Novel conjugative plasmids from the natural isolate Lactococcus lactis subspecies cremoris DPC3758: A repository of genes for the potential improvement of dairy starters

Journal of Dairy Science

Volumn 95, Issue 7, 2012, Pages 3593-3608

  Fallico, V ^a,b   Ross, R P ^a,c   Fitzgerald, G F ^b,c   McAuliffe, O ^a  

^a TEAGASC FOOD RESEARCH CENTRE   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Conjugative plasmid; Food grade selectable marker; Lactococcus lactis; Phage resistance

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BACTERIAL GENE; CATTLE; CHEESE; CHROMOSOME MAP; DNA SEQUENCE; FOOD CONTROL; GENETICS; LACTOCOCCUS LACTIS; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PLASMID; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; CHEESE; CHROMOSOME MAPPING; FOOD MICROBIOLOGY; GENES, BACTERIAL; LACTOCOCCUS LACTIS; MOLECULAR SEQUENCE DATA; PLASMIDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84862559540     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2011-5255     Document Type: Article

References (56)

1. Altschul S., Madden T., Schaffer A., Zhang J.H., Zhang Z., Miller W., Lipman D. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. FASEB J 1998, 12:A1326.
2. Ballesteros C., Poveda J.M., González-Viñas M.A., Cabezas L. Microbiological, biochemical and sensory characteristics of artisanal and industrial Manchego cheeses. Food Contr 2006, 17:249-255.
3. Chopin A., Chopin M.-C., Moillo-Batt A., Langella P. Two plasmid-determined restriction and modification systems in Streptococcus lactis. Plasmid 1984, 11:260-263.
4. Coffey A., Ross R.P. Bacteriophage-resistance systems in dairy starter strains: Molecular analysis to application. Antonie van Leeuwenhoek 2002, 82:303-321.
5. Cogan T.M., Barbosa M., Beuvier E., Bianchi-Salvadori B., Cocconcelli P.S., Fernandes I., Gomez J., Gomez R., Kalantzopoulos G., Ledda A., Medina M., Rea M.C., Rodriquez E. Characterization of the lactic acid bacteria in artisanal dairy products. J. Dairy Res. 1997, 64:409-421.
6. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641.
7. Delgado S., Mayo B. Phenotypic and genetic diversity of Lactococcus lactis and Enterococcus spp. strains isolated from Northern Spain starter-free farmhouse cheeses. Int. J. Food Microbiol. 2004, 90:309-319.
8. Djinovic-Carugo K., Gautel M., Ylänne J., Young P. The spectrin repeat: A structural platform for cytoskeletal protein assemblies. FEBS Lett 2002, 513:119-123.
9. Dougherty B.A., Hill C., Weidman J.F., Richardson D.R., Venter J.C., Ross R.P. Sequence and analysis of the 60kb conjugative, bacteriocin-producing plasmid pMRC01 from Lactococcus lactis DPC3147. Mol. Microbiol 1998, 29:1029-1038.
10. Finn R.D., Mistry J., Tate J., Coggill P.C., Heger A., Pollington J.E., Gavin O.L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E.L.L., Eddy S.R., Bateman A. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222.
11. Forde A., Fitzgerald G.F. Bacteriophage defence systems in lactic acid bacteria. Antonie van Leeuwenhoek 1999, 76:89-113.
12. Ito Y., Kawai Y., Arakawa K., Honme Y., Sasaki T., Saito T. Conjugative plasmid from Lactobacillus gasseri LA39 that carries genes for production of and immunity to the circular bacteriocin gassericin A. Appl. Environ. Microbiol. 2009, 75:6340-6351.
13. Jarvis A.W., Fitzgerald G.F., Mata M., Mercenier A., Neve H., Powell I.B., Ronda C., Saxelin M., Teuber M. Species and type phages of lactococcal bacteriophages. Intervirology 1991, 32:2-9.
14. Josephsen J., Klaenhammer T. Stacking of 3 different restriction and modification systems in Lactococcus lactis by cotransformation. Plasmid 1990, 23:71-75.
15. Khunajakr N., Liu C.-Q., Charoenchai P., Dunn N.W. A plasmid-encoded two-component regulatory system involved in copper-inducible transcription in Lactococcus lactis. Gene 1999, 229:229-235.
16. Leelawatcharamas V., Chia L.G., Charoenchai P., Kunajakr N., Liu C.-Q., Dunn N.W. Plasmid-encoded copper resistance in Lactococcus lactis. Biotechnol. Lett. 1997, 19:639-643.
