Complete genome sequence of Lactobacillus plantarum WCFS1

Abstract

The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single colony isolate of strain NCIMB8826 that was originally isolated from human saliva, has been determined, and contains 3,052 predicted protein-encoding genes. Putative biological functions could be assigned to 2,120 (70%) of the predicted proteins. Consistent with the classification of L. plantarum as a facultative heterofermentative lactic acid bacterium, the genome encodes all enzymes required for the glycolysis and phosphoketolase pathways, all of which appear to belong to the class of potentially highly expressed genes in this organism, as was evident from the codon-adaptation index of individual genes. Moreover, L. plantarum encodes a large pyruvate-dissipating potential, leading to various end-products of fermentation. L. plantarum is a species that is encountered in many different environmental niches, and this flexible and adaptive behavior is reflected by the relatively large number of regulatory and transport functions, including 25 complete PTS sugar transport systems. Moreover, the chromosome encodes >200 extracellular proteins, many of which are predicted to be bound to the cell envelope. A large proportion of the genes encoding sugar transport and utilization, as well as genes encoding extracellular functions, appear to be clustered in a 600-kb region near the origin of replication. Many of these genes display deviation of nucleotide composition, consistent with a foreign origin. These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome.

Figure 1

Genome-atlas view of the L. plantarum WCFS1 chromosome, with the predicted origin of replication at the top. The outer to inner circles show (i) positive strand ORFs (red); (ii) negative strand ORFs (blue); (iii) GC-skew (green); (iv) G+C content (black); (v) prophage-related functions (green) and IS-like elements (purple); and (vi) rDNA operons (black) and tRNA encoding genes (red). The GC% and GC skew (C-G)/(C+G) were calculated in a window of 4,000 nt, in steps of 75 nt. The G+C percentage was plotted as the number of G+C nucleotides in the plus strand divided by the window size, i.e., (G+C)/4,000; lowest and highest values are 30.8% and 51.8%. The upper and lower values of the GC skew were 0.22 and −0.27.

Figure 2

Nonrandom distribution of genes belonging to specific functional categories in the L. plantarum chromosome. The outer circle contains all genes encoding proteins involved in sugar transport (PTS are colored black, other transporters are colored blue), sugar metabolism (green), and biosynthesis and/or degradation of polysaccharides (red). The inner circle contains all genes predicted to encode secreted proteins; see also Table 1. Red, signal peptides; green, N-terminal lipoprotein anchor; blue, N-terminal signal anchor sequence.