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Ebright, Richard H.

Position: 
Board of Governors Professor of Chemistry and Chemical Biology

Richard H. Ebright Phone: 848-445-5179
E-mail: E-mail
FAX: 732-445-5735
Office: Waksman Institute Braun Building 201-A
Mail: Waksman Institute, 190 Frelinghuysen Road, Piscataway NJ 08854
Education Links
  • A.B., 1981, Ph.D. 1987, Harvard
  • Harvard Junior Fellow 1984-1987

Research Summary

Transcription--the synthesis of an RNA copy of genetic information in DNA--is the first step in gene expression and is the step at which most regulation of gene expression occurs. Richard H. Ebright's laboratory seeks to understand structures, mechanisms, and regulation of bacterial transcription complexes and to identify, characterize, and develop small-molecule inhibitors of bacterial transcription for application as antituberculosis agents and broad-spectrum antibacterial agents.

Structures of Transcription Complexes

Transcription initiation in bacteria requires RNA polymerase (RNAP) and the transcription initiation factor sigma. The bacterial transcription initiation complex contains six polypeptides (five in RNAP, one in sigma) and promoter DNA, and has a molecular mass of 0.5 MDa.

Understanding bacterial transcription initiation requires understanding the structures of polypeptides in bacterial transcription initiation complexes and the arrangements of these polypeptides relative to each other and relative to promoter DNA.

The Ebright lab uses x-ray crystallography to determine high-resolution structures of transcription initiation complexes, fluorescence resonance energy transfer (FRET) to define distances between pairs of site specifically incorporated fluorescent probes, photocrosslinking to define polypeptides near site-specifically incorporated photocrosslinking probes, and protein footprinting and residue scanning to define residues involved in contacts. In support of these activities, the lab develops procedures to incorporate fluorescent probes, photocrosslinking probes, and other biophysical and biochemical probes at specific sites within large multisubunit nucleoprotein complexes and develops automated docking algorithms to integrate structural, biophysical, biochemical, and genetic data in order to construct models for structures of complexes.

Structure of Transcription Complexes

Crystal structure of the bacterial transcription initiation complex. (A) Summary of protein-nucleic-acid interactions. Black residue numbers and lines, interactions by RNA polymerase (RNAP); green residue numbers and lines; interactions by the transcription initiation factor σ, blue, -10 element of DNA nontemplate strand; light blue, discriminator element of DNA nontemplate strand; pink, rest of DNA nontemplate strand; red, DNA template strand; magenta, ribodinucleotide primer GpA; violet, active-center Mg2+; asterisks, water-mediated interactions; cyan boxes, bases unstacked and inserted into pockets. Residues are numbered as in E coli RNAP and σ70. (B) Overall structure (RNAP β' non conserved domain omitted for clarity). RNAP, gray; σ, yellow. Other colors as in A. (C) Interactions of RNAP and σ with the transcription-bubble nontemplate strand, the transcription bubble template strand, and downstream dsDNA (RNAP β subunit and β' non conserved domain omitted for clarity). Colors as in B.

[See Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M., Arnold, E., and Ebright, R.H. (2012) Structural basis of transcription initiation. Science 338:1076-1080.]

Mechanism of Transcription

Transcription complexes are molecular machines that carry out complex, multistep reactions in transcription initiation and elongation:

  1. RNA polymerase (RNAP) binds to promoter DNA, to yield an RNAP-promoter closed complex.
  2. RNAP unwinds ~14 base pairs of promoter DNA surrounding the transcription start site, rendering accessible the genetic information in the template strand of DNA, and yielding an RNAP-promoter open complex.
  3. RNAP begins synthesis of RNA as an RNAP-promoter initial transcribing complex. During initial transcription, RNAP uses a "scrunching" mechanism, in which RNAP remains stationary on promoter DNA and unwinds and pulls downstream DNA into itself and past its active center in each nucleotide-addition cycle, resulting in generation of a stressed intermediate.
  4. After RNAP synthesizes an RNA product ~10-15 nucleotides in length, RNAP breaks its interactions with promoter DNA, breaks at least some of its interactions with sigma, escapes the promoter, and begins transcription elongation as a transcription elongation complex. Energy stored in the stressed intermediate generated by scrunching during initial transcription is used to drive breakage of interactions with promoter DNA and interactions with sigma during promoter escape.

