Complete Genome Sequence of the Prototype Lactic Acid Bacterium Lactococcus lactis subsp. cremoris MG1363

Abstract

Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category "carbohydrate metabolism and transport," by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the "lateral gene transfer hot spot" in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research.Lactococcus lactis, a mesophilic fermentative bacterium producing lactic acid from sugar (hexose) fermentation, is an important industrial microorganism with extensive and diverse uses in food fermentation. Strains of L. lactis are used as defined mixtures or in undefined combinations with other lactic acid bacteria (LAB) in the production of fermented milk products. The organism has adapted to growth in milk under stringent human selection for better performance with respect to taste, flavor, and texture of dairy products, and this process continues today (57,98,99). In 1985, the "dairy streptococci" were reclassified into two L. lactis subspecies, Lactococcus lactis subsp. lactis (previously Streptococcus lactis) and Lactococcus lactis subsp. cremoris (previously Streptococcus cremoris), to distinguish them from the streptococci sensu stricto, which contain a number of notorious human pathogens (82, 83).The strain used in this study, L. lactis subsp. cremoris MG1363, is the international prototype for LAB genetics, and the knowledge gained from fundamental research on this strain has been exploited for a wide variety of biotechnological applications. The large and unstable complement of plasmid DNA of the parent strain, L. lactis NCDO712, was eliminated by employing UV treatment and protoplast-curing strategies in the early 1980s (41). The resultant plasmid-free strain, L. lactis MG1363, is robust and genetically amenable, which has facilitated the analysis of introduced lactococcal and heterologous DNA. Sophisticated systems have been developed for the expression of proteins and peptides in this strain, and it has been used as a cell factory for a wide variety of heterologous products (e.g., antimicrobials, including bacteriocins [50], bacteriop...

Multifactorial diversity sustains microbial community stability

“…cremoris (Wegmann et al, 2007), IL1403 L. lactis ssp. lactis (Bolotin et al, 2001), SK11 L. lactis ssp.…”

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

“…Because the sequence homology between pLP712 and pSK11P stretches from the right inverted repeat of the IS946 element E to the right inverted repeat of the IS946 element A (disregarding insertion II), we postulate that inversion I was followed by homologous recombination between two divergently orientated IS946 elements (A and E) located on a pGdh442 derivative and pSK11P, resulting in the integration of the prtP-carrying fragment into pGdh442 (insertion I). We speculate that as a result of this event the opp-pepO operon normally located in this area of pGdh442 was lost from the pLP712 ancestor, but due to its crucial function, selective pressure favoured progeny that had the operon integrated into the hotspot region of the L. lactis genome (Wegmann et al, 2007). This idea is supported by the observation that a 12.6 kb fragment with a pGdh442-like gene organization, showing 98 % sequence identity stretching from pGdh442_18 to pGdh442_p23, appears to be integrated into the MG1363 hotspot region (Wegmann et al, 2007).…”

“…We speculate that as a result of this event the opp-pepO operon normally located in this area of pGdh442 was lost from the pLP712 ancestor, but due to its crucial function, selective pressure favoured progeny that had the operon integrated into the hotspot region of the L. lactis genome (Wegmann et al, 2007). This idea is supported by the observation that a 12.6 kb fragment with a pGdh442-like gene organization, showing 98 % sequence identity stretching from pGdh442_18 to pGdh442_p23, appears to be integrated into the MG1363 hotspot region (Wegmann et al, 2007). The flanking chromosome regions of this fragment do not indicate homologous recombination as the mechanism behind this event, but this area of the genome shows signs of heightened plasticity, which could have destroyed the evidence for a homologous recombination event.…”

The PurR regulon in Lactococcus lactis – transcriptional regulation of the purine nucleotide metabolism and translational machinery

“…As a fixed spacing between the 210 sequence and the PurBox is essential for its function as an activator site, a refined search for correctly positioned PurBoxes in the genome sequences of L. lactis IL1403 (Bolotin et al, 2001) and MG1363 (Wegmann et al, 2007) was conducted. Initially we examined the PurBox promoters already suggested in earlier work.…”