Evolutionary analysis in Enterobacterales of the Rcs-repressor protein IgaA unveils two cytoplasmic small β-barrel domains central for function

Abstract

The Rcs sensor system, comprised by the proteins RcsB/RcsC/RcsD and RcsF, is used by bacteria of the order Enterobacterales to withstand envelope damage. Under non-stress conditions, the system is repressed by the membrane protein IgaA. How IgaA has evolved within Enterobacterales in concert with the Rcs system has not been explored. Here, we report phylogenetic data supporting co-evolution of IgaA with the inner membrane proteins RcsC and RcsD. Functional assays showed that IgaA from representative genera as Shigella and Dickeya, but not those from Yersinia or the endosymbionts Photorhabdus and Sodalis, repress the Rcs system when expressed in a heterogenous host like Salmonella enterica serovar Typhimurium. IgaA structural features have therefore diverged among Enterobacterales. Modelling of IgaA structure unveiled one periplasmic and two cytoplasmic β-rich architectures forming partially-closed small β barrel (SBB) domains related to OB (oligonucleotide/oligosaccharide binding motif) fold domains. Interactions among conserved residues were mapped in a connector linking SBB-1 domain of cytoplasmic region cyt1 to SBB 2 domain of region cyt2 (residues E180 R265); the C-terminus of cyt1 facing cyt2 (R188 E194-D309 and T191-H326); and, between cyt2-cyt3 regions (H293-E328-R686). These interactions identify a previously unnoticed "hybrid" SBB-2 domain. We also identified interactions absent in the IgaA variants not functional in S. Typhimurium, including H192-P249, which links cyt1 to cyt2, R255-D313 and D287 R314. A short α-helix (α6) located in the SSB-1 domain is also missing in the non-complementing IgaA tested. Taken together, our data support a central role of the two cytoplasmic SBB domains in IgaA function and evolution.