# A Genomic Survey of Signalling in the Myxococcaceae
## 4 Discussion  
Myxobacterial genomes encode large numbers of signalling proteins; however, within a genus, they also have very small core genomes due to the large proportion of accessory genes in each genome [7; 8; 9]. Previous analysis of conservation of myxobacterial TCS genes suggested that gene gain/loss was one of the most frequent types of mutational events experienced by TCS genes [3]. Nevertheless, 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. We therefore investigated the conservation of regulatory gene family members within groups of myxobacterial genomes, and also assessed conservation of regulators associated with key myxobacterial behaviours. The numbers of regulatory proteins of different families/classes is remarkably constant between genomes within a group of related organisms, suggesting that they are disproportionately represented in the core genome compared to 'typical' genes (Figure 2). TCS genes seem to be even more enriched in the core genome compared to OCSs and TFs, which perhaps reflects the large numbers of TCSs in myxobacterial genomes. Because of their shared domain architectures and mechanisms of phosphotransfer, multiple TCS signalling pathways can be integrated into sophisticated regulatory modules and networks [42]. Potentially, this might reduce the loss of individual TCS genes from genomes, with selection instead acting at the level of the whole network or module. Fruiting body formation in _M. xanthus_ is regulated by a modular network dominated by TCS proteins. However, selection does not seem to be at the level of the module. The only module that is either present or absent from different genomes in its entirety is the DevTRS/CRISPR module (Supplementary Table S2), which is thought to primarily resist phage infection during sporulation, with only secondary effects on the timing of sporulation [22]. The other regulatory modules are always present in a genome, but in every case, some individual components are conserved, while others are dispensable (Figure 3). Robustness is a global property of modular biological networks, and the lack of conservation of 'key' fruiting regulatory proteins in species/strains which are proficient in fruiting implies the myxobacterial developmental network is evolutionarily robust. The impact of mutational loss can be reduced by the architecture of signalling networks [43]. It has long been recognised that robustness is an emergent property of certain network architectures. In particular, modularity is an organisingprinciple allowing the evolution of both robustness and computational complexity in gene regulatory networks [44; 45]. The ease with which suppressor and bypass mutations of developmental gene mutants can be isolated supports the notion that the developmental network is evolutionarily robust. Examples abound, but one good example involves the non-coding RNA Pxr, which inhibits the initiation of fruiting body development in the presence of nutrients [46]. In one study, a mutant strain unable to relieve Pxr inhibition in response to starvation could be restored to developmental proficiency by mutations within three separate genes, _pxr_ and two positive regulators of _pxr_ expression, leading the authors to conclude that reversion of developmental defects could be commonplace [47]. In another example, a third separate bypass suppressor mutation of the protease gene _bsgA_ was mapped to an operon encoding RNase D and an aminopeptidase [48]. The network must also be able to incorporate newly acquired or duplicated genes. Potentially, subtle changes in phenotype due to acquisition of a new gene might confer enough of a selective advantage to promote retention of that gene.