Escherichia coli utilizes the Aer protein to sense changes in the intracellular energy level and guide the bacteria to a niche where the cellular energy level is optimal. Aer contains a PAS sensory domain and an FI fragment in the N terminus and a chemotaxis signaling domain in the C terminus, separated by a putative transmembrane region. In this dissertation, I report that the linker region of Aer (residues 205-265), which joins the transmembrane region to the signaling domain, is a conserved signal transduction module in numerous methyl-accepting chemoreceptors, histidine kinases, adenylyl cyclases, and other sensory proteins in all three domains of life. The linker region is re-designated as a “HAMP” domain that might mediate sensing, propagation of transmembrane signals, or protein-protein interactions.
The Aer HAMP domain was essential for aerotaxis signaling. Deletion of part of the Aer HAMP domain eliminated binding of the FAD cofactor to the PAS domain and abolished aerotactic responses. An overexpressed Aer HAMP domain fragment inhibited Aer-mediated responses. Mutagenesis of the Aer HAMP domain identified essential residues for aerotaxis signaling. In the region 230-249, the AerV230D, R235C, R235E, L239Q, L239R, L241P, Q248R, and L249P mutations individually abolished FAD binding and thus, aerotaxis signaling. The D259H, V260A, S262G, and S265P mutations abolished responses but not FAD binding. The AerV264M mutation inverted aerotactic responses. Mutants with a novel “super swarming” phenotype were also identified. The mechanism by which the mutations interfered with aerotaxis signaling was studied. The Aer HAMP domain is proposed to contain three amphipathic helices. The first amphipathic sequence (residues 207-233) was required for proper folding of the N terminus of Aer. Mutations that abolished FAD binding were clustered in the second putative amphipathic helix (residues 234-251), whereas mutations in the third amphipathic helix did not abolish FAD binding. Based on these findings I propose a role for the Aer HAMP domain in aerotaxis signal transduction. Namely, subdomain 1 stabilizes folding of the N terminus and maintains membrane topology of the protein. Subdomain 2 interacts with the PAS domain and/or FI region to stabilize the FADbinding conformation and receives sensory signals. Subdomain 3 mediates dimerization and signal transduction from the HAMP domain to the signaling domain.
","abstract_html":"<p><em>Escherichia coli</em> utilizes the Aer protein to sense changes in the intracellular energy level and guide the bacteria to a niche where the cellular energy level is optimal. Aer contains a PAS sensory domain and an FI fragment in the N terminus and a chemotaxis signaling domain in the C terminus, separated by a putative transmembrane region. In this dissertation, I report that the linker region of Aer (residues 205-265), which joins the transmembrane region to the signaling domain, is a conserved signal transduction module in numerous methyl-accepting chemoreceptors, histidine kinases, adenylyl cyclases, and other sensory proteins in all three domains of life. The linker region is re-designated as a “HAMP” domain that might mediate sensing, propagation of transmembrane signals, or protein-protein interactions.</p> <p>The Aer HAMP domain was essential for aerotaxis signaling. Deletion of part of the Aer HAMP domain eliminated binding of the FAD cofactor to the PAS domain and abolished aerotactic responses. An overexpressed Aer HAMP domain fragment inhibited Aer-mediated responses. Mutagenesis of the Aer HAMP domain identified essential residues for aerotaxis signaling. In the region 230-249, the AerV230D, R235C, R235E, L239Q, L239R, L241P, Q248R, and L249P mutations individually abolished FAD binding and thus, aerotaxis signaling. The D259H, V260A, S262G, and S265P mutations abolished responses but not FAD binding. The AerV264M mutation inverted aerotactic responses. Mutants with a novel “super swarming” phenotype were also identified. The mechanism by which the mutations interfered with aerotaxis signaling was studied. The Aer HAMP domain is proposed to contain three amphipathic helices. The first amphipathic sequence (residues 207-233) was required for proper folding of the N terminus of Aer. Mutations that abolished FAD binding were clustered in the second putative amphipathic helix (residues 234-251), whereas mutations in the third amphipathic helix did not abolish FAD binding. Based on these findings I propose a role for the Aer HAMP domain in aerotaxis signal transduction. Namely, subdomain 1 stabilizes folding of the N terminus and maintains membrane topology of the protein. Subdomain 2 interacts with the PAS domain and/or FI region to stabilize the FADbinding conformation and receives sensory signals. Subdomain 3 mediates dimerization and signal transduction from the HAMP domain to the signaling domain.</p>","abstract_has_math":false,"creators":["Ma, Qinhong"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Dissertation","degree_discipline":"Microbiology, Molecular Biology and Biochemistry","degree_department":null,"school":null,"contributors":["Barry L. Taylor","Carlos A. Casiano","Hansel M. Fletcher","Mark S. Johnson","Jolinda A. Traugh"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2001,"date_issued":"2001-12-01T08:00:00Z","date_published":"2001-12-01T08:00:00Z","updated_at":"2026-07-24T02:53:08Z","subjects":["Microbiology","Molecular Genetics","Aerobiosis; Bacteria -- enzymology; Escherichia coli -- metabolism; Protein Structure, tertiary; Signal transduction -- physiology; Reverse Transcriptions; Electrons; Carrier Proteins -- genetics; Models, Molecular; Protein Binding"],"languages":["English"],"rights":["This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarsrepository.llu.edu/etd/722","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Barry L. Taylor","Carlos A. Casiano","Hansel M. Fletcher","Mark S. Johnson","Jolinda A. 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The author retains all other copyrights."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://scholarsrepository.llu.edu/etd/722"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Escherichia coli utilizes the Aer protein to sense changes in the intracellular energy level and guide the bacteria to a niche where the cellular energy level is optimal. Aer contains a PAS sensory domain and an FI fragment in the N terminus and a chemotaxis signaling domain in the C terminus, separated by a putative transmembrane region. In this dissertation, I report that the linker region of Aer (residues 205-265), which joins the transmembrane region to the signaling domain, is a conserved signal transduction module in numerous methyl-accepting chemoreceptors, histidine kinases, adenylyl cyclases, and other sensory proteins in all three domains of life. The linker region is re-designated as a “HAMP” domain that might mediate sensing, propagation of transmembrane signals, or protein-protein interactions.