During transcription elongation, RNAP uses a "stepping" mechanism, in which RNAP translocates relative to DNA in each nucleotide-addition step. Each nucleotide-addition cycle during initial transcription and transcription elongation can be subdivided into four sub-steps: (1) translocation of the RNAP active center relative to DNA (by scrunching in initial transcription; by stepping in transcription elongation); (2) binding of the incoming nucleotide; (3) formation of the phosphodiester bond; and (4) release of pyrophosphate.

Crystal structures have been reported for transcription elongation complexes without incoming nucleotides and for transcription elongation complexes with incoming nucleotides. Based on these crystal structures, it has been proposed that each nucleotide-addition cycle is coupled to an RNAP active-center conformational cycle, involving closing of the RNAP active center upon binding of the incoming nucleotide, followed by opening of the RNAP active center upon formation of the phosphodiester bond. According to this proposal, the closing and opening of the RNAP active center is mediated by the folding and the unfolding of an RNAP active-center structural element, the "trigger loop."

To understand transcription initiation, transcription elongation, and transcriptional regulation, it will be necessary to leverage the available crystallographic structural information, in order to define the structural transitions in RNAP and nucleic acid in each reaction, to define the kinetics of each reaction, and to define mechanisms of regulation of each reaction.

The Ebright lab is using FRET and photocrosslinking methods to define distances and contacts within trapped intermediates in transcription initiation and transcription elongation. In addition, the lab is using single-molecule FRET, single-molecule DNA nanomanipulation, and combined single-molecule FRET and single-molecule DNA nanomanipulation, to carry out single-molecule, millisecond-to-second timescale analysis of structural transitions.

Structure of Transcription Complexes

Determination of RNAP clamp conformation in solution. (A) Measurement of single-molecule FRET between fluorescent probes incorporated at the tips of the RNAP β’ pincer (clamp) and the RNAP β pincer. Open (red), partly closed (yellow), and closed (green) RNAP clamp conformational states are as observed in crystal structures. (B) Incorporation of fluorescent probes at the tips of the RNAP β’ pincer (clamp) and the RNAP β pincer, by unnatural amino acid mutagenesis to incorporate 4 azidophenylalanine at sites of interest in β’ and β subunits, followed by Staudinger ligation to incorporate fluorescent probes at 4 azidophenylalanines in β’ and β subunits, followed by in vitro reconstitution of RNAP from labelled β’ and β subunits and unlabelled α and ω subunits. (C) Relationship between single-molecule FRET efficiencies, E, and RNAP clamp conformational states. The red boxes denote the open (red), closed (green), and collapsed (blue) clamp states observed in this work for RNAP in solution.

[See Chakraborty, A., Wang, D., Ebright, Y., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., and Ebright, R. (2012) Opening and closing of the bacterial RNA polymerase clamp. Science 337, 591-595.]

Regulation of Transcription

Regulation of TranscriptionCrystal structure of a transcriptional activator (catabolite activator protein, CAP; cyan) in complex with its target in the transcriptional machinery (RNA polymerase α-subunit C-terminal domain,αCTD; green) and DNA (red). There are no large-scale conformational changes in the activator and target, and the interface between the activator and target is small (residues highlighted in navy and yellow)—consistent with the proposal that transcriptional activation involves a simple "recruitment" mechanism.

[See Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., and Ebright, R.H. 2002. Science 297:1562-1566.]

