Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation‐specific genes

Abstract

Summary Three classes of low‐G+C Gram‐positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat‐resistant endospores. Spore‐forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose‐degrading industrial strains, as well as human pathogens responsible for such diseases as anthrax, botulism, gas gangrene and tetanus. In the best‐studied model organism Bacillus subtilis, sporulation involves over 500 genes, many of which are conserved among other bacilli and clostridia. This work aimed to define the genomic requirements for sporulation through an analysis of the presence of sporulation genes in various firmicutes, including those with smaller genomes than B. subtilis. Cultivable spore‐formers were found to have genomes larger than 2300 kb and encompass over 2150 protein‐coding genes of which 60 are orthologues of genes that are apparently essential for sporulation in B. subtilis. Clostridial spore‐formers lack, among others, spoIIB, sda, spoVID and safA genes and have non‐orthologous displacements of spoIIQ and spoIVFA, suggesting substantial differences between bacilli and clostridia in the engulfment and spore coat formation steps. Many B. subtilis sporulation genes, particularly those encoding small acid‐soluble spore proteins and spore coat proteins, were found only in the family Bacillaceae, or even in a subset of Bacillus spp. Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages. These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation‐specific genes in Bacilli and Clostridia.

Small acid-soluble spore proteins of Clostridium acetobutylicum are able to protect DNA in vitro and are specifically cleaved by germination protease GPR and spore protease YyaC

“…Cac2372 (termed SspF) had a significantly enlarged size of 10.1 kDa in comparison with 7.2 kDa of SspA, SspB or SspD (Table 1) and seemed to be more distantly related ( Fig. 1) (Galperin et al, 2012). Regarding SASP consensus motifs, only slight similarities were obvious for Cac1663 and Cac1487 (Fig.…”

“…In the genome the proteins encoded by cac2365 and cac2372 were assigned as 'SspA protein', those of cac1522 and cac1620 as 'SASP', and cac1487 as 'SASP Tlp' (Nölling et al, 2001) and, recently, the last was renamed 'Tlp' (http://www.ncbi.nlm.nih.gov/ protein/Q97IZ9.1). Our analysis identified a new and sixth gene, cac1663, to encode a further SASP, also suggested by Galperin et al (2012).…”

“…1). The consensus matches in Cac1663 (51.4 %) and its overall identity of 25 % to SspH of B. subtilis lead to its classification as an SASP and its designation as SspH (Galperin et al, 2012) (Table 1). In contrast, Cac1487 (termed Tlp) revealed 46 % identity to SASP Tlp of B. subtilis but hardly matched the SASP motifs (32.4 %).…”

“…Three of them (Ssp1-3, 59-60 aa) are isoforms with about 90 % amino acid identity (Raju et al, 2007) and Ssp4 (90 aa) was detected later as it differs remarkably from Ssp1-3 in size and in amino acid identity (Li & McClane, 2008;Galperin et al, 2012). Two nearly identical a/b-type SASPs (w90 %) also exist in B. subtilis (SspA/ SspB), B. megaterium (SspA/SspC) and Clostridium bifermentans (SASP-a/SASP-b), and these SASPs are predominant in acidic protein extracts of dormant spores (Setlow, 1975b;Johnson & Tipper, 1981;Cabrera-Martinez et al, 1989).…”

“…Here, we present a comprehensive study of six putative SASPs of C. acetobutylicum including five genes, cac2365, cac1522, cac1620, cac2372 and cac1487, that have been annotated in the genome (Nölling et al, 2001), complemented by a new candidate gene, cac1663 (Galperin et al, 2012). The ability of all six recombinant proteins, C-terminally fused with a Strep-tag II, to protect DNA in vitro was analysed, and specific cleavage of SspB and SspD by recombinant GPR and YyaC of C. acetobutylicum was examined.…”