Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer

Abstract

In the past decade it has become clear that the lactic acid bacterium Lactobacillus plantarum occupies a diverse range of environmental niches and has an enormous diversity in phenotypic properties, metabolic capacity and industrial applications. In this review, we describe how genome sequencing, comparative genome hybridization and comparative genomics has provided insight into the underlying genomic diversity and versatility of L. plantarum. One of the main features appears to be genomic life-style islands consisting of numerous functional gene cassettes, in particular for carbohydrates utilization, which can be acquired, shuffled, substituted or deleted in response to niche requirements. In this sense, L. plantarum can be considered a "natural metabolic engineer".

Figure 1

Comparative genome hybridization (CGH) analysis of L. plantarum isolates. The genes are ordered based on their location in the genome sequence of L. plantarum WCFS1 (horizontal axis). Black bars indicate “absent” genes/regions. Red boxes indicate regions where large differences in presence/absence of genes correspond with a high base-deviation index. Adapted from Figure 2 of [15], with permission from the Society for Applied Microbiology and Blackwell Publishing Ltd.

Figure 2

Gene cassettes for sugar utilization. (A) General structure of a functional gene cassette; (B) example of rhamnose and galactitol utilization cassettes and their organization in two L. plantarum strains and other lactobacilli; (C) example of various sugar utilization cassettes and their organization in various lactobacilli. Orthologs in different strains/species are indicated by corresponding numbers and colors.

Figure 3

Genotype-phenotype linkage analysis by Random Forest classification. Growth (Yes) or non-growth (No) of 42 different L. plantarum strains on a variety of sugars was measured. Legend: the color coding used for integration of significance of genes for a certain phenotype with their presence/absence patterns for the different strains. A gene that is found to be important to distinguish strains of different phenotypes is assumed as important. Present (for the majority of strains): gene is present in at least p percent (default of 75%) of strains for a given phenotype. Absent (for the majority of strains): gene is absent in at least 75% of strains of a given phenotype. Examples are given of gene cassettes (using gene numbering of strain WCFS1) that are found to be important for phenotype classification of strains.

Figure 4

Diversity of tar genes for wall teichoic acid biosynthesis. Genome organization surrounding the ribitol-type teichoic acid biosynthesis genes tarIJKL in L. plantarum strains. The percentage nucleotide sequence identity is shown between reference strain WCFS1 and the other 5 strains (which themselves are nearly identical). CGH indicates whether these genes were identified by CGH in strains NC8 and ATCC14917; red boxes signify genes that were not identified by CGH. tarI: D-ribitol-5-phosphate cytidylyltransferase; tarJ: ribitol-5-phosphate 2-dehydrogenase; tarK: ribitol-phosphotransferase; tarL: ribitol-phosphotransferase.

Figure 5

Diversity of plantaricin (pln) gene clusters. Mosaic pln loci from strains of Lactobacillus plantarum. Lollipops indicate regulated promoters. The genes brnQ1 and napA1 at the upper end of the pln loci are not part of the pln regulon but they are included in the gene map to signify the upper boundary of the pln locus. Note that the lower ends of the pln loci of J51, NC8 and J23 are not completely sequenced. Reproduced from [55], with permission from Elsevier Inc.

Figure 6

Diversity of capsular polysaccharide biosynthesis genes. Comparison of genome organization surrounding the large cluster of cps biosynthesis genes. Genes are represented by blue and white arrows, in forward and reverse strands. Shades of connecting bars indicate high sequence identity (bright red) to low sequence identity (pink). The blue connecting bar indicates a reverse orientation. The 3 consecutive cps gene clusters in WCFS1 are indicated, and the rfbACBD genes. T indicates transposases of IS elements. Picture drawn with Artemis Comparison Tool (ACT)[66].

Figure 7

Modularity and variability of life-style gene cassettes. Life-style region corresponding to genes lp_3114-lp_3150 (from 2.78-2.82 Mb on the chromosome) in strain WCFS1, represented as gene cassettes. Each cassette contains 3-18 genes (see example in Figure 2A); identical colors indicate corresponding cassettes in other strains. Putative functions of proteins encoded in the cassettes are indicated.

Figure 8

Diversity of domain composition within the mannose-specific adhesion (Msa). Determined by sequencing of the msa gene in a subset of L. plantarum strains, highlighting the variation in numbers of mucus-binding (MUB) domains and PxxP-repeats. Adapted from [63], with permission from Wageningen Academic Publishers, the Netherlands.