17. Lillehaug D. An improved plaque assay for poor plaque-producing temperate lactococcal bacteriophages. J. Appl. Microbiol. 1997, 83:85-90.
18. Liu C.-Q., Charoechai P., Khunajakr N., Deng Y.-M., Widodo, Dunn N.W. Genetic and transcriptional analysis of a novel plasmid-encoded copper resistance operon from Lactococcus lactis. Gene 2002, 297:241-247.
19. Liu C.-Q., Su P., Khunajakr N., Deng Y.-M., Sumual S., Kim W.S., Tandianus J.E., Dunn N.W. Development of food-grade cloning and expression vectors for Lactococcus lactis. J. Appl. Microbiol. 2005, 98:127-135.
20. Lucey M., Daly C., Fitzgerald G. Analysis of a region from the bacteriophage resistance plasmid pCI528 involved in its conjugative mobilization between Lactococcus strains. J. Bacteriol. 1993, 175:6002-6009.
21. Madsen A., Josephsen J. Characterization of LlaCl, a new restriction-modification system from Lactococcus lactis subsp. cremoris W15. Biol. Chem. 1998, 379:443-449.
22. Madsen A., Josephsen J. Cloning and characterization of the lactococcal plasmid-encoded type II restriction/modification system, LlaDII. Appl. Environ. Microbiol. 1998, 64:2424-2431.
23. Marchler-Bauer A., Anderson J.B., Chitsaz F., Derbyshire M.K., DeWeese-Scott C., Fong J.H., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Lu S., Marchler G.H., Mullokandov M., Song J.S., Tasneem A., Thanki N., Yamashita R.A., Zhang D., Zhang N., Bryant S.H. CDD: Specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, 37:D205-D210.
24. McKay L.L., Baldwin K.A. Conjugative 40-megadalton plasmid in Streptococcus lactis subsp. diacetylactis DRC3 is associated with resistance to nisin and bacteriophage. Appl. Environ. Microbiol. 1984, 47:68-74.
25. Mills S., Coffey A., O'Sullivan L., Stokes D., Hill C., Fitzgerald G.F., Ross R.P. Use of lacticin 481 to facilitate delivery of the bacteriophage resistance plasmid, pCBG104 to cheese starters. J. Appl. Microbiol. 2002, 92:238-246.
26. Mills S., McAuliffe O.E., Coffey A., Fitzgerald G.F., Ross R.P. Plasmids of lactococci-Genetic accessories or genetic necessities?. FEMS Microbiol. Rev. 2006, 30:243-273.
27. Mruk I., Cichowicz M., Kaczorowski T. Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction-modification systems. Microbiology 2003, 149:3331-3341.
28. Murray N.E. Type I restriction systems: Sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev. 2000, 64:412-434.
29. Nomura M., Kobayashi M., Narita T., Kimoto-Nira H., Okamoto T. Phenotypic and molecular characterization of Lactococcus lactis from milk and plants. J. Appl. Microbiol. 2006, 101:396-405.
30. Notredame C., Higgins D.G., Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302:205-217.
31. O'Driscoll J., Glynn F., Fitzgerald G.F., van Sinderen D. Sequence analysis of the lactococcal plasmid pNP40: A mobile replicon for coping with environmental hazards. J. Bacteriol. 2006, 188:6629-6639.
32. O'Sullivan D., Coffey A., Fitzgerald G.F., Hill C., Ross R.P. Design of a phage-insensitive lactococcal dairy starter via sequential transfer of naturally occurring conjugative plasmids. Appl. Environ. Microbiol. 1998, 64:4618-4622.
33. O' Sullivan D., Ross R.P., Twomey D.P., Fitzgerald G.F., Hill C., Coffey A. Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker. Appl. Environ. Microbiol. 2001, 67:929-937.
34. O'Sullivan D., Twomey D.P., Coffey A., Hill C., Fitzgerald G.F., Ross R.P. Novel type I restriction specificities through domain shuffling of HsdS subunits in Lactococcus lactis. Mol. Microbiol. 2000, 36:866-875.
35. O'Sullivan D.J., Klaenhammer T.R. Rapid mini-prep isolation of high-quality plasmid DNA from Lactococcus and Lactobacillus spp. Appl. Environ. Microbiol. 1993, 59:2730-2733.
36. Rince A., Dufour A., Le Pogam S., Thuault D., Bourgeois C.M., Le Pennec J.P. Cloning, expression, and nucleotide sequence of genes involved in production of lactococcin DR, a bacteriocin from Lactococcus lactis subsp. lactis. Appl. Environ. Microbiol. 1994, 60:1652-1657.