The Aer HAMP domain was essential for aerotaxis signaling. Deletion of part of the Aer HAMP domain eliminated binding of the FAD cofactor to the PAS domain and abolished aerotactic responses. An overexpressed Aer HAMP domain fragment inhibited Aer-mediated responses. Mutagenesis of the Aer HAMP domain identified essential residues for aerotaxis signaling. In the region 230-249, the AerV230D, R235C, R235E, L239Q, L239R, L241P, Q248R, and L249P mutations individually abolished FAD binding and thus, aerotaxis signaling. The D259H, V260A, S262G, and S265P mutations abolished responses but not FAD binding. The AerV264M mutation inverted aerotactic responses. Mutants with a novel “super swarming” phenotype were also identified. The mechanism by which the mutations interfered with aerotaxis signaling was studied. The Aer HAMP domain is proposed to contain three amphipathic helices. The first amphipathic sequence (residues 207-233) was required for proper folding of the N terminus of Aer. Mutations that abolished FAD binding were clustered in the second putative amphipathic helix (residues 234-251), whereas mutations in the third amphipathic helix did not abolish FAD binding. Based on these findings I propose a role for the Aer HAMP domain in aerotaxis signal transduction. Namely, subdomain 1 stabilizes folding of the N terminus and maintains membrane topology of the protein. Subdomain 2 interacts with the PAS domain and/or FI region to stabilize the FADbinding conformation and receives sensory signals. Subdomain 3 mediates dimerization and signal transduction from the HAMP domain to the signaling domain.
"]},{"key":"dc:title","label":"Title","values":["HAMP Domain and Signaling Mechanism of the Aer Protein"]}]}],"canonical_facts":{"dc:contributor":["Barry L. Taylor","Carlos A. Casiano","Hansel M. Fletcher","Mark S. Johnson","Jolinda A. Traugh"],"dc:creator":["Ma, Qinhong"],"dc:description.abstract":["Escherichia coli utilizes the Aer protein to sense changes in the intracellular energy level and guide the bacteria to a niche where the cellular energy level is optimal. Aer contains a PAS sensory domain and an FI fragment in the N terminus and a chemotaxis signaling domain in the C terminus, separated by a putative transmembrane region. In this dissertation, I report that the linker region of Aer (residues 205-265), which joins the transmembrane region to the signaling domain, is a conserved signal transduction module in numerous methyl-accepting chemoreceptors, histidine kinases, adenylyl cyclases, and other sensory proteins in all three domains of life. The linker region is re-designated as a “HAMP” domain that might mediate sensing, propagation of transmembrane signals, or protein-protein interactions.
The Aer HAMP domain was essential for aerotaxis signaling. Deletion of part of the Aer HAMP domain eliminated binding of the FAD cofactor to the PAS domain and abolished aerotactic responses. An overexpressed Aer HAMP domain fragment inhibited Aer-mediated responses. Mutagenesis of the Aer HAMP domain identified essential residues for aerotaxis signaling. In the region 230-249, the AerV230D, R235C, R235E, L239Q, L239R, L241P, Q248R, and L249P mutations individually abolished FAD binding and thus, aerotaxis signaling. The D259H, V260A, S262G, and S265P mutations abolished responses but not FAD binding. The AerV264M mutation inverted aerotactic responses. Mutants with a novel “super swarming” phenotype were also identified. The mechanism by which the mutations interfered with aerotaxis signaling was studied. The Aer HAMP domain is proposed to contain three amphipathic helices. The first amphipathic sequence (residues 207-233) was required for proper folding of the N terminus of Aer. Mutations that abolished FAD binding were clustered in the second putative amphipathic helix (residues 234-251), whereas mutations in the third amphipathic helix did not abolish FAD binding. Based on these findings I propose a role for the Aer HAMP domain in aerotaxis signal transduction. Namely, subdomain 1 stabilizes folding of the N terminus and maintains membrane topology of the protein. Subdomain 2 interacts with the PAS domain and/or FI region to stabilize the FADbinding conformation and receives sensory signals. Subdomain 3 mediates dimerization and signal transduction from the HAMP domain to the signaling domain.
"],"dc:identifier":["https://scholarsrepository.llu.edu/etd/722"],"dc:language":["English"],"dc:rights":["This title appears here courtesy of the author, who has granted Loma Linda University a limited, non-exclusive right to make this publication available to the public. The author retains all other copyrights."],"dc:subject":["Microbiology","Molecular Genetics","Aerobiosis; Bacteria -- enzymology; Escherichia coli -- metabolism; Protein Structure, tertiary; Signal transduction -- physiology; Reverse Transcriptions; Electrons; Carrier Proteins -- genetics; Models, Molecular; Protein Binding"],"dc:title":["HAMP Domain and Signaling Mechanism of the Aer Protein"],"thesis:degree_discipline":["Microbiology, Molecular Biology and Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T02:53:08Z"}