User menu

Accès à distance ? S'identifier sur le proxy UCLouvain

Complete sequence and comparative genome analysis of the dairybacterium Streptococcus thermophilus

Primary tabs

Bolotin, Alexander [INRA] Quinquis, Benoît [INRA] Renault, Pierre [INRA] Sorokin, Alexei [INRA] Ehrlich, S. Dusko [INRA] Purnelle, Bénedicte [UCL] Prozzi, Deborah [UCL] Ngui, K. [UCL] Masuy, D. [UCL] Hancy, F. [UCL] Burteau, Sophie [UCL] Boutry, Marc [UCL] Delcour, Jean [UCL] Goffeau, André [UCL] Hols, Pascal [UCL]

The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.

Document type Article de périodique (Journal article) – Article de recherche
Publication date 2004
Language Anglais
Journal information "Nature Biotechnology" - Vol. 22, no.12, p. 1554-1158 (2004)
Peer reviewed yes
issn 1087-0156
e-issn 1546-1696
Publication status Publié
Affiliations UCL - SST/ISV - Institut des sciences de la vie
UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology
Links
  1. Fox, P.F. Cheese: Chemistry, Physics and Microbiology (Chapman & Hall, London, 1993).
  2. Tamine A.Y., J. Food Protection, 43, 939 (1980)
  3. Chausson, F. & Maurisson, E. L'économie Laitière en chiffres (Centre National Interprofessionnel de l'Economie Laitière, Paris, France, 2002).
  4. Mitchell Timothy J., The pathogenesis of streptococcal infections: from Tooth decay to meningitis, 10.1038/nrmicro771
  5. Tettelin H., Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae, 10.1126/science.1061217
  6. Ferretti J. J., McShan W. M., Ajdic D., Savic D. J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H. S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S. W., Roe B. A., McLaughlin R., Complete genome sequence of an M1 strain of Streptococcus pyogenes, 10.1073/pnas.071559398
  7. Tettelin H., Masignani V., Cieslewicz M. J., Eisen J. A., Peterson S., Wessels M. R., Paulsen I. T., Nelson K. E., Margarit I., Read T. D., Madoff L. C., Wolf A. M., Beanan M. J., Brinkac L. M., Daugherty S. C., DeBoy R. T., Durkin A. S., Kolonay J. F., Madupu R., Lewis M. R., Radune D., Fedorova N. B., Scanlan D., Khouri H., Mulligan S., Carty H. A., Cline R. T., Van Aken S. E., Gill J., Scarselli M., Mora M., Iacobini E. T., Brettoni C., Galli G., Mariani M., Vegni F., Maione D., Rinaudo D., Rappuoli R., Telford J. L., Kasper D. L., Grandi G., Fraser C. M., Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, 10.1073/pnas.182380799
  8. Glaser Philippe, Rusniok Christophe, Buchrieser Carmen, Chevalier Fabien, Frangeul Lionel, Msadek Tarek, Zouine Mohamed, Couvé Elisabeth, Lalioui Lila, Poyart Claire, Trieu-Cuot Patrick, Kunst Frank, Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease : Genome sequence of Streptococcus agalactiae, 10.1046/j.1365-2958.2002.03126.x
  9. Ajdic D., McShan W. M., McLaughlin R. E., Savic G., Chang J., Carson M. B., Primeaux C., Tian R., Kenton S., Jia H., Lin S., Qian Y., Li S., Zhu H., Najar F., Lai H., White J., Roe B. A., Ferretti J. J., Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen, 10.1073/pnas.172501299
  10. Ochman H., Elwyn S., Moran N. A., Calibrating bacterial evolution, 10.1073/pnas.96.22.12638
  11. Jansen Ruud., Embden Jan. D. A. van, Gaastra Wim., Schouls Leo. M., Identification of genes that are associated with DNA repeats in prokaryotes, 10.1046/j.1365-2958.2002.02839.x
