# A Genomic Survey of Signalling in the Myxococcaceae
## 4 Discussion
Gene duplication seems to have contributed to the large expansion in the size of myxobacterial genomes compared to the other Deltaproteobacterial Orders, with EBPs and TCSs notably prevalent [36], while acquisition by horizontal transfer might explain the origin of more than 20% of contemporary myxobacterial genes [49]. It is possible that TCSs are particularly abundant in the fruiting regulatory network because they are better able than other regulators to tolerate changes to network architecture and to engage in complex interactions with multiple partner regulators. In contrast to the fruiting body formation network, the Car system of _M. xanthus_ is essentially a linear signalling pathway, reliant on the sequential action of different categories of regulators. Unsurprisingly, all Car pathway genes are conserved in all genomes analysed (Figure 3, Supplementary Table S2). Such a pattern of conservation implies that the Car pathway regulates a phenotype with a strong selective advantage. Absence of carotenoid biosynthesis would make cells sensitive to singlet oxygen-mediated damage, resulting in death and a clear selective pressure. But, presumably, the metabolic costs of producing photoprotective carotenoids constitutively are also high enough to make retention of the signalling pathway evolutionarily favourable. Myxobacteria are generally considered to not produce the AHLs that mediate QS in diverse Gram-negative bacteria, although recently, a cryptic myxobacterial gene resembling an AHL synthase (_agpl_) was identified in the myxobacterium _Archangium gephyma_[50]. The _agpl_ gene was found to be able to induce production of AHLs in _Escherichia coli_, suggesting that Agpl may play a role in disrupting communication between prey. In addition, exogenously added AHLs have been found to promote the predatory behaviours of _M. xanthus_[26], suggesting that myxobacteria might eavesdrop on their prey. The conservation of an AHL cyclase suggests that active disruption of prey AHL-mediated QS might be a common behaviour of predatory myxobacteria. Conservation of CAI-I synthase homologues suggests that myxobacteria may communicate amongst themselves via this form of QS, while the occasional strain may also be able to use alternative QS molecules (Figure 3, Supplementary Table S2). CAI-I signalling has been most commonly associated with marine bacteria, and diverse chemical variants of CAI-I have been described [25; 51]. We predict that myxobacteria generally produce CAI-I variants and note that 90% of _Coralococcus_ spp. type strains are predicted by antiSMASH 5 to produce homoserine lactones and/or butylactones, with the latter being QS molecules associated with the phylum Actinobacteria [7; 52]. Further studies on QS in myxobacteria are needed to unravel what is likely to be a pervasive but idiosyncratic feature of their biology. Clearly, different types of signalling pathways and behaviours exhibit differing patterns of gene conservation. For some pathways (e.g., the Car pathway), every component gene is highly conserved, some (e.g., fruiting body formation) are largely conserved but particular genes are dispensable, while others are present sporadically within a taxon (e.g., AI-I and AI-II synthases). As well as the structure of the pathway (modular vs. linear) and its evolutionary robustness, the pattern of conservation is also likely to be affected by the number of genetic loci over which the regulatory genes are found. For example, pathways present at single loci (e.g., QS pathways) can be acquired/lost in their entirety by single mutagenic events, whereas networks comprising large numbers of components encoded at multiple loci (e.g., fruiting body formation) are more likely to gain/lose sub-components rather than entire modules. The availability of genome sequences means that knowledge gained by researching the molecular genetics of one model bacterium can be easily translated onto another organism by comparing their gene sets.