Our laboratory uses bacteria to study fundamental mechanisms of transcription regulation, as well as the biology of prions. With an emphasis on the development of genetic tools, our work also encompasses biochemical, structural and microscopy-based approaches.
Transcription by the multi-subunit RNA polymerases is a complex process consisting of multiple steps at which regulation can occur. To understand the relevant molecular interactions and regulatory mechanisms, we are taking advantage of the relative simplicity of the prokaryotic transcription machinery and the power of bacterial genetics. The RNA polymerase (RNAP) core enzyme is evolutionarily conserved from bacteria to man, as has been strikingly confirmed by crystallographic studies. Accordingly, insights into the function of the bacterial enzyme are likely to be relevant to the function of all multi-subunit RNAPs. Current work is focused particularly on regulatory mechanisms that target post-initiation stages of the transcription cycle. During the course of our transcription studies, we have developed a number of broadly applicable genetic assays for studying protein-protein interactions, including a widely used transcription-based bacterial two-hybrid assay that has facilitated a variety of projects in the lab.
A second project in the lab is focused on prions and protein-based heredity. Prions are infectious, self-propagating protein aggregates that are notorious for causing devastating neurodegenerative diseases in mammals. They have also been described in fungi, where they act as protein-based genetic elements. Despite the apparent conservation of prions in evolutionarily divergent members of the fungal Kingdom, prions were not known to exist in bacteria. Having first demonstrated that E. coli cells have the requisite molecular machinery to propagate a model yeast prion, we recently uncovered a bacterial prion-forming protein, the transcription termination factor Rho of Clostridium botulinum. At the same time, we have developed a set of genetic tools for detecting the conformational transitions that are diagnostic of prion formation. The identification of a bacterial protein with the ability to propagate as a prion points to a previously unrecognized source of epigenetic diversity in bacteria, and current work is directed at investigating the scope of prion-like phenomena in bacteria.
McPartland L, Heller DM, Eisenberg DS, Hochschild A*, Sawaya MR*. Atomic Insights into the genesis of cellular filaments by globular proteins. Nature Structural and Molecular Biology, 2018, in press.
Yuan AH, Hochschild A. A bacterial global regulator forms a prion. Science 2017; 355:198-201.
Berry KE, Hochschild A. A bacterial three-hybrid assay detects Escherichia coli Hfq-sRNA interactions in vivo. Nucleic Acids Res 2017; doi: 10.1093/nar/gkx1086
Heller DM, Tavag M, Hochschild A. CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB. PLoS Genet 2017; 13(9):e1007007
Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. The primary sigma factor can access the transcription elongation complex from solution in vivo. eLife 2015, 4: e10514.
Yuan AH, Garrity SJ, Nako E, Hochschild A. Prion propagation can occur in a prokaryote and requires the ClpB chaperone. eLife 2014; 3: e02949.
Sivanathan V and Hochschild A. Generating extracellular amyloid aggregates using E. coli cells. Genes Dev 2012; 26:2659-2667.