The difference between what an organism can do (genetic potential) and what it actually does (phenotype) is often regulated at the level of transcription. Our laboratory studies Bacillus subtilis, a Gram-positive soil bacterium and genetic model system. We are interested in the global patterns of transcriptional control and the mechanisms of the corresponding regulatory proteins and pathways.
Antibiotics that act on the cell envelope (including vancomycin and bacitracin) trigger global stress responses coordinated, in part, by alternative sigma subunits for RNA polymerase. Some of the genes induced by antibiotic stress play a direct role in antibiotic resistance, a growing problem among Gram positive pathogens.
Exposure of cells to reactive oxygen and nitrogen species (such as hydrogen peroxide, superoxide, and nitric oxide) induces the expression of multiple regulons coordinated by several different transcription factors. For example, we have described both PerR and OhrR as regulators that directly sense reactive oxygen species. Resistance to oxidative and nitrosative stress is important for many bacterial pathogens.
Metal ion homeostasis
To grow in the complex and varied environment of the soil, B. subtilis must be able to obtain all essential metal ions while at the same time excluding (or actively effluxing) toxic metal ions. We have described transcription factors that directly sense Fe(II), Mn(II), Zn(II), and Cu(I) and regulate the expression of the corresponding uptake and/or efflux systems.
Students in our laboratory can expect to gain experience in a wide range of techniques as applied to this model genetic system. Most research projects will include some or all of the following:
- genomics: whole-genome resequencing, TnSeq, ChIP-seq, computer-based approaches to defining regulons
- transcriptomics (RNA-seq) and metabolomics
- classical genetics: mariner mutagenesis, forward genetics, transformation, transduction
- molecular genetics: CRISPR-gene editing, site-directed and PCR-based mutagenesis
- biochemistry: protein purification, in vitro transcription, enzyme assays