A long term goal of this project is to understand the assembly, control, and function of nucleoprotein complexes that promote Hin-catalyzed site-specific DNA inversion. Work during the past funding period established the overall structure of the tetrameric catalytic core of the Hin synaptic complex, provided strong evidence that recombination of DNA strands was mediated by rotation of Hin subunit pairs within the tetramer, and showed how the Fis/enhancer system together with DNA supercoiling controls subunit rotation. Future work will entail an ensemble of genetic, biochemical, and structural approaches and will emphasize the mechanism by which the Fis/enhancer element activates initial reaction steps as well as controls the subunit rotation process. Mechanistic analysis will commence on an enzyme from a different class of serine recombinase, emphasizing its novel properties. A prominent theme of the project concerns the DNA binding properties and regulatory roles of nucleoid proteins on recombination and transcription reactions. New aspect on the control of phage lambda site specific recombination by nucleoid proteins will be pursued. X- ray crystal structure analyses of complexes bound by the nucleoid protein Fis will be extended to higher- order complexes which contain the phage lambda Xis protein and the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD). These structural studies will provide new information on the role of DNA conformational flexibility on indirect recognition and cooperative DNA binding by proteins. Cellular Fis levels vary enormously with respect to growth phase and growth rates, being the most abundant DNA binding protein in E. coli under rapid growth conditions but virtually absent in stationary phase. Mechanisms of transcriptional regulation by Fis through specific and non-specific DNA binding will be investigated. Recent in vitro evidence suggests Fis may play an important role in modulating chromosome structure because of its DNA-bending and looping activities. Fis effects on chromosome structure will be addressed by a combination of in vivo and in vitro approaches, including collaborative single-DNA molecule approaches as well as by bulk-phase in vitro and in vivo experiments.

Public Health Relevance

This research aims to understand the mechanism and control of specialized DNA recombination reactions, particulariy those of the less well understood serine recombinase family. A broader goal is to understand how abundant non-histone DNA binding and bending proteins modulate chromosome structure and control DNA recombination and gene expression.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
Project #
Application #
Study Section
Special Emphasis Panel (NSS)
Program Officer
Janes, Daniel E
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Los Angeles
Schools of Medicine
Los Angeles
United States
Zip Code
Mandali, Sridhar; Dhar, Gautam; Avliyakulov, Nuraly K et al. (2013) The site-specific integration reaction of Listeria phage A118 integrase, a serine recombinase. Mob DNA 4:2
Hancock, Stephen P; Ghane, Tahereh; Cascio, Duilio et al. (2013) Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucleic Acids Res 41:6750-60
Nafissi, Maryam; Chau, Jeannette; Xu, Jimin et al. (2012) Robust translation of the nucleoid protein Fis requires a remote upstream AU element and is enhanced by RNA secondary structure. J Bacteriol 194:2458-69
Xiao, Botao; Zhang, Houyin; Johnson, Reid C et al. (2011) Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation. Nucleic Acids Res 39:5568-77
Graham, John S; Johnson, Reid C; Marko, John F (2011) Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res 39:2249-59
Heiss, John K; Sanders, Erin R; Johnson, Reid C (2011) Intrasubunit and intersubunit interactions controlling assembly of active synaptic complexes during Hin-catalyzed DNA recombination. J Mol Biol 411:744-64
Graham, John S; Johnson, Reid C; Marko, John F (2011) Counting proteins bound to a single DNA molecule. Biochem Biophys Res Commun 415:131-4
Xiao, Botao; Johnson, Reid C; Marko, John F (2010) Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res 38:6176-85
Stella, Stefano; Cascio, Duilio; Johnson, Reid C (2010) The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev 24:814-26
Dowell, Noah L; Sperling, Adam S; Mason, Michael J et al. (2010) Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription. Genes Dev 24:2031-42

Showing the most recent 10 out of 72 publications