Genomic Characterization of Lactiplantibacillus plantarum Strains Possessing Differential Antiviral Immunomodulatory Activities

Abstract

Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the immunomodulatory effect are not known. In this work, the complete genomes of L. plantarum MPL16, CRL1506, CRL681 and TL2766 were used to perform comparative genomics with the aim of identifying the genes involved in their differential immunomodulatory effects. L. plantarum WCFS1, a strain with proven probiotic activity, was also used for comparisons. The analysis of the genes involved in the metabolic pathways of the five strains did not reveal differences in the metabolism of amino acids, lipids, nucleotides, cofactors and vitamins, nor in the genes associated with energy metabolism or the biosynthesis of lipoproteins and teichoic acids. However, differences were found between the five strains when considering carbohydrate metabolism pathways, particularly in the presence/absence of glycosylhydrolases and glycosyltransferases. In addition, a great variability was detected in the predicted surface proteins of each L. plantarum strain. These results suggest that the surface molecules expressed in the different strains of L. plantarum could be involved in their differential ability to modulate the innate antiviral immune response.

Lactiplantibacillus plantarum LOC1 Isolated from Fresh Tea Leaves Modulates Macrophage Response to TLR4 Activation

“…It was reported that surface-exposed proteins play key roles in the interactions of lactobacilli with their environments [ 27 , 28 ]. Therefore, we first evaluated the genes coding surface-exposed and secreted proteins in L. plantarum LOC1 and compared them with CRL1506 and WCSF1 strains ( Figure 9 ).…”

“…Therefore, we first evaluated the genes coding surface-exposed and secreted proteins in L. plantarum LOC1 and compared them with CRL1506 and WCSF1 strains ( Figure 9 ). The extracellular proteins in the LOC1 strain were studied by in silico analysis considering the subcellular location (surface-expressed or secreted), the secretory mechanism and the anchorage type, following the guidelines recently described by our group [ 28 ]. Notable differences were detected between L. plantarum LOC1, CRL1506 and WCSF1 when analyzing the 304 genes for extracellular proteins.…”

“…We also investigated the presence of genes involved in the adhesion to the gastrointestinal tract in the genome of L. plantarum LOC1. For this purpose, a bioinformatic analysis was carried out considering different types of molecules with mucus/mucin-binding domains, which were recently characterized and described in a comparative genomic study using strains of L. plantarum possessing differential immunomodulatory activities [ 28 ]. Then, the proteins MucBP1, MucBP2, MucBP3, MucBP4, MucBP5, MucBP-DUF1, MucBP-DUF2, Muc-MubB2-MBG, Muc-MubB2-YGX, Muc-MubB2, YceG and Ig-like were searched in the genome of the LOC1 strain ( Figure 10 ).…”

“…EPSs are also involved in the interaction of LAB with the host. It was shown that L. plantarum have four clusters for the biosynthesis of EPS [ 33 ] and recently we demonstrated that strains may differ markedly in the presence of those clusters in their genomes [ 28 ]. Thus, we performed a sequence comparison using L. plantarum WCFS1 as a reference to characterize the EPS clusters in the genome of the LOC1 strain ( Figure 11 ).…”

“…For the eps2 (or cps2) cluster, it was observed that L. plantarum LOC1 had the first five genes ( eps2A , eps2B , eps2C , eps2D and eps2E ) that have been reported to be highly conserved among L. plantarum strains [ 33 , 34 ]. The other genes of the eps2 cluster of the WCSF1 strain used as reference were not found in L. plantarum LOC1 and this is probably related to the fact that those genes possess very limited sequence homology between the corresponding regions from different strains [ 28 , 34 ]. It was shown that some strains including L. plantarum WCFS1 [ 34 ] possess a group of conserved genes called rfb ( rmlACBD genes), which are involved the biosynthesis of rhamnose precursors during the synthesis of EPS molecules [ 35 ].…”