Dr. Reid Johnson's research focuses on gene expression and chromosome biology in bacteria and yeast.
A long-term project of Johnson's lab has been to elucidate the enzymatic and regulatory mechanisms involved in promoting inversion of a segment of DNA in the Salmonella chromosome. The inversion reaction switches the expression of flagellar antigens, allowing the bacterium to evade a host immune response. The reaction requires the activities of a specific recombinase (Hin), a recombinational enhancer system (mediated by the Fis protein) and the chromatin-associated HU protein. These components are assembled into an "invertasome" structure that is the catalytically-active intermediate in the reaction. Current emphasis focuses on determining the 3-D structure of the invertasome complex, the molecular events involved in catalytic activation of Hin by Fis and the conformational changes required for DNA exchange. Approaches include mutant selections and characterizations, site-directed crosslinking, fluorescence transfer assays, high resolution electron microscopy, footprinting of DNA and protein and molecular modeling using information derived from X-ray crystal structures.
Another project Johnson studies is the Fis protein. Under rapid growth conditions, the Fis protein is the most abundant transcriptional activator in E. coli. However, Fis levels are extremely low in stationary phase or poor nutrient growth conditions. Johnson and his colleagues have previously identified a number of genes controlled by Fis and want to extend this analysis using current DNA microarray technology in order to understand its role in regulating gene expression as a function of cell growth. The researchers have been intensively studying the mechanism of transcriptional activation by Fis. Current emphasis is on identifying the molecular contacts between Fis and RNA polymerase using genetic and biochemical methods as well as x-ray crystallography.
A third focus is on HMGB chromatin proteins in yeast. Johnson and his colleagues are studying the DNA binding properties and biological functions of HMGB chromatin proteins in S. cerevisiae. These abundant DNA bending proteins positively or negatively influence transcription at a subset of promoters. Johnson's current studies are aimed at identifying genes whose expression is co-regulated by HMGBs, elucidating how HMGB proteins influence transcription at these genes and identifying and determining the functional consequences of reversible protein modifications and their role in chromosome biology.
Selected Cancer-Related Publications:
Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson RC, Clubb RT. Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly. Proc Natl Acad Sci U S A. 2007; 104(7): 2109-14.
Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod SM, Marko JF, Johnson RC. Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. J Mol Biol. 2006; 364(4): 777-98.
Dai Y, Wong B, Yen YM, Oettinger MA, Kwon J, Johnson RC. Determinants of HMGB proteins required to promote RAG1/2-recombination signal sequence complex assembly and catalysis during V(D)J recombination. Mol Cell Biol. 2005; 25(11): 4413-25.
Dhar G, Sanders ER, Johnson RC. Architecture of the hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands. Cell. 2004; 119(1): 33-45.
Wong B, Masse JE, Yen YM, Giannikopoulos P, Feigon J, Johnson RC. Binding to cisplatin-modified DNA by the S. cerevisiae HMGB protein NHP6A. Biochemistry. 2002; 41:5404-5414.