Complete Sequences of Four Plasmids ofLactococcus lactissubsp.cremorisSK11 Reveal Extensive Adaptation to the Dairy Environment

Abstract

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.

Multifactorial diversity sustains microbial community stability

“…The isolates of the other genetic lineages harbored a single unique plasmid profile for their corresponding lineage (Figure 4). Analogous to the previous reports (Feirtag et al, 1991;Siezen et al, 2005), functions that are relevant for growth in a dairy environment were found to be plasmid associated, including the citrate transport encoding gene (citP), extracellular protease (prtP) and lactose utilization (lac-operon; lacG) ( Supplementary Figure 8). On the basis of this analysis, cross-lineage plasmid transfer appears to be operational but not all host-plasmid combinations were encountered, suggesting certain incompatibilities.…”

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

“…S1), and putative D-Ldhs are only found in L. lactis plasmids pSK11P and pGdh442. Siezen et al (2005) (Tanous et al, 2007). Hence, there is no proof that the D-Ldh homologues found on pGdh442 and pSK11L are functional (Tanous et al, 2007;Siezen et al, 2005).…”

“…Siezen et al (2005) (Tanous et al, 2007). Hence, there is no proof that the D-Ldh homologues found on pGdh442 and pSK11L are functional (Tanous et al, 2007;Siezen et al, 2005). The pLP712_45 gene product has homology (Table S2) with an aketoacid dehydrogenase (E3 lipoamide dehydrogenase; Lpd), which is part of a family of multicomplex enzymes with many roles in metabolism that includes pyruvate dehydrogenase, a-ketoglutarate dehydrogenase, acetoin dehydrogenase, branched-chain a-ketoacid dehydrogenases (and the glycine cleavage system), depending on the bacterial species (Hein & Steinbüchel, 1994;Smith et al, 2002;Krüger et al, 1994).…”

“…They could all be related to common ancestor plasmids and have undergone rearrangements and deletions, and exchanged DNA regions with other plasmids and the chromosome. More than 80 % of pLP712 DNA can be attributed to pGdh442 (NC_009435) (Tanous et al, 2007), pSK11P (DQ149245) (Siezen et al, 2005), which carries the genes necessary for the proteolysis of caseins, and pSK11L (DQ149244) (Siezen et al, 2005), which carries the lactose metabolism genes. In the following description, these plasmids and their relatives are referred to by the name of the published representative.…”

Sequence analysis of the mobilizable lactococcal plasmid pGdh442 encoding glutamate dehydrogenase activity

“…This incompatibility could explain why the majority of strains exhibiting GDH activity carried by pGdh442 have been isolated from a plant or animal environment, while this activity has only rarely been detected in L. lactis strains with a history in dairy fermentation (Tanous et al, 2002). However, pGdh442 is probably compatible with the two plasmids that separately carry the genes responsible for lactose-fermenting ability and casein utilization in L. lactis SK11, because of the very low homology of their iterons (Siezen et al, 2005). …”