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Volume 158, Issue 12

Molecular characterization and structural instability of the industrially important composite metabolic plasmid pLP712 Free

Abstract

The widely used plasmid-free strain MG1363 was derived from the industrial dairy starter strain NCDO712. This strain carries a 55.39 kb plasmid encoding genes for lactose catabolism and a serine proteinase involved in casein degradation. We report the DNA sequencing and annotation of pLP712, which revealed additional metabolic genes, including peptidase F, -lactate dehydrogenase and α-keto acid dehydrogenase (E3 complex). Comparison of pLP712 with other large lactococcal lactose and/or proteinase plasmids from subsp. SK11 (pSK11L, pSK11P) and the plant strain NCDO1867 (pGdh442) revealed their close relationship. The plasmid appears to have evolved through a series of genetic events as a composite of pGdh442, pSK11L and pSK11P. We describe in detail a scenario by which the metabolic genes relevant to the growth of its host in a milk environment have been unified on one replicon, reflecting the evolution of as it changed its biological niche from plants to dairy environments. The extensive structural instability of pLP712 allows easy isolation of derivative plasmids lacking genes for casein degradation and/or lactose catabolism. Plasmid pLP712 is transferable by transduction and conjugation, and both of these processes result in significant molecular rearrangements. We report the detailed molecular analysis of insertion sequence element-mediated genetic rearrangements within pLP712 and several different mechanisms, including homologous recombination and adjacent deletion. Analysis of the integration of the lactose operon into the chromosome highlights the fluidity of the MG1363 integration hotspot and the potential for frequent movement of genes between plasmids and chromosomes in

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2012-12-01
2024-04-19
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., 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 [View Article][PubMed]
     [Google Scholar]
  2. Anba J., Bidnenko E., Hillier A., Ehrlich D., Chopin M. C. ( 1995). Characterization of the lactococcal abiD1 gene coding for phage abortive infection. J Bacteriol 177:3818–3823[PubMed]
     [Google Scholar]
  3. Anderson D. G., McKay L. L. ( 1983). Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl Environ Microbiol 46:549–552[PubMed]
     [Google Scholar]
  4. Bachmann H., Starrenburg M. J. C., Molenaar D., Kleerebezem M., van Hylckama Vlieg J. E. ( 2012). Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res 22:115–124 [View Article][PubMed]
     [Google Scholar]
  5. Bolotin A., Quinquis B., Sorokin A., Ehrlich D. S. ( 2004). Recent genetic transfer between Lactococcus lactis and enterobacteria. J Bacteriol 186:6671–6677 [View Article][PubMed]
     [Google Scholar]
  6. Burns G., Sykes P. J., Hatter K., Sokatch J. R. ( 1989). Isolation of a third lipoamide dehydrogenase from Pseudomonas putida . J Bacteriol 171:665–668[PubMed]
     [Google Scholar]
  7. Carver T. J., Rutherford K. M., Berriman M., Rajandream M.-A., Barrell B. G., Parkhill J. ( 2005). ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423 [View Article][PubMed]
     [Google Scholar]
  8. Christensson C., Pillidge C. J., Ward L. J. H., O’Toole P. W. ( 2001). Nucleotide sequence and characterization of the cell envelope proteinase plasmid in Lactococcus lactis subsp. cremoris HP. J Appl Microbiol 91:334–343 [View Article][PubMed]
     [Google Scholar]
  9. Davis J. J., Olsen G. J. ( 2010). Modal codon usage: assessing the typical codon usage of a genome. Mol Biol Evol 27:800–810 [View Article][PubMed]
     [Google Scholar]
  10. Davis J. J., Olsen G. J. ( 2011). Characterizing the native codon usages of a genome: an axis projection approach. Mol Biol Evol 28:211–221 [View Article][PubMed]
     [Google Scholar]
  11. Fallico V., McAuliffe O., Fitzgerald G. F., Ross R. P. ( 2011). Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain. Appl Environ Microbiol 77:6451–6462 [View Article][PubMed]
