Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion

Abstract

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species, considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the L. helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.

FIG. 1.

Genome atlas of L. helveticus DPC 4571. The circles represent the following (from outer to inner). Circle 1 (two strands, positive and negative) shows predicted ORFs assigned and colored according to 10 functional groupings based on BLASTP (3) similarity searches. Circle 2 (two strands, positive and negative) shows IS elements (blue) distinguished from all other features (gray). Circle 3 shows percent GC content (red represents high GC content, and green represents low GC content). Circle 4 shows GC skew. The positions of the putative genomic island and rRNA operon (asterisks) are also indicated. The atlas was created using GenomeViz software (18).

FIG. 2.

Phylogenetic supertree of sequenced lactobacilli and streptococci. Members of the L. acidophilus-L. delbrueckii group are circled, dairy cultures are shaded, and the Bacillus subtilis outgroup is boxed. The supertree was calculated from 32 individual ribosomal protein trees. All branches are supported at >75% bootstrap values.

FIG. 3.

Alignment of L. helveticus DPC 4571, L. acidophilus NCFM, L. johnsonii NCC533, and L. delbrueckii ATCC 11842 genomes using ACT. The lines between the genomes represent DNA-DNA similarities (BLASTN matches) between the two sequences.