From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile

Abstract

Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.

Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales

“…Most HGT events occurred at or near the branch tips of the reconciled gene-species phylogenetic trees, demonstrating a recent occurrence. This supports the idea that the ability to form spores in Firmicutes (in Bacilli and Clostridia) is an ancestral feature as other researchers have stated [27,85,88]. Moreover, these HGT events are further confirmed by the presence of IS sequences in genomes of the recipient species.…”

“…On the other hand, the lack of evidence for spore coat gene homologues in Hallolactobacillus, Jeotgalicoccus and B. beveridgei suggests that a major loss of genes occurred during their evolutionary history, as previously found for the Exiguobacterium genus. This may explain why they do not produce spores [88].…”

Host adaptation in gut Firmicutes is associated with sporulation loss and altered colonisation patterns

“…Our analysis places the non-gut-associated, SF order Halanaerobiales at the base of the phylogeny 33 . Subsequent, large-scale loss of sporulation within taxonomic orders such as the Lactobacillales is evident (all 344 genomes are predicted to be FSF), which has been observed before and attributed to adaptation to nutrient-rich habitats 19,34 . Interestingly, we also observe smaller scale sporulation loss within multiple distinct clades of the host-associated Erysipelotrichaceae , (26% are FSF), Peptostreptococcaceae (26% are FSF) and Lachnospiraceae (18% are FSF) families 35 .…”

Phenotypic reconstruction of the last universal common ancestor reveals a complex cell

“…While a positive correlation between the frequency of HGTs in distant lineages and genome size has been suggested 52 , several studies indicate that HGT in prokaryotes also depends on both physical and genetic proximity [53][54][55] . Moreover, there is accumulating evidence to suggest that some of the traits that we present such as motility, cell envelope and sporulation, were subject to little or rare HGT events during their evolutionary history in a number of prokaryotic lineages 22,23,25,45,55 .…”