Emergence of a Cell Wall Protease in the Streptococcus thermophilus Population

Abstract

Streptococcus thermophilus is perceived as a recently emerged food bacterium that evolved from a commensal ancestor by loss and gain of functions. Here, we provide data allowing a better understanding of this evolutionary scheme. A multilocus sequence typing approach that we developed showed that S. thermophilus diverges significantly from its potential ancestors of the salivarius group and displays a low level of allelic variability, confirming its likely recent emergence. An analysis of the origin and dissemination of the prtS gene was carried out within this evolutionary scheme. This gene encodes a protease that allows better growth in milk by facilitating casein breakdown to supply amino acids. The S. thermophilus protease exhibits 95% identity to the animal Streptococcus suis protein PrtS. Genomic analysis showed that prtS is part of an island flanked by two tandem insertion sequence elements and containing three other genes which present the best identities and synteny with the S. suis genome. These data indicate a potential origin for this "ecological" island in a species closely related to S. suis. The analysis of the distribution of the prtS gene in S. thermophilus showed that the gene is infrequent in historical collections but frequent in recent industrial ones. Moreover, this "ecological" island conferring an important metabolic trait for milk adaptation appears to have disseminated by lateral transfer in the S. thermophilus population. Taken together, these data support an evolutionary scheme of S. thermophilus where gene acquisition and selection by food producers are determining factors. The source and impact of genes acquired by horizontal gene transfer on the physiology and safety of strains should be addressed.

Biofilm Formation on Stainless Steel by Streptococcus thermophilus UC8547 in Milk Environments Is Mediated by the Proteinase PrtS

“…The genome analysis showed that S. thermophilus UC8547 contains the prtS gene on the mobile genetic element previously identified in the fast-acidifying S. thermophilus strains. This genomic island is located in the ciaH-rpsT chromosomal region, as observed in other S. thermophilus strains (6,8), downstream of the ciaH pseudogene and between two tandem ISSth1 elements (Fig. 6).…”

“…Interestingly, proteolytic activity and biofilm formation are associated with the prtS gene, which is located on a mobile genetic element that has been demonstrated to be a horizontally acquired trait (6)(7)(8). The mechanism of prtS island excision involves two copies of the ISSth1 insertion sequence flanking the prtS gene and is similar to that already described by Delorme et al (8) in different S. thermophilus strains, and to that observed by Dandoy et al (6), inserting by natural transformation the island in PrtS Ϫ strains. Unlike other S. thermophilus prtS islands (8), in UC8547, there is a single copy of IS1167.…”

“…Even if the exact source is not well known and its presence was originally correlated to Lactococcus lactis (5), the cell envelope proteinase PrtS in S. thermophilus could be indicated as an example of a gene acquired by HGT that recently appears to be highly conserved and therefore selected in the industrial strains (6). This is supported by the fact that in S. thermophilus, the prtS gene, coding for an LPXTGcontaining serine proteinase of the subtilisin family (5), is part of a genomic island flanked by conserved insertion sequence (IS) elements (6)(7)(8). This mobile island has been shown to be involved in recombination events involving the flanking IS elements that lead to the loss of the prtS genomic island (6)(7)(8), therefore influencing gene homeostasis and species heterogeneity (7).…”

“…This is supported by the fact that in S. thermophilus, the prtS gene, coding for an LPXTGcontaining serine proteinase of the subtilisin family (5), is part of a genomic island flanked by conserved insertion sequence (IS) elements (6)(7)(8). This mobile island has been shown to be involved in recombination events involving the flanking IS elements that lead to the loss of the prtS genomic island (6)(7)(8), therefore influencing gene homeostasis and species heterogeneity (7). The close proximity of these IS elements to genes involved in adaptation to milk environments reveals that their acquisition in this bacterium's genome could represent a relatively recent excision event (8).…”

“…This mobile island has been shown to be involved in recombination events involving the flanking IS elements that lead to the loss of the prtS genomic island (6)(7)(8), therefore influencing gene homeostasis and species heterogeneity (7). The close proximity of these IS elements to genes involved in adaptation to milk environments reveals that their acquisition in this bacterium's genome could represent a relatively recent excision event (8). prtS genetic adoption generated beneficial properties in S. thermophilus, like fast growth in milk substrate and the ability to hydrolyze casein with a consequent high acidification rate (6); moreover, additional unknown functions could be conferred by these horizontal genomic rearrangements compared to prtS-deficient strains.…”