Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure

Hong Qin,Adam Driks

doi:10.1186/1471-2148-13-261

Abstract

BackgroundThe Bacillus subtilis-group and the Bacillus cereus-group are two well-studied groups of species in the genus Bacillus. Bacteria in this genus can produce a highly resistant cell type, the spore, which is encased in a complex protective protein shell called the coat. Spores in the B. cereus-group contain an additional outer layer, the exosporium, which encircles the coat. The coat in B. subtilis spores possesses inner and outer layers. The aim of this study is to investigate whether differences in the spore structures influenced the divergence of the coat protein genes during the evolution of these two Bacillus species groups.ResultsWe designed and implemented a computational framework to compare the evolutionary histories of coat proteins. We curated a list of B. subtilis coat proteins and identified their orthologs in 11 Bacillus species based on phylogenetic congruence. Phylogenetic profiles of these coat proteins show that they can be divided into conserved and labile ones. Coat proteins comprising the B. subtilis inner coat are significantly more conserved than those comprising the outer coat. We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the B. subtilis-group genomes, but not in the B. cereus-group genomes. We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the B subtilis-clade and the B. cereus-clade.ConclusionsCoat proteins in the B. subtilis- and B. cereus-group species are under contrasting selective pressures. We speculate that the absence of the exosporium in the B. subtilis spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

Highlights

The Bacillus subtilis-group and the Bacillus cereus-group are two well-studied groups of species in the genus Bacillus
The defining feature of bacteria of the family Bacillaceae is the ability to form a specialized alternate cell type, the spore, which can withstand a wide range of environmental stresses, including toxic chemicals, heat, ultraviolet radiation and microbial predation [1,2,3,4]
The second clade is comprised of Bacillus subtilis and its close relatives, including Bacillus lichenniformis, Bacillus pumilus, Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis, and Bacillus vallismortis

Summary

Introduction

Bacteria in this genus can produce a highly resistant cell type, the spore, which is encased in a complex protective protein shell called the coat. The ability of spores to remain dormant for long time periods and to resist extreme conditions has made this cell type a major model for studies of cellular defenses against stress. The vast majority of research on these organisms has focused on only two Bacillus clades The first of these is the B. cereusgroup, which is comprised of the closely related species Bacillus anthracis, Bacillus cereus, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides and Bacillus weihenstephanensis [7]. Because the B. cereus-group and B. subtilis-group species comprise only a very small subset of the total diversity of the Bacillaceae [12], the biology of the majority of these organisms remains poorly understood [13]

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