Evolution of prokaryotic subtilases: Genome‐wide analysis reveals novel subfamilies with different catalytic residues

Abstract

Subtilisin-like serine proteases (subtilases) are a very diverse family of serine proteases with low sequence homology, often limited to regions surrounding the three catalytic residues. Starting with different Hidden Markov Models (HMM), based on sequence alignments around the catalytic residues of the S8 family (subtilisins) and S53 family (sedolisins), we iteratively searched all ORFs in the complete genomes of 313 eubacteria and archaea. In 164 genomes we identified a total of 567 ORFs with one or more of the conserved regions with a catalytic residue. The large majority of these contained all three regions around the "classical" catalytic residues of the S8 family (Asp-His-Ser), while 63 proteins were identified as S53 (sedolisin) family members (Glu-Asp-Ser). More than 30 proteins were found to belong to two novel subsets with other evolutionary variations in catalytic residues, and new HMMs were generated to search for them. In one subset the catalytic Asp is replaced by an equivalent Glu (i.e. Glu-His-Ser family). The other subset resembles sedolisins, but the conserved catalytic Asp is not located on the same helix as the nucleophile Glu, but rather on a beta-sheet strand in a topologically similar position, as suggested by homology modeling. The Prokaryotic Subtilase Database (www.cmbi.ru.nl/subtilases) provides access to all information on the identified subtilases, the conserved sequence regions, the proposed family subdivision, and the appropriate HMMs to search for them. Over 100 proteins were predicted to be subtilases for the first time by our improved searching methods, thereby improving genome annotation.

Non-canonical proteolytic activation of human prothrombin by subtilisin from Bacillus subtilis may shift the procoagulant–anticoagulant equilibrium toward thrombosis

“…These findings establish a new paradigm for the proteolytic activation of ProT, whereby nicking of Pre2 domain at different sites can evoke a common (physiological) mechanism of zymogen activation. The results reported in this work also indicate that proteases secreted by even non-virulent bacteria, such as B. subtilis, can shift the delicate procoagulantanticoagulant equilibrium toward thrombosis and pave the way to further investigate the ability of other subtilisin proteases (70), produced by known pathogenic bacteria (e.g. Shiga toxigenic E. coli, Streptococcus pyogenes, Pseudomonas aeruginosa, and Plasmodium falciparum) and sharing high sequence similarity with subtilisin form B. subtilis, to affect blood coagulation.…”

By their genes ye shall know them: genomic signatures of predatory bacteria

“…Further modification and breakdown of prey peptidic components into nutrients may be brought about by subtilisins and N-aminopeptidases. In most prokaryotes, secretion of subtilisins outside the cell may provide peptides and amino acids for cell growth or they may help invade host cells (Siezen et al, 2007); the N-aminopeptidases release N-terminal amino-acid residues, breakdown exogenously supplied peptides, and participate in the final steps of protein turnover, enabling the utilization of amino acids as nutrients (Ito et al, 2006;Kumar and Nandi, 2008). Accordingly, in B. bacteriovorus and Micavibrio, genes encoding these enzymes are produced during growth on a prey substrate and may thus be associated with internal degradation of the host (Lambert et al, 2010;Wang et al, 2011), along with the very strongly predator-enriched chymotrypsin proteases (Dori-Bachash et al, 2008;Lambert et al, 2010;Wang et al, 2011).…”

Novel Toxin-Antitoxin System Composed of Serine Protease and AAA-ATPase Homologues Determines the High Level of Stability and Incompatibility of the Tumor-Inducing Plasmid pTiC58

“…5). Subtilisin-like serine proteases are widely distributed from prokaryotes to higher eukaryotes (25). The proteases contain three invariant residues, His, Asn, and Ser, as an essential catalytic triad.…”