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:
McLean MM, Chang Y, Dhar G, Heiss JK, Johnson RC. Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion. Elife. 2013 Oct 22;2:e01211. doi: 10.7554/eLife.01211.
Dowell NL, Sperling AS, Mason MJ, Johnson RC. Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription. Genes Dev. 2010 Sep 15;24(18):2031-42.
Stella S, Cascio D, Johnson RC. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Genes Dev. 2010 Apr 15;24(8):814-26. doi: 10.1101/gad.1900610.
Dhar G, Heiss JK, Johnson RC. Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination. Mol Cell. 2009 Jun 26;34(6):746-59.
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 Jun;25(11):4413-25.