  12. Stackebrandt Erko, Teuber Michael, Molecular taxonomy and phylogenetic position of lactic acid bacteria, 10.1016/0300-9084(88)90204-0
  13. Zhang Jing-Ren, Idanpaan-Heikkila Ilona, Fischer Werner, Tuomanen Elaine I., Pneumococcal licD2 gene is involved in phosphorylcholine metabolism, 10.1046/j.1365-2958.1999.01291.x
  14. Comfort D., Clubb R. T., A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria, 10.1128/iai.72.5.2710-2722.2004
  15. Paterson Gavin K., Mitchell Timothy J., The biology of Gram-positive sortase enzymes, 10.1016/j.tim.2003.12.007
  16. Broadbent J.R., J. Dairy Sci., 86, 407 (2003)
  17. Dobrindt U, Whole genome plasticity in pathogenic bacteria, 10.1016/s1369-5274(00)00250-2
  18. Eisen Jonathan A, Heidelberg John F, White Owen, Salzberg Steven L, 10.1186/gb-2000-1-6-research0011
  19. Hickson Ian D., RecQ helicases: caretakers of the genome, 10.1038/nrc1012
  20. Bolotin A., Wincker P., Mauger S., Jaillon O., Malarme K., Weissenbach J., Ehrlich S. D., Sorokin A., The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403, 10.1101/gr.gr-1697r
  21. Bidnenko Vladimir, Seigneur Marie, Penel-Colin Marion, Bouton Marie-Florence, Dusko Ehrlich S., Michel Benedicte, sbcB sbcC null mutations allow RecF-mediated repair of arrested replication forks in rep recBC mutants, 10.1046/j.1365-2958.1999.01532.x
  22. Wren Brendan W., Microbial genome analysis: insights into virulence, host adaptation and evolution, 10.1038/35049551
  23. Cole S. T., Eiglmeier K., Parkhill J., James K. D., Thomson N. R., Wheeler P. R., Honoré N., Garnier T., Churcher C., Harris D., Mungall K., Basham D., Brown D., Chillingworth T., Connor R., Davies R. M., Devlin K., Duthoy S., Feltwell T., Fraser A., Hamlin N., Holroyd S., Hornsby T., Jagels K., Lacroix C., Maclean J., Moule S., Murphy L., Oliver K., Quail M. A., Rajandream M.-A., Rutherford K. M., Rutter S., Seeger K., Simon S., Simmonds M., Skelton J., Squares R., Squares S., Stevens K., Taylor K., Whitehead S., Woodward J. R., Barrell B. G., Massive gene decay in the leprosy bacillus, 10.1038/35059006
  24. Badger J. H., Olsen G. J., CRITICA: coding region identification tool invoking comparative analysis, 10.1093/oxfordjournals.molbev.a026133
  25. Delcher A., Improved microbial gene identification with GLIMMER, 10.1093/nar/27.23.4636
  26. Overbeek R., WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction, 10.1093/nar/28.1.123
  27. Delcher A. L., Kasif S., Fleischmann R. D., Peterson J., White O., Salzberg S. L., Alignment of whole genomes, 10.1093/nar/27.11.2369
  28. Hirsh Aaron E., Fraser Hunter B., Protein dispensability and rate of evolution, 10.1038/35082561
  29. Overbeek R., Fonstein M., D'Souza M., Pusch G. D., Maltsev N., The use of gene clusters to infer functional coupling, 10.1073/pnas.96.6.2896
  30. Huynen M. A., Bork P., Measuring genome evolution, 10.1073/pnas.95.11.5849
Bibliographic reference Bolotin, Alexander ; Quinquis, Benoît ; Renault, Pierre ; Sorokin, Alexei ; Ehrlich, S. Dusko ; et. al. Complete sequence and comparative genome analysis of the dairybacterium Streptococcus thermophilus. In: Nature Biotechnology, Vol. 22, no.12, p. 1554-1158 (2004)
Permanent URL http://hdl.handle.net/2078.1/118423