Transcription--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. Our lab 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. Our lab uses experimental approaches spanning structural biology, single-molecule biophysics, and drug discovery.
Structural basis of Rho-dependent transcription termination
Molodtsov, V., Wang, C., Firlar, E., Kaelber, H., and Ebright, R.H. (2023) Structural basis of Rho‑dependent transcription termination. Nature 614, 367–374.
Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription-translation-coupling quality control in Escherichia coli1-4. Here we report the preparation of complexes that are functional in factor-dependent transcription termination from Rho, NusG, RNA polymerase (RNAP), and synthetic nucleic acid scaffolds, and we report cryogenic electron microscopy structures of the complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer; have RNA threaded through the central channel of Rho; have 60 nucleotides of RNA interacting sequence-specifically with the exterior of Rho and 6 nucleotides of RNA interacting sequence-specifically with the central channel of Rho; have Rho oriented relative to RNAP such that ATP-dependent translocation by Rho exerts mechanical force on RNAP; and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho's function.
Redesign of rifamycin antibiotics to overcome ADP‑ribosylation-mediated resistance
Lan, T., Ganapathy, U., Sharma, S., Ahn, Y.-M., Zimmerman, M., Molodtsov, V., Hegde, P., Gengenbacher, M., Ebright, R.H., Dartois, V., Freundlich, J., Dick, T., and Aldrich, C. (2022) Angew. Chem. Intl. Ed. 61, e202211498.
Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.
In transcription antitermination by Qlambda, NusA induces refolding of Qlambda to form a nozzle that extends the RNA polymerase RNA-exit channel
Yin, Z., Bird, J., Kaelber, J., Nickels, B., and Ebright, R.H. In transcription antitermination by Qlambda, NusA induces refolding of Qlambda to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc. Natl. Acad. Sci. USA 119, 2205278119, 2022.
Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
Design, synthesis, and characterization of TNP-2198, a dual-targeted rifamycin-nitroimidazole conjugate with potent activity against microaerophilic and anaerobic bacterial pathogens
Ma, Z., He, S., Yuan, Y., Zhuang, Z., Liu, Y., Wang, H., Chen, J., Xu, X., Ding, C., Molodtsov, V., Lin, W., Robertson, G., Weiss, W., Pulse, M., Nguyen, P., Duncan, L., Doyle, T., Ebright, R.H., and Lynch, A. (2022) J. Med Chem. 65, 4481-4495.
TNP-2198, a stable conjugate of a rifamycin pharmacophore and a nitroimidazole pharmacophore, has been designed, synthesized, and evaluated as a novel dual-targeted antibacterial agent for the treatment of microaerophilic and anaerobic bacterial infections. TNP-2198 exhibits greater activity than a 1:1 molar mixture of the parent drugs and exhibits activity against strains resistant to both rifamycins and nitroimidazoles. A crystal structure of TNP-2198 bound to a Mycobacterium tuberculosis RNA polymerase transcription initiation complex reveals that the rifamycin portion of TNP-2198 binds to the rifamycin binding site on RNAP and the nitroimidazole portion of TNP-2198 interacts directly with the DNA template-strand in the RNAP active-center cleft, forming a hydrogen bond with a base of the DNA template strand. TNP-2198 is currently in Phase 2 clinical development for the treatment of Helicobacter pylori infection, Clostridioides difficile infection, and bacterial vaginosis.
Structural and mechanistic basis of sigma-dependent transcriptional pausing
Pukhrambam, C., Molodtsov, V., Kooshkbagh, M., Tareen, A., Vu, H., Skalenko, K., Su, M., Zhou, Y., Winkelman, J., Kinney, J., Ebright, R.H., and Nickels, B. Structural and mechanistic basis of sigma‑dependent transcriptional pausing. Proc. Natl. Acad. Sci. USA 119, e2201301119, 2022
In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein–DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR′ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2–4 bp, and σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2–3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2–3 bp—and only that state—is associated with the consensus sequence, T−3N−2Y−1G+1, (where −1 corresponds to the position of the RNA 3′ end), which is identical to the consensus for pausing in initial transcription and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T−3 resides in the DNA nontemplate strand. A cryoelectron microscopy structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T−3 of the consensus sequence exerts its effects by facilitating scrunching.
Structural and mechanistic basis of reiterative transcription initiation
Liu, Y., Winkelman, J., Yu, L., Pukhrambam, C., Zhang, Y., Nickels, B., and Ebright, R.H. Structural and mechanistic basis of reiterative transcription initiation. Proc. Natl. Acad. Sci. USA 119, e2115746119, 2022.
