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Applied and Environmental Microbiology, December 2005, p. 8371-8382, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8371-8382.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment

Roland J. Siezen,^1,2,3* Bernadet Renckens,^1,2,3 Iris van Swam,^1,3 Sander Peters,⁴ Richard van Kranenburg,^1,3, Michiel Kleerebezem,^1,3 and Willem M. de Vos¹

Wageningen Centre for Food Sciences, P.O. Box 557, 6700AN Wageningen,¹ Centre for Molecular and Biomolecular Informatics, Radboud University, P.O. Box 9010, 6500GL Nijmegen,² NIZO food research, P.O. Box 20, 6710BA Ede,³ Greenomics, Plant Research International, P.O. Box 16, 6700AA Wageningen, The Netherlands⁴

Received 28 June 2005/ Accepted 4 August 2005

Lactococcus lactis strains are known to carry plasmids encoding industrially important traits. L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372 bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous repB-containing replicons were found, all belonging to the family of lactococcal theta-type replicons. Twenty-three complete insertion sequence elements segment the plasmids into numerous modules, many of which can be identified as functional units or containing functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA). Newly identified plasmid-encoded functions could facilitate the uptake of various cations, while the pabA and pabB genes could be essential for folate biosynthesis. A competitive advantage could be obtained by using the putative flavin adenine dinucleotide-dependent D-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the activity of the predicted -acetolactate decarboxylase may contribute to the formation of an additional electron sink. Various stress response proteins are plasmid encoded, which could enhance strain robustness. A substantial number of these "adaptation" genes have not been described before on L. lactis plasmids. Moreover, several genes were identified for the first time in L. lactis, possibly reflecting horizontal gene transfer.

Supplemental material for this article may be found at http://aem.asm.org/.

Present address: Purac Biochem, P.O. Box 21, 4200AA Gorinchem,The Netherlands.

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