In bacteria, the 450 kDa RNA polymerase (RNAP) holoenzyme, comprising the evolutionarily conserved catalytic core (subunit composition ?2??'?) combined with the initiation-specific ? subunit, directs transcription initiation. Bacterial transcription depends on a primary ? factor that is essential for viability, as well as alternative ?'s that control specific regulons. A major mechanism to control transcription initiation is through regulation of ? activity. Dramatic insights have come from structural studies of ?'s and holoenzymes. Nevertheless, many challenges remain. In this competing continuation, we propose studies to further our understanding of ? factor structure and function, and interactions with accessory factors. Specifically, we propose to: 1. Determine the structural basis for ? interactions with the -10 element in the initiation of promoter melting. We will determine crystal structures of complexes between ? and in vitro- selected DNA aptamers that mimic ?/-10 element interactions critical for promoter melting. 2. Map the position of E. coli ?701.1 on the RNAP holoenzyme during different stages of promoter open complex formation. A protein-protein crosslinking/mapping approach (guided by our new structure of ?1.1) will be used. The crosslinking-based data will be combined with existing FRET-based distance constraints to generate structural models of ?701.1 in the context of the RNAP holoenzyme in holoenzyme alone, as well as in closed and open promoter complexes. 3. Structurally and functionally characterize ?/anti-? complexes: Staphylococcal aureus phage G1 ORF67. S. aureus phage G1 ORF67 binds to S. aureus ?A domain 4 and is a potent inhibitor of S. aureus transcription. We will determine crystal structures of complexes between phage G1 ORF67 and S. aureus ?A domain 4, and functionally characterize the mechanism of G1 ORF67 inhibition of S. aureus transcription. 4. Determine the structural basis for ?N interactions with its promoter DNA. We will determine the crystal structure of a complex between Aquifex aeolicus ?N and promoter DNA.

Public Health Relevance

Transcription is the major control point of gene expression and RNA polymerase is the central enzyme of transcription. Our long term goal is to understand the mechanism of transcription and its regulation. We focus on highly characterized prokaryotic RNA polymerases, which have a high degree of conservation of structure and function from bacteria to man. The ? factors are the key regulators of bacterial transcription initiation. Defective transcription regulation underlies many disorders. For example, many oncoproteins are transcriptional activator proteins. Moreover, the bacterial RNA polymerase is a proven target for antimicrobials, such as rifampicin (or its derivatives), widely used in combination therapy to treat tuberculosis. 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
Feklistov, Andrey (2013) RNA polymerase: in search of promoters. Ann N Y Acad Sci 1293:25-32
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; Darst, Seth A (2013) Crystallographic analysis of an RNA polymerase ýý-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
Feklistov, Andrey; Darst, Seth A (2011) Structural basis for promoter-10 element recognition by the bacterial RNA polymerase ? subunit. Cell 147:1257-69
Twist, Kelly-Anne F; Campbell, Elizabeth A; Deighan, Padraig et al. (2011) Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the ?-subunit flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 108:19961-6
Devi, Pukhrambam Grihanjali; Campbell, Elizabeth A; Darst, Seth A et al. (2010) Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation. Mol Microbiol 75:607-22
Opalka, Natacha; Brown, Jesse; Lane, William J et al. (2010) Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 8:
Lane, William J; Darst, Seth A (2010) Molecular evolution of multisubunit RNA polymerases: structural analysis. J Mol Biol 395:686-704
Lane, William J; Darst, Seth A (2010) Molecular evolution of multisubunit RNA polymerases: sequence analysis. J Mol Biol 395:671-85
Feklistov, Andrey; Darst, Seth A (2009) Promoter recognition by bacterial alternative sigma factors: the price of high selectivity? Genes Dev 23:2371-5

Showing the most recent 10 out of 48 publications