The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403

Abstract

Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group.

Figure 1

Distribution of IS elements and prophages in the IL1403 chromosome. Outer circle shows the scale in basepairs. IS981, IS983, and IS1077 are shown by yellow, red, and blue squares, respectively (enlarged for clarity). Red and blue arcs show the areas of IS983 and IS1077 insertions. pi prophages are shown in violet, and ps in black. Green circle shows GC skews (C−G/C+G) distribution (window 20 kb, step 5 kb), which indicates the origin (near bp 1) and terminus (near bp 1,260,000) of replication.

Figure 2

Linear map of the Lactococcus lactis ssp. lactis IL1403 chromosome. Coding regions are shown as arrows color-coded to the assigned functional categories. IS-elements and rRNA genes are shown as black arrows with white designation numbers inside. Symbols shown in pink identify genes in which frameshifts were detected.