37. Rincé A., Dufour A., Uguen P., Le Pennec J.-P., Haras D. Characterization of the lacticin 481 operon: The Lactococcus lactis genes lctF, lctE, and lctG encode a putative ABC transporter involved in bacteriocin immunity. Appl. Environ. Microbiol. 1997, 63:4252-4260.
38. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.-A., Barrell B. Artemis: Sequence visualization and annotation. Bioinformatics 2000, 16:944-945.
39. Ryan M.P., Rea M.C., Hill C., Ross R.P. An application in cheddar cheese manufacture for a strain of Lactococcus lactis producing a novel broad-spectrum bacteriocin, lacticin 3147. Appl. Environ. Microbiol. 1996, 62:612-619.
40. Salama M.S., Musafija-Jeknic T., Sandine W.E., Giovannoni S.J. An ecological study of lactic acid bacteria: Isolation of new strains of Lactococcus including Lactococcus lactis subspecies cremoris. J. Dairy Sci. 1995, 78:1004-1017.
41. Sanders M.E., Klaenhammer T.R. Characterization of phage-sensitive mutants from a phage-insensitive strain of Streptococcus lactis: Evidence for a plasmid determinant that prevents phage adsorption. Appl. Environ. Microbiol. 1983, 46:1125-1133.
42. Schirawski J., Hagens W., Fitzgerald G.F., van Sinderen D. Molecular characterization of cadmium resistance in Streptococcus thermophilus strain 4134: An example of lateral gene transfer. Appl. Environ. Microbiol. 2002, 68:5508-5516.
43. Schouler C., Clier F., Lerayer A.L., Ehrlich S.D., Chopin M.-C. A type IC restriction-modification system in Lactococcus lactis. J. Bacteriol. 1998, 180:407-411.
44. Schouler C., Gautier M., Ehrlich S.D., Chopin M.-C. Combinational variation of restriction modification specificities in Lactococcus lactis. Mol. Microbiol. 1998, 28:169-178.
45. Siezen R.J., Renckens B., van Swam I., Peters S., van Kranenburg R., Kleerebezem M., de Vos W.M. Complete sequences of four plasmids of Lactococcus lactis ssp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl. Environ. Microbiol. 2005, 71:8371-8382.
46. Sun Z., Zhong J., Liang X., Liu J., Chen X., Huan L. Novel mechanism for nisin resistance via proteolytic degradation of nisin by the nisin resistance protein NSR. Antimicrob. Agents Chemother. 2009, 53:1964-1973.
47. Tanous C., Chambellon E., Yvon M. Sequence analysis of the mobilizable lactococcal plasmid pGdh442 encoding glutamate dehydrogenase activity. Microbiology 2007, 153:1664-1675.
48. Terzaghi, B. E. 1988. Improved medium for lactic streptococci and their bacteriophages. Citation Classic Commentaries, Current Contents/Life Sci. 24:24. Accessed Apr. 3, 2012. http://garfield.library.upenn.edu/classics1988/A1988N613100001.pdf.
49. Trotter M., Mills S., Ross R.P., Fitzgerald G.F., Coffey A. The use of cadmium resistance on the phage-resistance plasmid pNP40 facilitates selection for its horizontal transfer to industrial dairy starter lactococci. Lett. Appl. Microbiol. 2001, 33:409-414.
50. van Kranenburg R., de Vos W.M. Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in Lactococcus lactis. J. Bacteriol. 1998, 180:5285-5290.
51. van Kranenburg R., Golic N., Bongers R., Leer R.J., de Vos W.M., Siezen R.J., Kleerebezem M. Functional analysis of three plasmids from Lactobacillus plantarum. Appl. Environ. Microbiol. 2005, 71:1223-1230.
52. van Kranenburg R., Kleerebezem M., de Vos W.M. Nucleotide sequence analysis of the lactococcal EPS plasmid pNZ4000. Plasmid 2000, 43:130-136.
53. Yoon K.P., Misra T.K., Silver S. Regulation of the cadA cadmium resistance determinant of Staphylococcus aureus plasmid pI258. J. Bacteriol. 1991, 173:7643-7649.
54. Zdobnov E.M., Apweiler R. InterProScan-An integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.
55. Zhang W., Yu D., Sun Z., Chen X., Bao Q., Meng H., Hu S., Zhang H. Complete nucleotide sequence of plasmid plca36 isolated from Lactobacillus casei Zhang. Plasmid 2008, 60:131-135.
56. Zhang Z., Schwartz S., Wagner L., Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 2000, 7:203-214.