Microbiology

John R. Kirby, PhD

Portrait

Associate Professor of Microbiology

Contact Information

Office: 3-632 BSB
Iowa City, IA 52242
Office Phone: 319-335-7818

Lab: 3-615D BSB
Iowa City, IA 52242
Phone: 319-335-7938

Email: john-kirby@uiowa.edu
Web: Kirby Lab Website

Education

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

All Publications

Willett J, Tiwari N, Müller S, Hummels K, Houtman J, Fuentes E, Kirby J.  Specificity residues determine binding affinity for two-component signal transduction systems.  MBio.  2013 November 5. 4(6):pii: e00420-13.
[Link]

Schlievert P, Merriman J, Salgado-Pabón W, Mueller E, Spaulding A, Vu B, Chuang-Smith O, Kohler P, Kirby J.  Menaquinone analogs inhibit growth of bacterial pathogens.  Antimicrob Agents Chemother.  2013 November. 57(11):5432-7.
[Link]

Müller S, Willett J, Bahr S, Scott J, Wilson J, Darnell C, Vlamakis H, Kirby J.  Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.  Genome Announc.  2013 June 20. 1(3):pii: e00392-13.
[Link]

Müller S, Willett J, Bahr S, Darnell C, Hummels K, Dong C, Vlamakis H, Kirby J.  Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.  Genome Announc.  2013 May 9. 1(3):pii: e00217-13.
[Link]

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.
[Link]

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.
[Link]

Kirby J.  Designer bacteria degrades toxin.  Nat Chem Biol.  2010 June. 6(6):398-9.
[Link]

Berleman J, Kirby J.  Deciphering the hunting strategy of a bacterial wolfpack.  FEMS Microbiol Rev.  2009 September. 33(5):942-57.
[Link]

Scharf B, Aldridge P, Kirby J, Crane B.  Upward mobility and alternative lifestyles: a report from the 10th biennial meeting on Bacterial Locomotion and Signal Transduction.  Mol Microbiol.  2009 July. 73(1):5-19.
[Link]

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

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.
[Link]

Mignot T, Kirby J.  Genetic circuitry controlling motility behaviors of Myxococcus xanthus.  Bioessays.  2008 August. 30(8):733-43.
[Link]

Thomas S, Wagner R, Arakaki A, Skolnick J, Kirby J, Shimkets L, Sanford R, Löffler F.  The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria.  PLoS One.  2008 May 7. 3(5):e2103.
[Link]

Kirby J, Berleman J, Müller S, Li D, Scott J, Wilson J.  Chemosensory Signal Transduction Systems in Myxococcus xanthus.  ASM Press.  2008. 

Zusman D, Scott A, Yang Z, Kirby J.  Chemosensory pathways, motility and development in Myxococcus xanthus.  Nat Rev Microbiol.  2007 November. 5(11):862-72.
[Link]

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

Kirby J.  In vivo mutagenesis using EZ-Tn5.  Methods Enzymol.  2007. 421:17-21.
[Link]

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

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.
[Link]

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

Vlamakis H, Kirby J, Zusman D.  The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility.  Mol Microbiol.  2004 June. 52(6):1799-811.
[Link]

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.
[Link]

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.
[Link]

Kirby J, Kristich C, Saulmon M, Zimmer M, Garrity L, Zhulin I, Ordal G.  CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis.  Mol Microbiol.  2001 November. 42(3):573-85.
[Link]

Kirby J.  Chemotaxis genes, fibrils and PE taxis in Myxococcus xanthus.  Trends Microbiol.  2001 May. 9(5):205.
[Link]

Kirby J, Niewold T, Maloy S, Ordal G.  CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis.  Mol Microbiol.  2000 January. 35(1):44-57.
[Link]

Kirby J, Saulmon M, Kristich C, Ordal G.  CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis.  J Biol Chem.  1999 April 16. 274(16):11092-100.
[Link]

Ordal G, Kirby J.  Chemotaxis.  John Wiley & Sons, New York.  1999. 1:413-5.

Ordal G, Kirby J.  Methyltransferase.  John Wiley & Sons, New York.  1999. 3:1491-2.

Ordal G, Kirby J.  Protein Methylation.  John Wiley & Sons, New York.  1999. 3:1486-8.

Ordal G, Kirby J.  Transducer Proteins.  John Wiley & Sons, New York.  1999. 4:2593-995.

Kirby J, Kristich C, Feinberg S, Ordal G.  Methanol production during chemotaxis to amino acids in Bacillus subtilis.  Mol Microbiol.  1997 May. 24(4):869-78.
[Link]

Rasario M, Kirby J, Bochar D, Ordal G.  Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD.  Biochemistry.  1995 March 21. 34(11):3823-31.
[Link]

Kirsch M, Peters P, Hanlon D, Kirby J, Ordal G.  Chemotactic methylesterase promotes adaptation to high concentrations of attractant in Bacillus subtilis.  J Biol Chem.  1993 September 5. 268(25):18610-6.
[Link]

Thoelke M, Kirby J, Ordal G.  Novel methyl transfer during chemotaxis in Bacillus subtilis.  Biochemistry.  1989 June 27. 28(13):5585-9.
[Link]

Ordal G, Parker H, Kirby J.  Complementation and characterization of chemotaxis mutants of Bacillus subtilis.  J Bacteriol.  1985 November. 164(2):802-10.
[Link]

Date Last Modified: 07/31/2013 - 10:51:40