This proposal focuses on transcription initiation and elongation by bacterial RNA polymerase (RNAP). Transcription initiation and elongation involve a series of steps: (i) RNAP binds to promoter DNA, yielding an RNAP-promoter closed complex; (ii) RNAP unwinds promoter DNA, yielding an RNAP-promoter open complex; (iii) RNAP synthesizes the first ~11 nucleotides of RNA as an RNAP-promoter initial transcribing complex, using a scrunching mechanism, in which RNAP remains stationary on promoter DNA and pulls in adjacent DNA in each nucleotide-addition cycle; and (iv) RNAP breaks its interactions with promoter DNA and synthesizes the remaining nucleotides of RNA as an RNAP-DNA elongation complex, using a stepping mechanism, in which RNAP moves forward on DNA in each nucleotide-addition cycle. Each of these steps is a potential target for transcriptional regulators Understanding transcription initiation, transcription elongation, and transcriptional regulation wil require defining the structural transitions in protein and DNA at each step, the kinetics of structural transitions, and the mechanisms by which regulators affect structural transitions. In the current period, we identified a new crystal form that enables high-resolution structural studies of the RNAP-promoter open complex (RPo) and the RNAP-promoter initial transcribing complex (RPitc), we determined the first high-resolution structure of RPo, and we delineated a DNA sequence element recognized by RNAP (the core recognition element, CRE). In other work in the current period, we developed a single-molecule-fluorescence assay that enables the monitoring of RNAP clamp conformation in solution, and we defined RNAP clamp conformation at each step in transcription initiation. The proposed work will build on the findings of the curret period. The proposed work will use x-ray crystallography, single-molecule biophysics, biochemistry, and genetics to address five specific aims:
Specific Aim 1 : Determination of the structural basis of de novo transcription initiation Specific Aim 2: Determination of the structura basis of initial transcription Specific Aim 3: Analysis of RNAP-CRE interactions in transcription initiation Specific Aim 4: Analysis of RNAP-CRE interactions in transcription elongation Specific Aim 5: Analysis of RNAP clamp conformation in transcription elongation The results will contribute to understanding bacterial transcription and transcriptional regulation, and will contribute to design and synthesis of small-molecule inhibitors of bacterial transcription, for use in antibacterial therapy. Since bacterial RNAP shows sequence, structural, and mechanistic similarities to eukaryotic RNAP, the results also will contribute to understanding eukaryotic transcription and transcriptional regulation.

Public Health Relevance

Bacterial RNA polymerase (RNAP) is a molecular machine that carries out reactions essential for bacterial gene expression and bacterial growth. Two classes of current antibacterial drugs function by inhibiting RNAP. The proposed work will provide information essential for understanding the mechanism of action of RNAP and for rational design of improved and novel antibacterial drugs that function by inhibiting RNAP.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
Project #
Application #
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Rutgers University
Organized Research Units
United States
Zip Code
Winkelman, Jared T; Vvedenskaya, Irina O; Zhang, Yuanchao et al. (2016) Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science 351:1090-3
Vvedenskaya, Irina O; Vahedian-Movahed, Hanif; Zhang, Yuanchao et al. (2016) Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. Proc Natl Acad Sci U S A 113:E2899-905
Bird, Jeremy G; Zhang, Yu; Tian, Yuan et al. (2016) The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 535:444-7
Feng, Yu; Zhang, Yu; Ebright, Richard H (2016) Structural basis of transcription activation. Science 352:1330-3
Chakraborty, Anirban; Mazumder, Abhishek; Lin, Miaoxin et al. (2015) Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation. Methods Mol Biol 1276:101-31
Vvedenskaya, Irina O; Zhang, Yuanchao; Goldman, Seth R et al. (2015) Massively Systematic Transcript End Readout, ""MASTER"": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. Mol Cell 60:953-65
Hassan, Hossam M; Degen, David; Jang, Kyoung Hwa et al. (2015) Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp. J Antibiot (Tokyo) 68:206-9
Feng, Yu; Degen, David; Wang, Xinyue et al. (2015) Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure 23:1470-81
Degen, David; Feng, Yu; Zhang, Yu et al. (2014) Transcription inhibition by the depsipeptide antibiotic salinamide A. Elife 3:e02451
Tang, Wufeng; Liu, Shuang; Degen, David et al. (2014) Synthesis and evaluation of novel analogues of ripostatins. Chemistry 20:12310-9

Showing the most recent 10 out of 19 publications