In standard transcription initiation, RNA polymerase (RNAP) synthesizes an initial RNA product complementary to the DNA template. In an alternative pathway of transcription initiation, termed “reiterative transcription initiation,” observed at promoters containing homopolymeric sequences at the transcription start site, RNAP synthesizes an initial RNA product having a 5′ sequence containing a variable number, up to tens to hundreds, of nucleotides noncomplementary to the DNA template. Here, using crystallography, cryoelectron microscopy, photocrosslinking, and single-molecule DNA nanomanipulation, we show that RNA extension in reiterative transcription initiation involves slipping of RNA relative to DNA within a short RNA–DNA hybrid and generates RNA that exits RNAP through a previously unobserved RNA path (“alternative RNA path”) and previously unobserved RNA exit (“alternative RNA exit”).
Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism
Mazumder, A., Ebright, R.H., and Kapanidis, A., Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism. eLife 10, e70090, 2021.
Transcription initiation starts with unwinding of promoter DNA by RNA polymerase (RNAP) to form a catalytically competent RNAP-promoter complex (RPo). Despite extensive study, the mechanism of promoter unwinding has remained unclear, in part due to the transient nature of intermediates on path to RPo. Here, using single-molecule unwinding-induced fluorescence enhancement to monitor promoter unwinding, and single-molecule fluorescence resonance energy transfer to monitor RNAP clamp conformation, we analyse RPo formation at a consensus bacterial core promoter. We find that the RNAP clamp is closed during promoter binding, remains closed during promoter unwinding, and then closes further, locking the unwound DNA in the RNAP active-centre cleft. Our work defines a new, ‘bind-unwind-load-and-lock’, model for the series of conformational changes occurring during promoter unwinding at a consensus bacterial promoter and provides the tools needed to examine the process in other organisms and at other promoters.
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
Skalenko, K., Li, L., Zhang, Y., Vvedenskaya, I., Winkelman, J., Cope, A., Taylor, D., Shah, P., Ebright, R.H., Kinney, J., Zhang, Y., and Nickels, B., Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proc. Natl. Acad. Sci. USA 118, e2106388118, 2021.
Primer-dependent transcription initiation—the use of RNA primers as initiating entities in transcription initiation—yields RNA products having a 5′-hydroxyl. Here, we show that primer-dependent initiation in vivo in Escherichia coli involves predominantly dinucleotide primers, involves any of the 16 possible dinucleotide primers, and depends on promoter sequences in, upstream, and downstream of the primer binding site. Crystal structures explain the structural basis of sequence dependence at the promoter position immediately upstream of the primer binding site, namely, interchain base stacking between the promoter template-strand nucleotide and primer 5′ nucleotide. Taken together, our findings provide a mechanistic and structural description of primer-dependent initiation in E. coli.
Structural basis of transcription-translation coupling
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G, Su M, and Ebright RH, Science 369, 1359-1365, 2020.
In bacteria, transcription and translation are coupled processes, in which movement of RNA polymerase (RNAP) synthesizing mRNA is coordinated with movement of the first ribosome translating mRNA. Coupling is modulated by the transcription factors NusG–which is thought to bridge RNAP and ribosome–and NusA. Here, we report cryo-EM structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P-site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A; previously termed “expressome”). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.
XACT-Seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing
Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, and Nickels BE, Molecular Cell 79, 797-811, 2020.
Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a "stepping" mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a "scrunching" mechanism, has not. We report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolution (XACT-seq; "crosslink-between-active-center-and-template sequencing"). We apply this method to detect and quantify pausing in initial transcription at 411 (∼4,000,000) promoter sequences in vivo in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4 to 5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard coded by sequence elements similar to those for transcription-elongation pausing.
Closing and opening of the RNA polymerase trigger loop
Mazumder A, Lin M, Kapanidis A, and Ebright RH, Proc. Natl. Acad. Sci. USA 117, 15642–15649, 2020
During transcription elongation at saturating nucleotide concentrations, RNA polymerase (RNAP) performs ∼50 nucleotide-addition cycles every second. The RNAP active center contains a structural element, termed the trigger loop (TL), that has been suggested, but not previously shown, to open to allow a nucleotide to enter and then to close to hold the nucleotide in each nucleotide-addition cycle. Here, using single-molecule fluorescence spectroscopy to monitor distances between a probe incorporated into the TL and a probe incorporated elsewhere in the transcription elongation complex, we show that TL closing and opening occur in solution, define time scales and functional roles of TL closing and opening, and, most crucially, demonstrate that one cycle of TL closing and opening occurs in each nucleotide-addition cycle.