     [Google Scholar]
  12. Flórez A. B., Ammor M. S., Mayo B. ( 2008). Identification of tet(M) in two Lactococcus lactis strains isolated from a Spanish traditional starter-free cheese made of raw milk and conjugative transfer of tetracycline resistance to lactococci and enterococci. Int J Food Microbiol 121:189–194 [View Article][PubMed]
     [Google Scholar]
  13. Gasson M. J. ( 1983). Plasmid complements of Streptococcus lactis NCDO 712 and other lactic streptococci after protoplast-induced curing. J Bacteriol 154:1–9[PubMed]
     [Google Scholar]
  14. Gasson M. J., Hill S. H. A., Anderson P. H. ( 1987). Molecular genetics of metabolic traits in lactic streptococci. Streptococcal Genetics242–245 Ferretti J. J., Curtiss R. Washington: American Society for Microbiology;
     [Google Scholar]
  15. Gasson M. J., Swindell S., Maeda S., Dodd H. M. ( 1992). Molecular rearrangement of lactose plasmid DNA associated with high-frequency transfer and cell aggregation in Lactococcus lactis 712. Mol Microbiol 6:3213–3223 [View Article][PubMed]
     [Google Scholar]
  16. Gerber S. D., Solioz M. ( 2007). Efficient transformation of Lactococcus lactis IL1403 and generation of knock-out mutants by homologous recombination. J Basic Microbiol 47:281–286 [View Article][PubMed]
     [Google Scholar]
  17. Hein S., Steinbüchel A. ( 1994). Biochemical and molecular characterization of the Alcaligenes eutrophus pyruvate dehydrogenase complex and identification of a new type of dihydrolipoamide dehydrogenase. J Bacteriol 176:4394–4408[PubMed]
     [Google Scholar]
  18. Hugenholtz J. ( 2008). The lactic acid bacterium as a cell factory for food ingredient production. Int Dairy J 18:466–475 [View Article]
     [Google Scholar]
  19. Jensen P. R., Hammer K. ( 1993). Minimal requirements for exponential growth of Lactococcus lactis . Appl Environ Microbiol 59:4363–4366[PubMed]
     [Google Scholar]
  20. Kelly W. J., Ward L. J. H., Leahy S. C. ( 2010). Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures. Genome Biol Evol 2:729–744[PubMed]
     [Google Scholar]
  21. Kondo J. K., McKay L. L. ( 1982). Transformation of Streptococcus lactis protoplasts by plasmid DNA. Appl Environ Microbiol 43:1213–1215[PubMed]
     [Google Scholar]
  22. Krüger N., Oppermann F. B., Lorenzl H., Steinbüchel A. ( 1994). Biochemical and molecular characterization of the Clostridium magnum acetoin dehydrogenase enzyme system. J Bacteriol 176:3614–3630[PubMed]
     [Google Scholar]
  23. MacCormick C. A., Griffin H. G., Gasson M. J. ( 1995). Construction of a food-grade host/vector system for Lactococcus lactis based on the lactose operon. FEMS Microbiol Lett 127:105–109 [View Article][PubMed]
     [Google Scholar]
  24. Maeda S., Gasson M. J. ( 1986). Cloning, expression and location of the Streptococcus lactis gene for phospho-β-d-galactosidase. J Gen Microbiol 132:331–340[PubMed]
     [Google Scholar]
  25. McKay L. L., Baldwin K. A. ( 1974). Simultaneous loss of proteinase- and lactose-utilizing enzyme activities in Streptococcus lactis and reversal of loss by transduction. Appl Microbiol 28:342–346[PubMed]
     [Google Scholar]
  26. McKay L. L., Cords B. R., Baldwin K. A. ( 1973). Transduction of lactose metabolism in Streptococcus lactis C2. J Bacteriol 115:810–815[PubMed]
     [Google Scholar]
  27. McKay L. L., Baldwin K. A., Efstathiou J. D. ( 1976). Transductional evidence for plasmid linkage of lactose metabolism in Streptococcus lactis C2. Appl Environ Microbiol 32:45–52[PubMed]
     [Google Scholar]
  28. Mills S., McAuliffe O. E., Coffey A., Fitzgerald G. F., Ross R. P. ( 2006). Plasmids of lactococci – genetic accessories or genetic necessities?. FEMS Microbiol Rev 30:243–273 [View Article][PubMed]
     [Google Scholar]
  29. Morello E., Bermúdez-Humarán L. G., Llull D., Solé V., Miraglio N., Langella P., Poquet I. ( 2008). Lactococcus lactis, an efficient cell factory for recombinant protein production and secretion. J Mol Microbiol Biotechnol 14:48–58 [View Article][PubMed]
     [Google Scholar]
