Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex

Abstract

Escherichia coli and Salmonella enterica are models for many experiments in molecular biology including chemotaxis, and most of the results obtained with one organism have been generalized to another. While most components of the chemotaxis pathway are strongly conserved between the two species, Salmonella genomes contain some chemoreceptors and an additional protein, CheV, that are not found in E. coli. The role of CheV was examined in distantly related species Bacillus subtilis and Helicobacter pylori, but its role in bacterial chemotaxis is still not well understood. We tested a hypothesis that in enterobacteria CheV functions as an additional adaptor linking the CheA kinase to certain types of chemoreceptors that cannot be effectively accommodated by the universal adaptor CheW. Phylogenetic profiling, genomic context and comparative protein sequence analyses suggested that CheV interacts with specific domains of CheA and chemoreceptors from an orthologous group exemplified by the Salmonella McpC protein. Structural consideration of the conservation patterns suggests that CheV and CheW share the same binding spot on the chemoreceptor structure, but have some affinity bias towards chemoreceptors from different orthologous groups. Finally, published experimental results and data newly obtained via comparative genomics support the idea that CheV functions as a “phosphate sink” possibly to off-set the over-stimulation of the kinase by certain types of chemoreceptors. Overall, our results strongly suggest that CheV is an additional adaptor for accommodating specific chemoreceptors within the chemotaxis signaling complex.

Cooperation of two distinct coupling proteins creates chemosensory network connections

“…CheW, however, had a greater ability to activate CheA than CheV1. This observation is consistent with the data presented by Ortega and Zhulin that CheV proteins limit CheA kinase output and thus can function with chemoreceptors that have a high intrinsic ability to activate CheA (17). These authors proposed that this limitation is due to CheV acting as a phosphate sink, a protein that can be phosphorylated by CheA to direct phosphates away from other targets (17).…”

“…Because of the high degree of similarity and the fact that TlpD is soluble in its full-length form, we used TlpD to characterize chemoreceptor-coupling protein interactions. It is possible, however, that CheW and CheV1 interact with the other chemoreceptors with varying strength or preference (7,17). Finally, we saw that both CheV1 and CheW interacted with each other (Fig.…”

“…This finding sheds light on why cheV1 and cheW mutants are nonchemotactic, whereas both proteins are capable of typical coupling protein functions as we show here. Large chemosensory arrays are critical for chemotaxis because they allow the high positive cooperativity (Hill coefficients of [15][16][17][18][19][20], a property that underlies the high sensitivity and ability to amplify the chemotaxis system's response to ligands (3,8,35). Indeed, isolated core chemoreceptor-CheW-CheA signaling complexes are able to regulate CheA but with little positive cooperativity (36).…”

“…Our work suggests that some microbes have altered CheW such that the array-forming function is split between two coupling proteins. Indeed, the residues that form interface 2 are conserved among enteric CheW but not among CheW as a whole (7,17). Other support comes from models that suggested complexes lacking CheA and having only CheW-socalled CheW-only linkers-create high cooperativity in signal sensing (38).…”

“…There is evidence suggesting that some chemoreceptors might operate with particular coupling proteins, displaying greater affinity for one coupling protein than for another (15,16). CheW and CheV may also have some affinity bias toward different chemoreceptors (17).…”