In bacteria, the 450 kDa RNA polymerase (RNAP) holoenzyme, comprising the evolutionarily conserved catalytic core combined with the initiation-specific ? subunit, directs transcription initiation. Bacterial transcription depends on a primary factor that is essential for viability. In addition, most bacteria contain multiple alternative ?'sthat control regulons in response to environmental cues. The principal control point of gene expression in bacteria is transcription initiation, and a major mechanism by which bacteria regulate transcription initiation is through regulation of ? activity. Dramatic insights have come from structural studies of bacterial RNAPs. Nevertheless, many challenges remain, including understanding the complex process of transcription initiation and its control by ? factors and modulators of ?-factor function. Specifically, we propose to: 1. Determine the structural basis for the recognition of the -10 element by alternative ?'s. In the last project period, we determined high-resolution crystal structures of a primary ? bound to the - 10 element sequence. How do alternative ?'s recognize and facilitate melting of their cognate -10 elements, which bear no relationship to the primary ? -10 element? To address this question, we will determine structures of alternative ?'s bound to their -10 element sequence. 2. Structurally characterize the role of ?N region I in promoter recognition. The ?N family of ? factors (also called ?54) is evolutionarily unrelated to the ?70 family and functions through a distinct mechanism. In the last funding period, we determined crystal structures of ?N/promoter DNA complexes, but these structures lack the N-terminal ?N region I, which controls promoter melting. We will determine crystal structures of full-length ?N bound to promoter DNA constructs. 3. Determine the structure of a Sau phage G1 ORF67/Sau ?A4/DNA complex. In the last funding period, our studies revealed that ORF67 targets transcription in a promoter-specific manner by disrupting RNAP ?-subunit/UP-element interactions, but the molecular basis for how this is achieved was not clear from our ORF67/?A4 structures. To understand the molecular details of ORF67 function, we will determine the crystal structure of an ORF67/?A4/promoter DNA ternary complex. 4. Determine the structure of a new family of anti-?: Streptomyces venezuelae ?BldN/RsbN. An ECF ?/anti-? pair, ?BldN/RsbN, plays a critical role in the cellular differentiation of Streptomyces into aerial hyphae and spores. The biological cue sensed by RsbN to release ?BldN is unknown, and sequence analysis also indicates RsbN represent a new class of anti-?. A crystal structure of the ?BldN/RsbN complex will help address these questions.

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
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Sledjeski, Darren D
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
Wang, Guanshi; Hauver, Jesse; Thomas, Zachary et al. (2016) Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry. Cell 167:1839-1852.e21
Bae, Brian; Feklistov, Andrey; Lass-Napiorkowska, Agnieszka et al. (2015) Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife 4:
Hubin, Elizabeth A; Tabib-Salazar, Aline; Humphrey, Laurence J et al. (2015) Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA. Proc Natl Acad Sci U S A 112:7171-6
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
Osmundson, Joseph; Darst, Seth A (2013) Biochemical insights into the function of phage G1 gp67 in Staphylococcus aureus. Bacteriophage 3:e24767
Feklistov, Andrey; Darst, Seth A (2013) Crystallographic analysis of an RNA polymerase ?-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:950-5
Montero-Diez, Cristina; Deighan, Padraig; Osmundson, Joseph et al. (2013) Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system. J Bacteriol 195:3621-8
Feklistov, Andrey (2013) RNA polymerase: in search of promoters. Ann N Y Acad Sci 1293:25-32
Osmundson, Joseph; Dewell, Scott; Darst, Seth A (2013) RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PLoS One 8:e76572
Bae, Brian; Davis, Elizabeth; Brown, Daniel et al. (2013) Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of ?70 domain 1.1. Proc Natl Acad Sci U S A 110:19772-7

Showing the most recent 10 out of 56 publications