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li L, Molodtsov V, Lin W, Ebright RH, and Zhang Y, Proc. Natl. Acad. Sci USA 117, 5801-5809, 2020
The “σ-finger” of bacterial initiation factor σ binds within RNA polymerase active-center cleft and blocks the path of nascent RNA. It has been hypothesized that the σ-finger must be displaced during initial transcription. By determining crystal structures defining successive steps in initial transcription, we demonstrate that the σ-finger is displaced in a stepwise fashion, driven by collision with the RNA 5′-end, as nascent RNA is extended from ∼5 nt to ∼10 nt during initial transcription. We further show that this is true for both the primary σ-factor and alternative σ-factors, and that the nascent RNA length at which displacement occurs is determined by the extent to which the σ-finger penetrates the active center of RNA polymerase.
Structural basis of Q-dependent antitermination
Yin, Z., Kaelber, J., and Ebright, R.H., Proc. Natl. Acad. Sci. USA 116, 18384-18390, 2019
Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins.
Structural basis of ECF-σ-factor-dependent transcription initiation
Lin, W., Mandal, S., Degen, D., Cho, M., Feng, Y., Das, K., and Ebright, R.H., Nature Commun. 10, 710, 2019
Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.
Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3)
Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH, Molecular Cell 7:60-71, 2018
Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP "clamp." The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter -10 and -35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives.
Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase
Maffioli S, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH, Cell 169:1240-1248, 2017
Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6′-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.
Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH, Molecular Cell 66, 169-179, 2017
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8–4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds—Nα-aroyl-N-aryl-phenylalaninamides (AAPs)—that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.
Affinity selection-mass spectrometry identifies a novel antibacterial RNA polymerase inhibitor
Walker, SS, Degen D, Nickbarg E, Carr D, Soriano A, Mandal M B, Painter RE, Sheth PR, Xiao L, Sher X, Murgolo N, Su J, Olsen DB, Ebright RH, Young K., ACS Chemical Biology 2, 1346-1352, 2017
The growing prevalence of drug resistant bacteria is a significant global threat to human health. The antibacterial drug rifampin, which functions by inhibiting bacterial RNA polymerase (RNAP), is an important part of the antibacterial armamentarium. Here, in order to identify novel inhibitors of bacterial RNAP, we used affinity-selection mass spectrometry to screen a chemical library for compounds that bind to Escherichia coli RNAP. We identified a novel small molecule, MRL-436, that binds to RNAP, inhibits RNAP, and exhibits antibacterial activity. MRL-436 binds to RNAP through a binding site that differs from the rifampin binding site, inhibits rifampin-resistant RNAP derivatives, and exhibits antibacterial activity against rifampin-resistant strains. Isolation of mutants resistant to the antibacterial activity of MRL-436 yields a missense mutation in codon 622 of the rpoC gene encoding RNAP β′ subunit or a null mutation in the rpoZ gene encoding RNAP ω subunit, confirming that RNAP is the functional cellular target for the antibacterial activity of MRL-436, and indicating that RNAP β′ subunit residue 622 and RNAP ω subunit are required for the antibacterial activity of MRL-436. Similarity between the resistance determinant for MRL-436 and the resistance determinant for the cellular alarmone ppGpp suggests a possible similarity in binding site and/or induced conformational state for MRL-436 and ppGpp.
The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA
Bird J, Zhang Y, Tian Y, Panova N, Barvík I, Greene, L Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE, Nature 535, 444-447, 2016
The chemical nature of the 5′ end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency [1,2], and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation3. Recently it has been shown that some bacterial RNA species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic RNA. In particular, RNA species containing a 5′-end nicotinamide adenine dinucleotide (NAD+) or 3′-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria [3,4,5,6]. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps [6,7,8]. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms.
Structural basis of transcription activation
Feng Y, Zhang Y, Ebright RH, Science 352, 1330-1333, 2016
Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)–promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σA holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.
Multiplexed protein-DNA cross-linking: scrunching in transcription start site selection
Winkelman J, Vvedenskaya I, Zhang Y, Zhang Y, Bird J, Taylor D, Gourse R, Ebright RH, Nickels B, Science 351, 1090-1093, 2016.
