ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes.

Iztok Dogsa,Roberto Vera,Ziva Marsetic,Sándor Pongor,Ines Mandic-Mulec,Sanjarbek Hudaiberdiev,Kumari Sonal Choudhary,Raymond Schuch

doi:10.1371/journal.pone.0096122

Abstract

The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand. Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013). After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions. The census data show that in addition to B. subtilis and close relatives, 20 comQXPA-like loci are predicted to occur outside the B. subtilis clade. These include some species of Clostridiales order, but none outside the phylum Firmicutes. Characteristic gene-overlap patterns were observed in comQXPA loci, which were different for the B. subtilis-like and non-B. subtilis-like clades. Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

Highlights

B. subtilis is one of the most studied prokaryotes and a frequently used model organism for Gram positive bacteria
The complex nature of the ComQXPA quorum sensing system justifies questioning whether or not related circuit architectures occur outside the B. subtilis species
Visibly more varied clade as ‘‘non-B. subtilis-like’’ since it contains no B. subtilis sequences. This clade contains a few species from the Bacillus genus (B. isronensis, B. coagulans, B. azotoformansname and B. cereus), and species from Lysinbacillus, Geobacillus, Anoxybacillus, Desulfosporosinus and more distantly related organisms such as Clostridiales. (Note that the same clades appear on the ComP and ComA trees, shown in Figures S2 and S3)

Summary

Introduction

B. subtilis is one of the most studied prokaryotes and a frequently used model organism for Gram positive bacteria It is capable of secreting a wide variety of molecules, including ribosomally and non-ribosomally produced peptides, polyketides, etc (for a recent review see [1,2]). Some of these play the role of quorum sensing (QS) molecules that coordinate social response of various bacterial populations in a cell density dependent manner [3]. We focus on the major B. subtilis quorum sensing comQXPA locus that operates through the ribosomally synthesized signaling peptide ComX. We use the term ‘‘signal’’ without reference to evolutionary adaptation, but to denote a chemical compound that alters the functioning of a bacterial cell

Methods

Results

Conclusion