Assigning chemoreceptors to chemosensory pathways inPseudomonas aeruginosa

Abstract

In contrast to , a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein-protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor-pathway interactions.

Repurposing a macromolecular machine: Architecture and evolution of the F7 chemosensory system

“…We analysis predicts three chemosensory gene clusters, one each from the F6 (MEALZ_3148 -MEALZ_3158), F7 (MEALZ_2869-MEALZ_2879) and F8 classes (MEALZ_2939 -MEALZ_2942, Table S2). Cryo-ET of M. alcaliphilum revealed two array types: putative F6 arrays with 25.6±2.8 nm between the IM and the CheA/ CheW layer, as expected for 40H chemoreceptors (18), and, in 25% of cells, taller arrays with a distance of 35.1±2.8 nm between the IM and baseplate (Fig. 1D).…”

“…In cryotomograms of S. oneidensis cells grown anaerobically in batch culture, we observed a single membrane-bound array, usually located at the cell pole in close proximity to the single flagellar motor. The distance between the IM and the CheA/CheW baseplate was 24.5±2.7 nm, as expected for 40H chemoreceptors of the F6 system (18). When cells were grown anaerobically in continuous flow bioreactors, however, we observed the novel taller array type in ~10% of cells, often (but not always) at the same cell pole as the F6 array (Table S1).…”

“…S2 (some Xanthomonadales contained multiple copies of Aer2-like receptors in their F7 gene clusters, some Shewanellaceae lacked McpA-like receptors and none of the Enteric genomes had either). All 130 identified Aer2-like receptors belonged to the 36H heptad class, consistent with their belonging to F7 systems (9,18). The McpA-like receptors could not be assigned to a heptad class.…”

“…In contrast, 36H F7 Tar-like receptors have a periplasmic N-terminal sensor sandwiched by two transmembrane regions and a single HAMP domain (31). Interestingly, this topology is the same as that of the majority of 40H F6 receptors that control flagellar motility in γ-Proteobacteria with stage 1 and 2 F7 systems (18). Thus, the F7 system's takeover of the flagellar motor involved acquisition of a sensory input (an N-terminal periplasmic sensor domain) similar to that of the F6 system that used to control the motor.…”

“…MCPs are classified by length according to the number of heptad repeats they contain (17). The length of the shorter array (24 nm) corresponds to receptors belonging to the 40H class that is often associated with F6 systems (18,9), so we assume this array is the F6 system. The additional taller membrane-associated array, present in ~30% of the cells (Table S1), was often (but not always) found at the same cell pole as the putative F6 array and had a distance of 40.3±1.8 nm between the IM and the CheA/CheW baseplate (Fig.…”