Orthologous and paralogous FFRPs in E. coli and related proteobacteria

Feast/farnine regulatory proteins (FFRP) comprise a diverse family of transcription factors. Orthologues of types of eubacterial FFRPs, Lrp, AsnC, YbaO and TinR, were identified. Organisms having these FFRPs were found limited into smaller groups in succession: Lrp in the 0 and 7 subclasses of Proteobacteria, AsnC in the facultatively anaerobic order in the gamma subclass, YbaO in the same order in its Vibrionaceae and Enterobacteriaceae families only, and TinR in the species Salmonella enterica in the Enterobacteriaceae family. Yet in a distance map (i.e. an unrooted phylogenetic tree), e.g. TinR did not branch from the YbaO cluster, but the four FFRP groups remained outside to each other. These facts can be explained by assuming duplication of the ancestor gene of ybaO and tinR inside a common ancestor of Vibrionaceae and Enterobacteriaceae. One of the two genes was modified to ybaO, and the other was unused for a number of years until it adapted the new function of tinR inside S. enterica after diversification of Vibrionaceae and Enterobacteriaceae. Using various outgroups, the common root of the four FFRP types was localized to the connection between AsnC and the other three types, so that the second differentiation took place between Lrp and the common ancestor of YbaO and TinR.