Extremely Variable Conservation of  -Type Small, Acid-Soluble Proteins from Spores of Some Species in the Bacterial Order Bacillales

Abstract

␥-Type small, acid-soluble spore proteins (SASP) are the most abundant proteins in spores of at least some members of the bacterial order Bacillales, yet they remain an enigma from both functional and phylogenetic perspectives. Current work has shown that the ␥-type SASP or their coding genes (sspE genes) are present in most spore-forming members of Bacillales, including at least some members of the Paenibacillus genus, although they are apparently absent from Clostridiales species. We have applied a new method of searching for sspE genes, which now appear to also be absent from a clade of Bacillales species that includes Alicyclobacillus acidocaldarius and Bacillus tusciae. In addition, no ␥-type SASP were found in A. acidocaldarius spores, although several of the DNA-binding ␣/␤-type SASP were present. These findings have elucidated the phylogenetic origin of the sspE gene, and this may help in determining the precise function of ␥-type SASP.Bacterial spores of species of the Firmicutes phylum contain a number of small, acid-soluble proteins (SASP) that comprise 10 to 15% of the protein in the spore's central region or core (30, 32). The following two types of major SASP have been identified in spores: (i) ␣/␤-type SASP that are products of a multi-ssp gene family and have extremely similar sequences both within and across species and (ii) ␥-type SASP that are almost always encoded by a single sspE gene; this is the most abundant protein found in spores of a number of species and comprises 5 to 8% of total spore protein (18-20, 29-32, 39). In contrast to the highly conserved sequences of ␣/␤-type SASP, sequences of ␥-type SASP are not well conserved across species, and this has allowed the use of sspE and SASP-␥ sequences to distinguish closely related Bacillus strains and species (17).In Bacillus subtilis, genes encoding both ␣/␤-type and ␥-type SASP are transcribed in parallel late in spore development when the various SASP are synthesized, and the transcription of ssp genes is mediated by the RNA polymerase sigma factor, G (22). The SASP are degraded soon after spores complete the germination process and begin outgrowth, and one function of these proteins is to serve as a reservoir of amino acids (aa) for protein synthesis early in outgrowth (12,30,32). The latter is an important function, since spores become deficient in a number of amino acid biosynthetic enzymes during spore formation and synthesize these enzymes only during spore outgrowth. In addition to serving as a reservoir of amino acids, the ␣/␤-type SASP have an additional function, as these proteins saturate spore DNA and protect it from many types of damage and are thus very important for long-term spore survival (30-32). However, other than serving as an amino acid reservoir, no additional function has been demonstrated for ␥-type SASP (12, 30, 32).In the current work, we have examined genome sequence information for spore-forming Firmicutes and have confirmed that (i) spore-forming Clostridiales species appear to lack sspE genes; (ii) most bu...

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

“…Aside from SASPs of the α/β group, most B. subtilis SASPs have a relatively narrow phylogenetic distribution and are found almost exclusively in Bacilli . Thus, the major SASP of the γ‐type, SspE, is encoded in most bacilli but is absent in any clostridial genome sequenced to date (Table S3 and Vyas et al ., 2011). Among minor SASPs, only SspH, SspI and Tlp are found in any clostridia, although each of these three is found in almost all bacilli.…”

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

“…Taken together, in silico analysis suggested SspA, SspB, SspD and SspF of C. acetobutylicum as SASPs, whereas SspH and Tlp disclosed less conserved DNA-binding motifs of a/btype SASPs of aerobic and anaerobic spore-formers (Setlow, 2007;Vyas et al, 2011). In comparison with SASPs of B. subtilis, all those of C. acetobutylicum revealed a non-conserved enlarged spacer of 4-6 aa between the Nand C-terminal SASP motif (Fig.…”

“…Due to the binding motif, the tlp promoter seemed to be controlled by the forespore-specific s F of C. acetobutylicum (Paredes et al, 2004;Jones, 2011). Downstream of each ssp gene a dyad-symmetrical DNA sequence is located, probably representing stem-loops of rho-independent transcription terminators (Connors et al, 1986;Vyas et al, 2011) (Fig. 3c).…”

“…3(a) shows the DNA region of the sspA gene highlighting the transcription start point 41 bp upstream of the start codon. The untranslated region of the mRNA comprises a ribosome-binding site at a typical distance of 6-7 bases upstream of the ATG codon (Vyas et al, 2011) and the upstream promoter region shows a 210 box and a 235 box with high similarities to the consensus of forespore-specific s G of C. acetobutylicum (Dürre, 2005) and s G of B. subtilis (Wang et al, 2006). Remarkably, all derived ssp gene promoters of C. acetobutylicum revealed at least 4 of 5 nt identical to the s G 235 consensus box and 4 of 7 nt identitical to the s G 210 box (Fig.…”

“…Major and minor SASPs could be categorized into two classes: (i) a/b-type and (ii) c-type (Setlow, 1988). The latter are not able to bind DNA and are expected to be restricted to the genus Bacillus (Francesconi et al, 1988;Vyas et al, 2011). Usually, most SASPs are encoded by monocistronic genes termed ssp, which are expressed only in the developing forespore compartment, and immediately after protein biosynthesis a/btype SASPs bind DNA up to saturation with the effect of DNA protection by dense packaging (Lee et al, 2008;Ge et al, 2011).…”