PAS domains are widespread signal sensors that share a conserved three-dimensional αβ fold that consists of a central β-sheet flanked by several α- helices. The aerotaxis receptor Aer from Escherichia coli and the Aer2 chemoreceptor from Pseudomonas aeruginosa both contain PAS domains. Aer senses oxygen (O2) indirectly via an FAD cofactor bound to its PAS domain, while Aer2 directly binds O2 to its PAS b-type heme cofactor. The Aer and Aer2 PAS domains both interact with a signal transduction domain known as a HAMP domain. The PAS-HAMP arrangement differs between Aer and Aer2, with Aer- PAS residing adjacent to its HAMP domain, and Aer2-PAS being sandwiched linearly between three N-terminal and two C-terminal HAMP domains. The differences between these PAS-HAMP architectures raise the possibility of two different PAS-HAMP signaling mechanisms: a lateral PAS-HAMP signaling mechanism for Aer, and a linear PAS-HAMP signaling mechanism for Aer2. This dissertation focuses on uncovering the PAS-HAMP transduction mechanisms and clarifying the signaling of conserved residues in Aer and Aer2 PAS. In Aer, I determined that a region on the PAS β-scaffold was sequestered by direct interaction with the HAMP domain. These data support a novel lateral PAS-HAMP arrangement that is crucial for Aer signaling. In Aer2, I demonstrated that unique PAS domain residues are involved in heme-binding, oxygen-binding and PAS signal initiation. My data provide the first functional corroboration of the Aer2 PAS signaling mechanism previously proposed from structure. The work presented in this dissertation demonstrates two variations of PAS-HAMP signaling mechanisms, both involving a global conformational change of the PAS domain that is transmitted from the PAS β-scaffold to the HAMP domain. My Aer and Aer2 studies provide the first direct evidence that HAMP domains can be activated by either linear or lateral interaction with a sensor module. Studying PAS-HAMP signaling mechanisms will help in understanding how sensing domains activate chemosensory systems that are involved in the survival of both commensal and pathogenic bacteria.

LLU Discipline

Microbiology and Molecular Genetics


Basic Sciences


School of Medicine

First Advisor

Taylor, Barry L.

Second Advisor

Watts, Kyle J.

Third Advisor

Duerksen-Hughes, Penelope J.

Fourth Advisor

Herrmann, Paul

Fifth Advisor

Johnson, Mark S.

Sixth Advisor

Mohan, Subburaman

Degree Name

Doctor of Philosophy (PhD)

Degree Level


Year Degree Awarded


Date (Title Page)




Library of Congress/MESH Subject Headings

Bacteria - Pathogenicity; Bacteriology; Escherichia coli; Aer protein; Pseudomonas aeruginosa;

Subject - Local

PAS domains; Aerotaxis receptors; Signal transduction domain; Commensal bacteria; pathogenic bacteria



Page Count


Digital Format


Digital Publisher

Loma Linda University Libraries

Usage 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.


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Loma Linda University. Del E. Webb Memorial Library. University Archives