Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.

Lokesh P Tripathi,R Sowdhamini

doi:10.1186/1471-2164-9-549

Abstract

BackgroundSerine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms.ResultsA total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes.ConclusionDomain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes. Many domain combinations were found unique to specific prokaryotic species, suggesting functional specialisation in various cellular and physiological processes.

Highlights

Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life
The present analysis reveals a high abundance of the trypsin-like proteins in Bdellovibrio bacteriovorus (24 gene products; Table 1)
A closer inspection of the distribution of the DD-peptidase-like proteins in the prokaryotic species considered in the present study reveals a high representation in the genomes of some pathogenic bacteria: Bacillus anthracis Ames (14 gene products), Bacillus thuringiensis konkukian (17 gene products), Bradyrhizobium japonicum (17 gene products), Mycobacterium tuberculosis

Summary

Introduction

Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. The proper functioning of a cell is facilitated by a precise regulation of protein levels, which in turn is maintained by a balance between the rates of protein synthesis and degradation. Protein degradation mediated by proteolysis is an important mechanism for recycling of the amino acids into the cellular pool and to possibly generate energy during starvation. Serine proteases are ubiquitous enzymes with a nucleophilic Ser residue at the active site and believed to constitute nearly one-third of all the known proteolytic enzymes. They include exopeptidases and endopeptidases belonging to different protein families grouped into clans

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