# A Genomic Survey of Signalling in the Myxococcaceae
## 3 Results
### Conservation of Regulatory Proteins Involved in Key Myxococcaeal Behaviours  
To further investigate the evolution of regulatory networks in Myxococcaeal genomes, we assessed the conservation of regulatory proteins in three 'case studies' of myxobacterial behaviours: carotenoid synthesis, fruiting body formation and quorum sensing. The regulatory mechanisms underpinning each of these phenomena are well-described and involve different classes of regulatory proteins. Identification of homologues was undertaken using BLAST, using the _M. xanthus_ DK1622 protein as a query sequence (Supplementary Table S2).  
Supplementary Table S2 also shows the pattern of conservation of regulators involved in the three behaviours. Regulatory proteins were designated as 'absent' from a group of \(n\) genomes if no homologues were identified in at least \(n\)-1 genomes. If the same number of homologues were found in at least \(n\)-1 genomes, the protein was denoted 'constant', and if the numbers of homologues were different in at least two genomes, the protein was classified as 'variable'. Regulators were then classified as 'core' (if homologues were found to be present at a constant number in all groups of genomes), 'conserved' (if present but found in different numbers within groups or in different groups of genomes), or 'accessory' (if absent from at least one group of genomes, or at least two genomes within a 'variable' group of genomes). Figure 3 shows the pattern of conservation of regulatory proteins involved in carotenogenesis, fruiting body formation and QS.  
Figure 2: The percentage of RRs and TFs + OCSs found in the pan-genome core for the four groups of genomes.  
Figure 3: Conservation of signalling pathway proteins in Myxococcaceae. Regulatory proteins are shown as ovals. Positive regulation is shown with pointed arrows, and negative regulation with blunt-headed arrows. (**A**) Carotenoid production. In the dark (top), CarQ is held inactive by CarR, while CarA and CarH repress expression of the constitutively active _crt_ promoter. In the light (bottom), CarH is directly inactivated while CarF - inactivates CarR, releasing CarQ to direct transcription of  
carQRS_, producing CarS which binds to CarA, relieving repression of the crt genes, which encode enzymes for the biosynthesis of carotenoids (lycopene shown as an example). (**B**) Fruiting body formation. Gene products work together in modules (dark grey boxes). Starvation triggers the production of the secondary messengers c-di-GMP and (p)ppGpp and activates the EBP (enhancer binding protein) cascade and the Mrp module. The A-signalling, C-signalling, FruA and Nla24/DmxB modules are stimulated by secondary messengers and regulatory modules. Various 'development timer' proteins regulate the timing of fruiting, and the DevTRS/CRISPR module modulates the timing of sporulation. 'Other' proteins regulate fruiting, but their relationship to other modules is not clear. **(C)** Quorum signalling. Four common Gram-negative bacterial quorum signals (AI-I, AI-II, CAI-I and HAI-I), and their corresponding synthase and receptor/regulator proteins, are shown. Also shown is the quorum-quenching AHL acylase, PvdQ. Whether regulatory proteins are core, conserved, or dispensable, is indicated based on their pattern of evolutionary conservation. Core proteins are found at a constant number per genome across the Myxococcaceae and are highlighted in bold text. Conserved proteins are found in all groups of Myxococcaceae genomes, but in variable numbers, and are indicated with a pale grey background and dashed outline. Dispensable proteins are absent from some groups of Myxococcaeal genomes and are shown with a transparent background, and grey text.