Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors

Abstract

As an important model for transmembrane signaling, methylaccepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N-and Cterminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.chemotaxis ͉ methyl-accepting chemotaxis protein ͉ signal transduction

Bacterial chemoreceptors: high-performance signaling in networked arrays

“…Sequence comparisons of >2000 chemoreceptors from 152 species revealed high conservation for 10 of 11 principal trimer contact residues across all families [7]. The one exceptional site (residue 373 in Tsr) is a phenylalanine in the E. coli chemoreceptor …”

“…The resulting interplay between motor control and sensory adaptation produces directed motile behavior. E. coli chemoreceptors are the most extensively studied representatives of the MCP super-family, central components of homologous systems that mediate tactic responses [5,6] across the phylogenetic diversity of bacteria and archaea [7].In E. coli chemotaxis proteins cluster in membrane-associated patches [8]. Interaction within patches is thought to contribute to notable features of the signaling system: high sensitivity, wide dynamic range, extensive cooperativity and precise adaptation.…”

“…For instance, the kinase control modules of chemoreceptors from E. coli and from the evolutionarily distant species, Thermotoga maritima, are both anti-parallel, four-helix bundles formed by the dimerization of helical hairpins [25,34]. Impressively, recent analysis of >2000 kinase control module sequences from ~150 species revealed an orderly pattern of sequence relatedness [7]. Seven major receptor classes were distinguished by pairs of heptad (sevenresidue) insertions or deletions symmetrically placed on each side of the membrane-distal hairpin turn, thus preserving register and packing of the coiled-coil.…”

“…Figure I). The residues promoting dimer-dimer interactions in the trimer are highly conserved throughout the MCP superfamily [7] and are identical in the five E. coli receptors. These structural features suggested that trimer formation might be important for receptor function and that E. coli receptors of different types might form mixed trimers-of-dimers in vivo.…”

“…Conformational signals in the kinase control module are transmitted by rearrangements of helix-helix contacts at the subunit interface (see text for details). The carboxyl terminus of some receptors carries a conserved pentapeptide sequence (NWETF or NWESF in the single-letter amino acid code) that interacts with the two enzymes of adaptational modification (CheR and CheB) and enhances the rates of the reactions they catalyze [69,70].The sequence and 3D structure of kinase control modules are conserved across the diversity of bacteria and archaea [7]. Sequence conservation is more subtle among HAMP modules [42,45] but 3D structure is probably shared for the approximately two-thirds of all chemoreceptors that contain the module [43].…”