Transcription is the major control point of gene expression and RNA polymerase (RNAP), conserved from bacteria to man, is the central enzyme of transcription. Our long term goal is to understand the mechanism of transcription and its regulation. Determining three-dimensional structures of RNAP and its complexes with DNA, RNA, and regulatory factors, is an essential step. We focus on highly characterized prokaryotic RNAPs. To this end, we bring to bear a combined biochemical and biophysical approach. Here we propose structure/function studies of transcription complexes in different stages of the transcription cycle, aimed towards adding to our understanding of RNAP regulation by the product of transcription itself, RNA. Specifically, we propose to: 1. Use X-ray crystallography to determine high-resolution structures of Thermus RNAP paused transcription complexes, with and without NusA or NusA domains, at the his pause site. Transcriptional pausing plays key roles in the regulation of gene expression by coordinating RNAP with other regulatory events. Transcriptional pausing couples transcription and translation to control the expression of many amino acid biosynthesis operons in a process called attenuation. These regulatory pauses, such as at the his pause site, are stabilized by an RNA hairpin that forms in the just transcribed RNA transcript, likely through an allosteric mechanism. In addition, extrinsic factors, such as the conserved elongation factor NusA, can further stabilize the pause. We've crystallized a paused elongation complex and collected diffraction data to 3.8 E-resolution. Further experiments are proposed to i) improve the resolution limit of these crystals, ii) trap additional relevant conformational states of the paused complex, and iii) crystallize a complex containing NusA or NusA domains. 2. Structurally characterize the 6S RNA/RNAP-holoenzyme complex. The 6S RNA, a key player in the response of the bacterial transcriptional program to nutrient limitation in stationary phase, binds with marked specificity to C70-holoenzyme and inhibits its function. The 6S RNA mimics the DNA in an open promoter complex, and can serve as a transcription template, providing a mechanism for releasing the 6S RNA when nutrients become plentiful. We will: i) Use biochemical and biophysical approaches to map E. coli C70-holoenzyme interactions with 6S RNA, ii) Use X-ray crystallography to determine structures of 6S RNA/RNAP-holoenzyme complexes.

Public Health Relevance

We focus on highly characterized bacterial RNA polymerases, which have a high degree of conservation of structure and function from bacteria to man. The bacterial RNA polymerase is a proven target for antimicrobials, such as rifampicin (or its derivatives), widely used in combination therapy to treat tuberculosis, but bacterial strains resistant to rifampicin arise with appreciable frequency, compromising treatment. Insights into the mechanism of bacterial transcription can lead to new avenues for the development of antimicrobials.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Flicker, Paula F
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Rockefeller University
Other Domestic Higher Education
New York
United States
Zip Code
Bae, Brian; Nayak, Dhananjaya; Ray, Ananya et al. (2015) CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. Proc Natl Acad Sci U S A 112:E4178-87
Hein, Pyae P; Kolb, Kellie E; Windgassen, Tricia et al. (2014) RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement. Nat Struct Mol Biol 21:794-802
Weixlbaumer, Albert; Leon, Katherine; Landick, Robert et al. (2013) Structural basis of transcriptional pausing in bacteria. Cell 152:431-41