Biosciences Graduate Program

John R. Kirby, PhD


Professor of Microbiology

Contact Information

Office: 3-632 Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Office Phone: 319-335-7818

Lab: 3-615D Bowen Science Building
51 Newton Rd
Iowa City, IA 52242
Phone: 319-335-7938

Web: Kirby Lab Website


BS, Biochemistry, University of Illinois Urbana-Champaign
PhD, Biochemistry, University of Illinois Urbana-Champaign

Post Doctoral, Molecular Cell Biology, University of California, Berkeley

Education/Training Program Affiliations

Biosciences Graduate Program
Department of Microbiology Graduate Program
Interdisciplinary Graduate Program in Genetics
Interdisciplinary Graduate Program in Translational Biomedicine
Medical Scientist Training Program

Research Summary

We are interested in chemosensory signal transduction systems that regulate motility and development in the bacterial model organisms, Myxococcus xanthus and Bacillus subtilis. Chemosensory systems are chemotaxis-like two component systems that regulate a variety of cellular functions ranging from flagellar based motility to sporulation.

Chemosensory regulation of Motility, Physiology & Development in M. xanthus. Analysis of signal transduction systems that allow cells to detect and mediate responses to environmental factors, including neighbor contact, is the major subject of investigation in our lab. M. xanthus is a soil bacterium that displays a multicellular life cycle. Cells feed on other organisms and form complex fruiting structures, culminating in spore production when starved. These processes require Type IV pilus-based motility and depend on chemotaxis and complex intercellular signaling. M. xanthus utilizes over 120 two-component systems, including eight homologous chemosensory signaling pathways to regulate its complex lifestyle. While some of these che homologs are involved in the regulation of motility and predation, others have been shown to affect a variety of cellular functions including gene expression and carotenoid biosynthesis. Our projects focus on the chemosensory regulation of gene expression, lipoprotein-dependent stress responses, type IV pilus assembly, and membrane composition.

Mechanism of Chemotaxis in Bacillus subtilis. Analysis of the B. subtilis chemotaxis system focuses our work on CheC, CheD, and CheV. Homologs to these proteins are not found in E. coli but are present in the majority of known chemotactic Bacteria and Archaea. Our projects include the characterization of CheD deamidase activity and HAMP domain interactions, targets and regulation of CheC phosphatase activity, and regulation of signaling by the unique receptor-kinase coupling protein, CheV. The broad distribution of CheC, CheD and CheV identified by genome sequencing allows us to conclude that B. subtilis is the best paradigm for the study of chemotaxis in prokaryotes.

Center, Program and Institute Affiliations

Center for Biocatalysis and Bioprocessing

Selected Publications

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Willett J, Kirby J.  Genetic and Biochemical Dissection of a HisKA Domain Identifies Residues Required Exclusively for Kinase and Phosphatase Activities.  PLoS Genet.  2012 November. 8(11):e1003084.

Willett J, Kirby J.  CrdS and CrdA comprise a two-component system that is cooperatively regulated by the Che3 chemosensory system in Myxococcus xanthus.  MBio.  2011 August 2. 2(4):e00110-11.

Kirby J.  Chemotaxis-like regulatory systems: unique roles in diverse bacteria.  Annu Rev Microbiol.  2009. 63:45-59.

Berleman J, Scott J, Chumley T, Kirby J.  Predataxis behavior in Myxococcus xanthus.  Proc Natl Acad Sci U S A.  2008 November 4. 105(44):17127-32.

Berleman J, Kirby J.  Multicellular development in Myxococcus xanthus is stimulated by predator-prey interactions.  J Bacteriol.  2007 August. 189(15):5675-82.

Berleman J, Chumley T, Cheung P, Kirby J.  Rippling is a predatory behavior in Myxococcus xanthus.  J Bacteriol.  2006 August. 188(16):5888-95.

Müller S, Shen H, Hofmann D, Schairer H, Kirby J.  Integration into the phage attachment site, attB, impairs multicellular differentiation in Stigmatella aurantiaca.  J Bacteriol.  2006 March. 188(5):1701-9.

Rao C, Kirby J, Arkin A.  Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles.  Phys Biol.  2005 July 14. 2(3):148-58.

Rao C, Kirby J, Arkin A.  Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis.  PLoS Biol.  2004 February. 2(2):E49.

Kirby J, Zusman D.  Chemosensory regulation of developmental gene expression in Myxococcus xanthus.  Proc Natl Acad Sci U S A.  2003 February 18. 100(4):2008-13.

Date Last Modified: 07/01/2014 - 08:36:00