The activities of bacterial transcription initiation complexes are regulated in response to environmental, cell-type, and developmental signals. In most cases, regulation is mediated by factors that bind to specific DNA sites in or near a promoter and inhibit (repressors) or stimulate (activators) one or more of the steps on the transcription initiation pathway.
To provide the first complete structural and mechanistic descriptions of activation, the Ebright lab studies two of the simplest examples of activation in bacteria: (1) activation of the lac //promoter by catabolite activator protein (CAP) and (2) activation of the gal promoter by CAP. These model systems each involve only a single activator molecule and a single activator DNA site and, as such, are more tractable than typical examples of activation in bacteria and substantially more tractable than typical examples of activation in eukaryotes (which can involve tens of activator molecules and activator DNA sites).

The lab has established that activation at lac involves an interaction between CAP and the RNA polymerase (RNAP) alpha-subunit C-terminal domain that facilitates closed-complex formation. Activation at gal involves this same interaction and also interactions between CAP and the RNAP alpha-subunit N-terminal domain, and between CAP and sigma, that facilitate isomerization of closed complex to open complex.

Together with collaborators, the lab is using electron microscopy, x-ray crystallography, and NMR to determine the structures of the interfaces between CAP and its targets on RNAP. In addition, the lab is using FRET, photocrosslinking, and single-molecule FRET and single-molecule DNA nanomanipulation methods to define when each CAP-RNAP interaction is made as RNAP enters the promoter and when each interaction is broken as RNAP leaves the promoter.

Inhibitors of Transcription; Antibacterial Drug Discovery

Bacterial RNA polymerase (RNAP) is a proven target for broad-spectrum antibacterial therapy. The suitability of bacterial RNAP as a target for broad-spectrum antibacterial therapy follows from the fact that bacterial RNAP is an essential enzyme (permitting efficacy), the fact that bacterial RNAP-subunit sequences are highly conserved (providing a basis for broad-spectrum activity), and the fact that bacterial RNAP-subunit sequences are not highly conserved in human RNAPI, RNAPII, and RNAPIII (providing a basis for therapeutic selectivity).
The rifamycin antibacterial agents--rifampin, rifapentine, rifabutin, and rifamixin--bind to and inhibit bacterial RNAP. The rifamycins bind to a site on bacterial RNAP adjacent to the RNAP active center and prevent extension of RNA chains beyond a length of 2–3 nucleotides. The rifamycins are in current clinical use in treatment of Gram-positive and Gram-negative bacterial infections. The rifamycins are of particular importance in treatment of tuberculosis; the rifamycins are first-line antituberculosis agents and are among the only antituberculosis agents able to clear infection and prevent relapse. The clinical utility of the rifamycin antibacterial agents is threatened by the existence of bacterial strains resistant to rifamycins. Resistance to rifamycins typically involves substitution of residues in or adjacent to the rifamycin-binding site on bacterial RNAP--i.e., substitutions that directly interfere with rifamycin binding.

In view of the public health threat posed by drug-resistant and multidrug-resistant bacterial infections, there is an urgent need for new classes of broad-spectrum antibacterial agents that (1) target bacterial RNAP (and thus have the same biochemical effects as rifamycins), but that (2) target sites within bacterial RNAP that do not overlap the rifamycin-binding site (and thus do not show cross-resistance with rifamycins).

The Ebright lab has identified new drug targets within the structure of bacterial RNAP. Each of these new targets can serve as a potential binding site for compounds that inhibit bacterial RNAP and thereby kill bacteria. Each of these new targets is present in most or all bacterial species, and thus compounds that bind to these new targets are active against a broad spectrum of bacterial species. Each of these new targets is different from targets of current antibiotics, and thus compounds that bind to these new targets are not cross-resistant with current antibiotics. For each of these new targets, the lab has identified at least one lead compound that binds to the target, and the lab has synthesized analogs of the lead compound comprising optimized lead compounds. Several of the lead compounds and optimized lead compounds are extremely promising: they exhibit potent activity against a broad spectrum of bacterial pathogens (including Staphylococcus aureus MSSA, Staphylococcus aureus MRSA, Enterococcus faecalis, Enterococcus faecium, Clostridium difficile, Mycobacterium tuberculosis, Bacillus anthracis, Francisella tularensis, Burkholderia mallei, and Burkholderia pseudomallei) and exhibit no cross-resistance with current antibiotics.

