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.Lactobacillus species are employed in the production of a wide range of fermented milk, meat, and plant products and are also routinely isolated from the vagina and gastrointestinal (GI) tract. This broad range of environmental niches is reflected in the diversity of species belonging to the genus Lactobacillus.

Transcriptional and functional analysis of galactooligosaccharide uptake bylacSinLactobacillus acidophilus

“…The related genetic loci were inclusive within the acidophilus subfamily of lactobacilli (L. acidophilus, L. ultunensis, and L. helveticus), whereas other species (e.g., Lactobacillus fermentum and L. plantarum) include lacS-positive strains and strains that have no homologs of either lacS or lacA. The retention of lacS and lacA homologs in L. helveticus is consistent with the known genetic lineage and adaptation of these lactobacilli to milk (48). In that process, L. helveticus eliminated a number of GITrelated functions (e.g., bile salt hydrolase and mucin binding proteins) but retained the lac-related genes while losing most gal-related genes except the galactose-1-phosphate uridylyltransferase gene (galT).…”

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

“…It has been shown in numerous systems that repeating elements (repeats and/or IS; Dataset S8) can be mediators of genomic plasticity (61,62,78); however, the direct impacts of these repeats are not always so clear. For example, high IS density in the genome of Lactobacillus acidophilus has been described (79), and despite the propensity of these elements to inactivate genes and facilitate recombination of genomic structure (61), the genome of this isolate still displays high levels of synteny with other sequenced Lactobacilli. Because it has also been shown that partial IS sequences can inhibit transposition (78,80), it is possible that these repeats/pseudogenes have not been deleted because they are controlling transposition in the transposase-heavy IMS101.…”

Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut

“…In this context, the typical milk-adapted L. bulgaricus and L. helveticus genomes 24,42 contain an arsenal of genes that encode enzymes dedicated to the metabolism of typical milk-derived sugars and other carbohydrates. 9 A clear sign of adaptation of the human GIT is represented by the enrichment of mucus-binding proteins and enzymes that are predicted to be involved in breakdown of complex carbohydrates.…”