Jeffrey F Gardner

Jeffrey F Gardner

Office: (217) 333-7287
Lab: (217) 333-7289

Mail to: Microbiology
601 S Goodwin
Urbana, IL 61801

Professor of Microbiology

Research Topics

Genetics, Protein-Nucleic Acid Interactions


B.A. (Biology), Boston University, 1969
Ph.D. (Biology), Marquette University, 1975
Postdoctoral (Biochemistry), University of Wisconsin, 1975-1977

Teaching Interests

Mechanism of site-specific recombination by bacteriophages and conjugative transposons; mechanisms of protein recognition of DNA

The research in my laboratory is centered around the genetics and biochemistry of DNA binding proteins. Three of the proteins we are studying are required for site-specific recombination by bacteriophage λ. One phage-encoded protein, Integrase (Int), participates in the formation of a higher-order protein-DNA complex called the intasome and performs the strand exchanges that form recombinant products. We have isolated mutants that produce Int proteins that are defective in performing distinct steps in the recombination pathway such as intasome formation, synapsis, and strand exchange. The mutant proteins are currently being used to carry out biochemical analyses of the recombination reaction and to construct a structure-function map of Int protein. We are also using a genetic approach to isolate Int mutants that bind altered recognition sites to determine which amino acid residues interact with DNA.

A second phage-encoded protein, Xis, is required for excisive recombination. It participates in the formation of the excisive intasome by bending DNA and by binding cooperatively with Int to form the active recombinogenic complex. We have used a genetic approach to isolate xis mutants that are defective for excisive recombination in vivo. Our results have shown that the amino-terminal domain of Xis is required for DNA binding and that the carboxyl terminal domain is required for cooperative interactions with Int. Future studies will include studies on the mechanism of cooperativity between Xis and Int.

Integration Host Factor (IHF) is a host-encoded protein that is required for both integrative and excisive recombination. In addition, it participates in a variety of cellular processes such as gene expression and regulation, plasmid replication, and the movement of some transposable elements. IHF is a heterodimer that bends DNA when it binds. We have used a genetic approach to isolate IHF binding-site mutants and have used the information to determine which base-pairs in the recognition site are important for recognition by the protein. We have also used a genetic selection to isolate suppressor mutants in the genes that encode the IHF sub-units. The suppressors recognize variant IHF binding sites and the amino acids substituted are believed to be the ones that contact the DNA. We are currently using a biochemical approach towards characterizing the binding properties of the suppressor proteins. A future project involves X-Ray crystal structure analysis of suppressor IHF-DNA complexes.

Another project (in collaboration with Dr. A. Salyers, Department of Microbiology) is centered around site-specific recombination of conjugative transposons (CTns). CTns are large self-transmissible elements that excise from the host chromosome by site-specific recombination to form a circular intermediate. The circular intermediate is nicked at the transfer origin and a single stranded copy is transferred to the recipient cell. A double stranded circular intermediate is produced and integrated into the recipient's genome. CTns are important because they often carry genes that make cells resistant to antibiotics.

Current projects include determining target sites in recipient DNA, defining sites in CTn DNA that bind integrase and host factors, determining the identity of host factors, and developing in vitro recombination reactions to study the mechanism of recombination. We have been successful in developing an in vitro integration system that requires DNA substrates, integrase and host factors. Studies on excision are in progress.

Representative Publications

Keeton, C. M. and Gardner, J. F. (2012). “The Roles of Exc Protein and DNA Homology in the CTnDOT Excision Reaction.” J. Bacteriology (In Press).

Kim, S. and Gardner, J. F. (2011). “Resolution of Holliday Junction Recombination Intermediates by Wild Type and Mutant IntDOT Proteins.” J. Bacteriology 193: 1351 – 1358.

Laprise, J., Yoneji, S. and Gardner, J. (2009). “Homology-Dependent Interactions Determine the Order of Strand Exchange by IntDOT Recombinase.” Nucleic Acids Research 38, 958 – 969.

Kim, S., Swalla, B. M. and Gardner, J. F. (2009). “A Structure-Function Analysis of IntDOT.” J. Bacteriol. 192, 575 - 586.

Wood, M. M., DiChiara, J. M., Yoneji, S. and Gardner, J. F. (2010). “CTnDOT Integrase Interactions with Attachment Site DNA and the Control of Directionality of the Recombination Reaction.” J. Bacteriol. 192, 3934 – 3943.

Malanowska, K., Cioni. J., Swalla, B., Salyers, A. and Gardner, J. F. (2009) “Mutational Analysis and Homology-Based Modeling of the IntDOT Core-Binding Domain.”  J. Bacteriol. 191, 2330-2339.

Rajeev, L., Malanowska, C. and Gardner, J. F. (2009).  “Challenging a Paradigm:  The Role of Homology in Tyrosine Recombinase Reactions.”  MMBC 73, 300 – 309.

Rajeev, L., A. M. Segall, and J. F. Gardner. 2007. The Bacteroides NBU1 Integrase performs a homology independent strand exchange to form a Holliday junction intermediate. J Biol Chem 282:31228-31237.

Complete Publications List