In support of this work, the lab is identifying new small-molecule inhibitors of bacterial RNAP by analysis of microbial and plant natural products, by high-throughput screening, and by virtual screening. The lab also is using genetic, biochemical, biophysical, and crystallographic approaches to define the mechanism of action of each known, and each newly identified, small-molecule inhibitor of bacterial RNAP, and the lab is using microbiological approaches to define antibacterial efficacies, resistance spectra, and spontaneous resistance frequencies of known and new small-molecule inhibitors of bacterial RNAP.

The lab seeks to address the following objectives: to develop new classes of antituberculosis agents and broad-spectrum antibacterial agents, to develop antibacterial agents effective against pathogens resistant to current antibiotics, to develop antibacterial agents effective against pathogens of high relevance to public health, and to develop antibacterial agents effective against pathogens of high relevance to biodefense.

Small-Molecule Inhibitors of Bacterial TranscriptionStructural basis of transcription inhibition by myxopyronin: contacts between RNA polymerase and myxopyronin.

  1. Binding pocket for myxopyronin. Cyan, surface representation of the binding pocket and adjacent hydrophobic pocket. Gray, ribbon representation of RNA polymerase backbone. Green, myxopyronin carbon atoms; red, myxopyronin oxygen atoms. RNA polymerase residues are numbered both as in T thermophilus RNA polymerase and as in E. coli RNA polymerase (in parentheses).
  2. Contacts between RNA polymerase and myxopyronin (stereoview). Gray, RNA polymerase backbone (ribbon representation) and RNA polymerase sidechain carbon atoms (stick representation); green, myxopyronin carbon atoms; red, oxygen atoms; blue, nitrogen atoms. "W," ordered bound water molecule. Dashed lines, H-bonds.
  3. Schematic summary of contacts between RNA polymerase and myxopyronin. "W", ordered bound water molecule. Red dashed lines, H-bonds. Blue arcs, van der Waals interactions.

[See Mukhopadhyay, J., Das, ., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., and Ebright, R. (2008) The RNA polymerase "switch region" is a target of inhibitors Cell 135, 295-307.]


Awards & Honors

  • Searle Scholar Award, 1989
  • Johnson & Johnson Discovery Research Fellow, 1990
  • American Society for Biochemistry and Molecular Biology/Schering-Plough Research Achievement Award, 1995
  • Walter J. Johnson Prize, 1995
  • American Academy of Microbiology Fellow,1996
  • Howard Hughes Medical Institute Investigator, 1997
  • Rutgers University Board of Trustees Research Excellence Award, 1998
  • American Association for the Advancement of Science Fellow, 2004
  • Infectious Diseases Society of America Fellow, 2011
  • Theobald Smith Society Waksman Award, 2012

Publications

Heyduk, T., Lee, J., Ebright, Y., Blatter, E., Zhou, Y., and Ebright, R. (1993) CAP interacts with RNA polymerase in solution in the absence of promoter DNA. Nature 364, 548-549.

Chen, Y., Ebright, Y., and Ebright, R. (1994) Identification of the target of a transcription activator protein by protein-protein photocrosslinking. Science 265, 90-92.

Pendergrast, P.S., Ebright, Y., and Ebright, R. (1994) High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates. Science 265, 959-961.

Blatter, E., Ross, W., Tang, H., Gourse, R., and Ebright, R. (1994) Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78, 889-896.

Busby, S. and Ebright, R. (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79, 743-746.

Tang, H., Sun, X., Reinberg, D., and Ebright, R. (1996) Protein-protein interactions in eukaryotic transcription initiation: structure of the pre-initiation complex. Proc. Natl. Acad. Sci. USA 93, 1119-1124.

Pellegrini, M. and Ebright, R. (1996) Artificial DNA binding peptides. J. Amer. Chem. Soc. 118, 5831-5835.

