A Genomic Survey of Signalling in the Myxococcaceae.

David E Whitworth,Allison Zwarycz

doi:10.3390/microorganisms8111739

Abstract

As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.

Highlights

During the evolution of new species from common ancestors, phenotypic differences often emerge as a result of lineage-specific changes in underlying signalling pathways and regulatory genes
Previous analysis of conservation of myxobacterial two-component systems (TCSs) genes suggested that gene gain/loss was one of the most frequent types of mutational events experienced by TCS genes [3]
We would expect that some TCS genes belong to the core genome and are indispensable, while other TCS genes would belong to the accessory pan-genome and would be absent from some organisms

Summary

Introduction

During the evolution of new species from common ancestors, phenotypic differences often emerge as a result of lineage-specific changes in underlying signalling pathways and regulatory genes. It is important to understand how signalling gene sets change as organisms evolve and to be able to relate those changes to formal taxonomies. Understanding the mutability of signalling gene sets can provide us with insights into the ecology of contemporary organisms and the molecular mechanisms of their phenotypes. The myxobacteria (order Myxococcales) are renowned for having exceptionally large numbers of signalling genes in their genomes [1,2,3]. Myxobacterial genomes encode numerous transcription factors (TFs), including DNA-binding transcriptional regulators (TRs), alternative sigma factors and DNA-binding OCSs

Methods

Results

Conclusion