  30. Nardi M., Renault P., Monnet V. ( 1997). Duplication of the pepF gene and shuffling of DNA fragments on the lactose plasmid of Lactococcus lactis . J Bacteriol 179:4164–4171[PubMed]
     [Google Scholar]
  31. Payne J., MacCormick C. A., Griffin H. G., Gasson M. J. ( 1996). Exploitation of a chromosomally integrated lactose operon for controlled gene expression in Lactococcus lactis . FEMS Microbiol Lett 136:19–24 [View Article][PubMed]
     [Google Scholar]
  32. Platteeuw C., van Alen-Boerrigter I., van Schalkwijk S., de Vos W. M. ( 1996). Food-grade cloning and expression system for Lactococcus lactis . Appl Environ Microbiol 62:1008–1013[PubMed]
     [Google Scholar]
  33. Ravin V., Sasaki T., Räisänen L., Riipinen K.-A., Alatossava T. ( 2006). Effective plasmid pX3 transduction in Lactobacillus delbrueckii by bacteriophage LL-H. Plasmid 55:184–193 [View Article][PubMed]
     [Google Scholar]
  34. Siezen R. J., Renckens B., van Swam I., Peters S., van Kranenburg R., Kleerebezem M., de Vos W. M. ( 2005). Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71:8371–8382 [View Article][PubMed]
     [Google Scholar]
  35. Smith A. W., Roche H., Trombe M.-C., Briles D. E., Håkansson A. ( 2002). Characterization of the dihydrolipoamide dehydrogenase from Streptococcus pneumoniae and its role in pneumococcal infection. Mol Microbiol 44:431–448 [View Article][PubMed]
     [Google Scholar]
  36. Sonnhammer E. L. L., Durbin R. ( 1995). A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1–GC10 [View Article][PubMed]
     [Google Scholar]
  37. Stentz R., Bongaerts R. J., Gunning A. P., Gasson M., Shearman C. ( 2010). Controlled release of protein from viable Lactococcus lactis cells. Appl Environ Microbiol 76:3026–3031 [View Article][PubMed]
     [Google Scholar]
  38. Swindell S. ( 1992). The influence of conjugation and transposition on Lactococcus lactis genome organisation http://www.srswindell.com/phd
     [Google Scholar]
  39. Taïbi A., Dabour N., Lamoureux M., Roy D., LaPointe G. ( 2010). Evaluation of the genetic polymorphism among Lactococcus lactis subsp. cremoris strains using comparative genomic hybridization and multilocus sequence analysis. Int J Food Microbiol 144:20–28 [View Article][PubMed]
     [Google Scholar]
  40. Tanous C., Chambellon E., Sepulchre A.-M., Yvon M. ( 2005). The gene encoding the glutamate dehydrogenase in Lactococcus lactis is part of a remnant Tn3 transposon carried by a large plasmid. J Bacteriol 187:5019–5022 [View Article][PubMed]
     [Google Scholar]
  41. Tanous C., Chambellon E., Yvon M. ( 2007). Sequence analysis of the mobilizable lactococcal plasmid pGdh442 encoding glutamate dehydrogenase activity. Microbiology 153:1664–1675 [View Article][PubMed]
     [Google Scholar]
  42. van Kranenburg R., van Swam I. I., Marugg J. D., Kleerebezem M., de Vos W. M. ( 1999). Exopolysaccharide biosynthesis in Lactococcus lactis NIZO B40: functional analysis of the glycosyltransferase genes involved in synthesis of the polysaccharide backbone. J Bacteriol 181:338–340[PubMed]
     [Google Scholar]
  43. van Rooijen R. J., de Vos W. M. ( 1990). Molecular cloning, transcriptional analysis, and nucleotide sequence of lacR, a gene encoding the repressor of the lactose phosphotransferase system of Lactococcus lactis . J Biol Chem 265:18499–18503[PubMed]
     [Google Scholar]
  44. van Rooijen R. J., van Schalkwijk S., de Vos W. M. ( 1991). Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis . J Biol Chem 266:7176–7181[PubMed]
     [Google Scholar]
  45. Wegmann U., O’Connell-Motherway M., Zomer A. L., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M. J. & other authors ( 2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189:3256–3270 [View Article][PubMed]
     [Google Scholar]
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Molecular characterization and structural instability of the industrially important composite metabolic plasmid pLP712
Microbiology 158, 2936 (2012); https://doi.org/10.1099/mic.0.062554-0
/content/journal/micro/10.1099/mic.0.062554-0
/content/journal/micro/10.1099/mic.0.062554-0
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