Niu, W., Kim, Y., Tau, G., Heyduk, and Ebright, R. (1996) Transcription activation at Class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell 87, 1123-1134.

Miller, A., Wood, D., Ebright, R., and Rothman-Denes, L. (1997) RNA polymerase β: a target for DNA-binding-independent activation. Science 275, 1655-1657.

Kim, T.-K., Lagrange, T., Reinberg, D., and Ebright, R. (1997) Trajectory of DNA in the RNA polymerase II transcription preinitiation complex Proc. Natl. Acad. Sci. USA 94, 12268-12273.

Lagrange, T., Kapanidis, A., Tang, H., Reinberg, D., and Ebright, R. (1998) New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes & Development, 12, 34-44.

Estrem, S., Ross, W., Gaal., Chen, Z.W.S., Niu, W., Ebright, R., and Gourse, R. (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxyl-terminal domain of RNA polymerase alpha subunit. Genes & Development 13, 2134-2147.

Tan, Q., Linask, K.L., Ebright, R. and Woychik, N. (2000) Activation mutants in yeast RNA polymerase subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes & Development 14, 339-348.

Kim, T.-K., Ebright, R., and Reinberg, D. (2000) Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288, 1418-1421.

Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. (2000) Structural organization of the RNA polymerase-promoter open complex. Cell 101, 601-611.

Minakhin, L., Bhagat, S. Brunning, A., Campbell, E., Darst, S., Ebright, R. and Severinov, K. (2001) Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly Proc. Natl. Acad. Sci. USA 98, 892-897.

Mukhopadhyay, J., Kapanidis, A., Mekler, V., Kortkhonjia, E., Ebright, Y., and Ebright, R. (2001) Translocation of sigma70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106, 453-463.

Kapanidis, A., Ebright, Y., and Ebright, R. (2001) Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling using (Ni2+:nitrilotriacetic acid)n-fluorochrome conjugates. J. Amer. Chem. Soc. 123, 12123-12125.

Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Structural organization of RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108, 599-614.

Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Structural basis of transcription activation: structure of the CAP-aCTD-DNA complex. Science 297, 1562-1566.

Lloyd, G., Niu, W., Trebbutt, J., Ebright, R., and Busby, S. (2002) Requirement for two copies of RNA polymerase α subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters. Genes & Development 16, 2557-2565.

Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Structural organization of RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108, 599-614.

Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Structural basis of transcription activation: structure of the CAP-αCTD-DNA complex. Science 297, 1562-1566.

Chen, H., Tang, H., and Ebright, R.H. (2003) Functional interaction between RNA polymerase a subunit C-terminal domain and δ70 in UP-element- and activator-dependent transcription. Mol. Cell 11, 1621-1623.

Bayro, M., Mukhopadhyay, J., Swapna, G.V.T., Huang, J., Ma, L.-C., Sineva, E., Dawson, P., Montelione, G., and Ebright, R. (2003) Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. J. Amer. Chem. Soc. 125, 12382-12383.

Revyakin, A., Ebright, R., and Strick, T. (2004) Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation. Proc. Natl. Acad. Sci. USA 101, 4776-4780.

Nickels, B., Mukhopadhyay, J., Garrity, S., Ebright, R., and Hochschild, A. (2004) δ70 mediates a promoter-proximal pause at the lac promoter. Nature Structl. Mol. Biol. 11, 544-550.

Mukhopadhyay, J., Sineva, E., Knight, J., Levy, R., and Ebright, R. (2004) Antibacterial peptide microcin J25 (MccJ25) inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol. Cell. 14, 739-751.

Knight, J., Mekler, V., Mukhopadhyay, J., Ebright, R., Levy, R. (2005) Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J. 88, 925-938.

Revyakin, A., Ebright, R., and Strick, T. (2005) Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments. Nature Meths. 2, 127-138.

Lee, N.K., Kapanidis, A., Wang, Y., Michalet, X., Mukhopadhyay, J., Ebright, R.H., and Weiss, S. (2005) Accurate FRET measurements within diffusing single biomolecules using alternating-laser excitation. Biophys. J. 88, 2939 2953.

