Fleischmann, R.D. 1997. Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18: 1207-1216.
19. Gasson, MJ. 1983. Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J. Bacteriol. 154: 1-9.
20. Godon, J.J., Delorme, C., Bardowski, J., Chopin, M.C., Ehrlich, S.D., and Renault, P. 1993. Gene inactivation in Lactococcus lactis: Branched-chain amino acid biosynthesis. J. Bacteriol. 175: 4383-4390.
21. Griffin, H.G., Swindell, S.R., and Gasson, M.J. 1992. Cloning and sequence analysis of the gene encoding L-lactate dehydrogenase from Lactococcus lactis: Evolutionary relationships between 21 different LDH enzymes. Gene 122: 193-197.
22. Jensen, P.R. and Hammer, K. 1993. Minimal requirements for exponential growth of Lactococcus lactis. Appl. Environ. Microbiol. 59: 4363-4366.
23. +, a gene required for chromosomal but not plasmid DNA transformation. J. Bacteriol. 177: 3235-3240.
24. Kravchenko, V.V., Gileva, I.P., Dobrynin, V.N., Filipov, S.A., and Korobko, V.G. 1988. Location of the initiation codon AUG in relation to the 5′-end of mRNA mediates the effectiveness of translation in E. coli cells. Bioorg. Khim. 14: 1387-1392.
25. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
26. Le Bourgeois, P., Lautier, M., Mata, M., and Ritzenthaler, P. 1992. Physical and genetic map of the chromosome of Lactococcus lactis subsp. lactis IL1403. J. Bacteriol. 174: 6752-6762.
27. Le Bourgeois, P., Lautier, M., van den Berghe, L., Gasson, M., and Ritzenthaler, P. 1995. Physical and genetic map of the chromosome of Lactococcus lactis subsp. cremoris MG1363 chromosome: Comparison with that of Lactococcus lactis subsp. lactis IL1403 reveals a large genome inversion. J. Bacteriol. 177: 2840-2850.
28. Lee, M.S. and Morrison, D.A. 1999. Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J. Bacteriol. 181: 5004-5016.
29. Le Loir, Y., Gruss, A., Ehrlich, S.D., and Langella, P. 1998. A nine-residue synthetic propeptide enhances secretion efficiency of heterologous proteins in Lactococcus lactis. J. Bacteriol. 180: 1895-1903.
30. Lopez de Felipe, F.L., Kleerebezem, M., de Vos, W.M., and Hugenholtz, J. 1998. Cofactor engineering: A novel approach to metabolic engineering in Lactococcus lactis by controlled expression of NADH oxidase. J. Bacteriol. 180: 3804-3808.
31. Mickelson, M.N. 1972. Glucose degradation, molar growth yields, and evidence for oxidative phosphorylation in Streptococcus agalactiae. J. Bacteriol. 109: 96-105.
32. Ochman, H., Elwyn, S., and Moran, N.A. 1999. Calibrating bacterial evolution. Proc. Natl. Acad. Sci. 96: 12638-12643.
33. Pestova, E.V. and Morrison, D.A. 1998. Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector. J. Bacteriol. 180: 2701-2710.
34. Pogliano, J.A. and Beckwith, J. 1994. SecD and SecF facilitate protein export in Escherichia coli. EMBO J. 13: 554-561.
35. Poolman, B. 1993. Energy transduction in lactic acid bacteria. FEMS Microbiol. Rev. 12: 125-147.
36. Pouquet, I., Saint, V., Seznec, E., Simoes, N., Bolotin, A., and Gruss, A. 2000. HtrA in the unique surface housekeeping protease in Lactococcus lactis and is required for natural protein processing. mol. Microbiol. 35: 1042-1051.
37. Quentin, Y., Fichant, G., and Denizot, F. 1999. Inventory, assembly and analysis of Bacillus subtilus ABC transport systems. J. mol. Biol. 287: 467-484.
38. Rollan, G., de Nadra, M.C.M., Holgado, P.R., and Oliver, G. 1985. Aspartate metabolism in Lactobacillus murinus CNRS 313. I. Aspartase. J. Gen. Appl. Microbiol. 31: 403-409.
39. Sanders, J.W., Leenhouts, K.J., Haandrikman, A.J., Venema, G., and Kok, J. 1995. Stress response in Lactococcus lactis: Cloning, expression analysis, and mutation of the lactococcal Superoxide dismutase gene. J. Bacteriol. 177: 5254-5260.
40. Sanders, J.W., Leenhouts, K., Burghoorn, J., Brands, J.R., Venema, G., and Kok J. 1998. A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation. mol. Microbiol. 27:299-310.
41. Schleifer, K.H., Kraus, J., Dvorak, C, Kilpper-Bälz, R., Collins, M.D., and Fischer, W. 1985. Transfer of Streptococcus lactis and related streptococci to the genus Lactococcus gen. nov. Syst. Appl. Microbiol. 6: 183-195.
42. Sijpesteijn, A.K. 1970. Induction of cytochrome formation and stimulation of oxidative dissimilation by hemin in Streptococcus lactis and Leuconostoc mesenteroides. Antonie Leeuwenhoek 36: 335-348.
43. Sorokin, A., Lapidus, A., Capuano, V., Galleron, N., Pujic, P., and Ehrlich, S.D. 1996. A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing. Genome Res. 6: 448-453.
44. Steidler, L., Hans, W., Schotte, L., Neirynck, S., Obermeier, F., Falk, W., Fiers, W., and Remaut, E. 2000. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289: 1352-1355.
45. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.
46. Tedin, K., Moll, I., Grill, S., Resch, A., Graschopf, A., Gualerzi, C.O., and Blasi, U. 1999. Translation initiation factor 3 antagonizes authentic start codon selection on leaderless mRNAs. Mol. Microbiol. 31: 67-77.
47. Ten Brink, B., Otto, R., Hansen, U.P., and Konings, W.L. 1985. Energy recycling by lactate flux in growing and non-growing cells of Streptococcus cremoris. J. Bacteriol. 162: 383-390.
48. Tettelin, H., Saunders, N.J., Heidelberg, J., Jeffries, A.C., Nelson, K.E., Eisen, J.A., Ketchum, K.A., Hood, D.W., Peden, J.F., Dodson, R.J., et al. 2000. Complete genome sequence of Naisseria meningitidis serogroup B strain MC58. Science 287: 1809-1815.
49. Valyasevi, R., Sandine, W.E., and Geller, B.L. 1990. The bacteriophage kh receptor of Lactococais lactis subsp. cremoris KH is the rhamnose of the extracellular wall polysaccharide. Appl. Environ. Microbiol. 56: 1882-1889.
50. Van Etten, W.J. and Janssen, G.R. 1998. An AUG initiation codon, not codon-anticodon complementarity, is required for the translation of unleadered mRNA in Escherichia coli. Mol. Microbiol. 27: 987-1001.
51. Van Kranenburg, R., Marugg, J.D., van Swam, I.I., Willem, N.J., and de Vos, W.M. 1997. Molecular characterization of the plasmid-encoded eps gene cluster essential for exopolysaccharide biosynthesis in Lactococcus lactis. Mol. Microbiol. 24: 387-397.
52. Yvon, M., Chambellon, E., Bolotin, A., and Roudot-Algaron, F. 2000. Characterisation and role of the branched-chain aminotransferase (BcaT) isolated from Lactococcus lactis subsp. cremoris NCDO763 Appl. Environ. Microbiol. 66: 571-577.