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.

FIG. 1.

Genome atlas of the chromosome of L. lactis MG1363. The first base pair of dnaA in the oriC region is designated position 1, and the putative terminus is at position 1255251. The inversion relative to L. lactis IL1403 is indicated. Starting from the inside, the circles depict the following. Circle no. 1 (red) represents the GC skew; the origin and terminus are clearly marked by the change in GC skew. Circle no. 2 (blue/green) shows the GC percentage of the CDSs on the genome, where green peaks are (six) tRNA genes or rRNA regions; regions with a lower GC content possibly originate from a lateral gene transfer event. Circle no. 3 marks the presence of IS elements (red) and prophages/phage remnants (green) and the location of the integration hot spot (yellow) and sex factor (light blue). Regions with many IS elements often coincide with sequences of relatively high AT, and IS elements are overrepresented in the integration hot spot. Circle no. 4 depicts the genes that are unique to L. lactis MG1363, i.e., that do not occur in L. lactis IL1403. The outer two circles are color coded according to the COG classification of the genes present on the forward (circle no. 6) and reverse (circle no. 5) strands.

FIG. 2.

Integration hot-spot repeat sequences. The underlined sequences indicate inverted repeats. The asterisk indicates the fact that the transposase gene of IS905 is a pseudogene. (A) Sequence present in at least 27 plasmids from L. lactis subsp. lactis, L. lactis subsp. cremoris, and L. lactis bv. diacetylactis and plasmids of Lactobacillus helveticus, Lactobacillus delbrueckii subsp. lactis, Tetragenococcus halophila, Pediococcus acidilactici, Leuconostoc citreum, L. monocytogenes, and L. innocua, and also the genomes of Lactobacillus sakei, Lactobacillus delbrueckii subsp. lactis, and Lactobacillus delbrueckii subsp. paracasei and different strains of S. thermophilus. (B) Sequence present in at least nine plasmids from L. lactis subsp. lactis, L. lactis subsp. cremoris, and L. lactis bv. diacetylactis and plasmids of L. helveticus, Lactobacillus lindneri, Lactobacillus brevis, L. sakei, and L. plantarum, and also the genomes of Lactobacillus paracasei subsp. paracasei and S. thermophilus. (C) Sequence, or part thereof, present in at least 24 plasmids from L. lactis subsp. lactis and L. lactis subsp. cremoris. The inverted repeat is present in the genomes of different strains of S. thermophilus and Acetobacter pasteurianus and plasmids of Staphylococcus epidermidis (two), S. aureus (six), Staphylococcus xylosus, Staphylococcus haemolyticus (two), and L. monocytogenes and L. innocua.

FIG. 3.

Chromosomal inversions in L. lactis. (A) Dot plot of the nucleotide sequences of the chromosomes of L. lactis IL1403 (red) and L. lactis SK11 (black) (both on the y axis) against that of L. lactis MG1363 (x axis). (B) Chromosomal inversions in L. lactis MG1363 and L. lactis NCDO763. The colored squares indicate homologous sequence pairs involved in the inversions, while the numbers indicate the coordinates in the L. lactis MG1363 genome sequence of the fragments involved. Horizontal black bars show the positions of the integration hot spot and the sex factor. ter, putative terminus of replication. See the text for details.

FIG. 4.

Growth of L. lactis on sugars. Utilization by L. lactis MG1363 (open bars) and L. lactis IL1403 (black bars) of various sugar sources as measured by a significant (<60) difference in dye intensity development (indicated in arbitrary units on the y axis) on Biolog plates (7).