Nickels, B. Garrity, S., Mekler, V., Minakhin, L., Severinov, K., Ebright, R.H., and Hochschild, A. (2005) Altering the interaction between δ70 and the β-flap of Escherichia coli RNA polymerase provides evidence for a barrier to the extension of the nascent RNA during early elongation. Proc. Natl. Acad. Sci USA 102, 4488 4493.

Ebright, R. and Ebright, Y. (2005) Bis-transition-metal-chelate probes. US Patent #6,919,333.

Tuske, S., Sarafianos, S., Wang, X., Hudson, B., Sineva, E., Mukhopadhyay, J., Birktoft, J, Leroy, O., Ismail, S., Clark, A., Dharia, C., Napoli, A., Laptenko, O., Lee, J., Borukhov, S., Ebright, R., and Arnold, E., (2005) Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122, 541-552.

Vrentas, C., Gaal, T., Ross, W., Ebright, R., and Gourse, R. (2005) Response of RNA polymerase to ppGpp: requirement for the w subunit and relief of this requirement by DksA. Genes Dev. 19, 2378-2387.

Kapanidis, A., Margeat, E., Laurence, T., Doose, S., Ho, S.O., Mukhopadhyay, J., Kortkhonjia, E., Mekler, V., Ebright, R., and Weiss, S. (2005) Retention of transcription initiation factor δ70 in transcription elongation: single molecule analysis. Mol. Cell 20, 347-356.

Margeat, E., Kapanidis, A., Tinnefield, P., Wang, Y., Mukhopadhyay, J., Ebright, R., and Weiss, S. (2006) Direct observation of abortive initiation and promoter escape within immobilized single transcription complexes. Biophys. J. 20, 347-356.

Tadigotla, V., O'Maoileidigh, D., Sengupta, A., Epshtein, V., Ebright, R., Nudler, E., and Ruckenstein, A. (2006) Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl. Acad. Sci. USA 103, 4439-4444.

Seul, M. and Ebright, R. (2006) Color-encoding and in-situ interrogation of matrix-coupled chemical compounds. US Patent #7,083,914.

Popovych, N., Sun, S., Ebright, R., and Kalodimos, C. (2006) Dynamically driven protein allostery. Nature Structl. Mol. Biol. 13, 831-838.

Revyakin, A., Liu, C., Ebright, R.H. and Strick, T. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139-1143.

Kapanidis, A., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S. and Ebright, R.H. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144-1147.

Ebright, R. and Ebright, Y. (2006) Reagents and procedures for high-specificity labelling. US Patent #7,141,655.

Cellai, S., Vannini, N., Naryshkin, N., Kortkhonjia, E., Ebright, R., and Rivetti, C. (2007) Upstream promoter sequences and aCTD mediate stable DNA wrapping within the RNA polymerase open promoter complex. EMBO Reports 8, 271-278.

Ebright, R. and Ebright, Y. (2007) Ultra-high-specificity fluorescent labelling. US Patent #7,282,373.

Ebright, R. and Ebright, Y. (2008) Bis-transition-metal-chelate probes. US Patent #7,371,745.

Ebright, R. and Ebright, Y. (2008) Reagents and procedures for multi-label high-specificity labelling. US Patent #7,381,572.

Severinov, K., Pavlova, O., Sineva, E., Zakeyeva, I., and Ebright, R. (2008) Mutational derivatives of peptide antibiotic microcin J25 with increased antibacterial action. US Patent #7,442,762.

Feklistov, A., Mekler, V., Jiang, Q., Westblade, L., Irschik, H., Jansen, R., Mustaev, A., Darst, S., and Ebright, R.H. (2008) Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center. Proc. Natl. Acad. Sci. USA 105, 14820-14825.

Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., and Ebright, R. (2008) The RNA polymerase "switch region" is a target of inhibitors Cell 135, 295-307.

Pavlova, O., Mukhopadhyay, J., Sineva, E., Ebright, R., and Severinov, K. (2008) Systematic structure-activity analysis of microcin J25 (MccJ25). J. Biol. Chem. 283, 25589-25595.

Kim, Y., Ebright, Y., Goodman, A., Reinberg, D., and Ebright, R. (2008) Non-radioactive, ultrasensitive site-specific protein-protein photocrosslinking: interactions of a-helix 2 of TATA-binding protein with general transcription factor TFIIA and with transcriptional repressor NC2. Nucl. Acids Res. 36, 6143-6154.

Naryshkin, N., Druzhinin S., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. (2009) Static and kinetic site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes. Meths. Mol. Biol. 543, 403-437.

Popovych, N., Tzeng, S.-R., Tonelli, M., Ebright¬, R., and Kalodimos, C. (2009) Structural basis of cAMP-mediated allosteric control of the catabolite activator protein, Proc. Natl. Acad. Sci. USA 106, 6927-6932.

Goldman, S., Ebright, R., and Nickels, B. (2009) Direct detection of abortive RNA transcripts in vivo. Science 324, 927-928.

Hudson, B., Quispe, J., Lara, S., Kim, Y., Berman, H., Arnold, E., Ebright, R., and Lawson, C. (2009) Three-dimensional structure of an intact activator-dependent transcription initiation complex. Proc. Natl. Acad. Sci. USA 106, 19830-19835.

Ho, M., Hudson, B., Das, K., Arnold, E., and Ebright, R. (2009) Structures of RNA polymerase-antibiotic complexes. Curr. Opin. Structl. Biol. 19, 715-723.

Chakraborty, A., Wang, D., Ebright, Y., and Ebright, R. (2010) Azide-specific labelling of biomolecules by Staudinger-Bertozzi ligation: phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy. Meths. Enzymol. 472, 19-30.

Grohmann, D., Nagy, J., Chakraborty, A., Klose, D., Fielden, D., Ebright, R., Michaelis, J., and Werner, F. (2011) The initiation factor TFE and the elongation factor Spt4/5 compete for binding to the RNAP clamp during transcription initiation and elongation. Mol. Cell 43, 263-274.

Xiao, Y., Wei, X., Ebright, R., and Wall, D. (2011) Antibiotic production by myxobacteria plays a role in predation. J. Bacteriol. 193, 4626-4633.

Kuznedelov, K., Semenova, E., Knappe, T., Mukahmedjarov, D., Srivastava, A., Chatterjee, S., Ebright, R., Marahiel, M., and Severinov, K. (2011) The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase. J. Mol. Biol. 412, 842-848.

Srivastava, A., Talaue, M., Liu, S., Degen, D., Ebright, R.Y., Sineva, E., Chakraborty, A., Druzhinin, S., Chatterjee, S., Mukhopadhyay, J., Ebright, Y., Zozula, A., Shen, J., Sengupta, S., Niedfeldt, R., Xin, C., Kaneko, T., Irschik, H., Jansen, R., Donadio, S., Connell, N., and Ebright, R. (2011) New target for inhibition of bacterial RNA polymerase:
"switch region." Curr. Opin. Microbiol. 14, 532-543.

Ebright, R. Switch region: target and method for inhibition of bacterial RNA polymerase. US Patent #8,114,583.

Ebright, R. (2012) Target and method for inhibition of bacterial RNA polymerase. US Patent #8,198,021.

Ebright, R. (2012) RNA exit channel: target and method for inhibition of bacterial RNA polymerase. US Patent #8,206,898.

Chakraborty, A., Wang, D., Ebright, Y., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., and Ebright, R. (2012) Opening and closing of the bacterial RNA polymerase clamp. Science 337, 591-595.

Srivastava, A., Degen, D., Ebright, Y., and Ebright, R. (2012) Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus. Antimicrob. Agents Chemother. 56, 6250-6255.

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Research Areas: 
Biophysical Chemistry

Rutgers, The State University of New Jersey