In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.
Structural basis of transcription inhibition by CBR hydroxamidines and CBR pyrazoles
Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH, Structure 23, 1470-1481, 2015.
CBR hydroxamidines are small-molecule inhibitors of bacterial RNA polymerase (RNAP) discovered through high-throughput screening of synthetic-compound libraries. CBR pyrazoles are structurally related RNAP inhibitors discovered through scaffold hopping from CBR hydroxamidines. CBR hydroxamidines and pyrazoles selectively inhibit Gram-negative bacterial RNAP and exhibit selective antibacterial activity against Gram-negative bacteria. Here, we report crystal structures of the prototype CBR hydroxamidine, CBR703, and a CBR pyrazole in complex with E. coli RNAP holoenzyme. In addition, we define the full resistance determinant for CBR703, show that the binding site and resistance determinant for CBR703 do not overlap the binding sites and resistance determinants of other characterized RNAP inhibitors, show that CBR703 exhibits no or minimal cross-resistance with other characterized RNAP inhibitors, and show that co-administration of CBR703 with other RNAP inhibitors results in additive antibacterial activities. The results set the stage for structure-based optimization of CBR inhibitors as antibacterial drugs.
Interactions between RNA polymerase and the ''core recognition element" counteract pausing
Vvedenskaya I, Vahedian-Movahed H, Bird J, Knoblauch J, Goldman S, Zhang Y, Ebright RH, Nickels B, Science 344, 1285-1289, 2014
Transcription elongation is interrupted by sequences that inhibit nucleotide addition and cause RNA polymerase (RNAP) to pause. Here, by use of native elongating transcript sequencing (NET-seq) and a variant of NET-seq that enables analysis of mutant RNAP derivatives in merodiploid cells (mNET-seq), we analyze transcriptional pausing genome-wide in vivo in Escherichia coli. We identify a consensus pause-inducing sequence element, G-10Y-1G+1 (where -1 corresponds to the position of the RNA 3′ end). We demonstrate that sequence-specific interactions between RNAP core enzyme and a core recognition element (CRE) that stabilize transcription initiation complexes also occur in transcription elongation complexes and facilitate pause read-through by stabilizing RNAP in a posttranslocated register. Our findings identify key sequence determinants of transcriptional pausing and establish that RNAP-CRE interactions modulate pausing.
Transcription inhibition by the depsipeptide antibiotic salinamide A
Degen D, Feng Y, Zhang Y, Ebright K, Ebright Y, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH, eLife, 3, e02451, 2014
We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap,' comprising the 'bridge-helix N-terminal hinge,' 'F-loop,' and 'link region.' We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.
GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides
Zhang Y, Degen D, Ho M, Sineva E, Ebright K, Ebright Y, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske, S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, and Ebright RH, eLife 3, e02450, 2014
Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance.
Structural basis of transcription initiation
Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho M, Arnold E, and Ebright RH, Science 338, 1076-1080, 2012
During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, sigma A, and a promoter DNA fragment corresponding to the transcription bubble and downstream dsDNA of the RNAP-‑promoter open complex. The structures show that sigma recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases, and that RNAP recognizes the ‑-4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between sigma and template-‑strand ssDNA pre‑organize template-strand ssDNA to engage the RNAP active center.
Opening and closing of the bacterial RNA polymerase clamp
Chakraborty A, Wang D, Ebright Y, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R, Nixon BT, Knight J, Weiss S, Ebright RH, Science 337, 591-595, 2012
Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription initiation and elongation. We find that the clamp predominantly is open in free RNAP and early intermediates in transcription initiation but closes upon formation of a catalytically competent transcription initiation complex and remains closed during initial transcription and transcription elongation. We show that four RNAP inhibitors interfere with clamp opening. We propose that clamp opening allows DNA to be loaded into and unwound in the RNAP active-center cleft, that DNA loading and unwinding trigger clamp closure, and that clamp closure accounts for the high stability of initiation complexes and the high stability and processivity of elongation complexes.
Richard H. Ebright, Ph.D., is Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and Laboratory Director at the Waksman Institute of Microbiology. He directs a laboratory of approximately ten postdoctoral associates, graduate students, and technicians and serves as project leader on three National Institutes of Health research grants ("Prokaryotic Transcription Termination," "Therapeutics for Drug-Resistant Bacteria," and "Treatments for Tuberculosis and Non-Tuberculous Mycobacterial Lung Infections: Dual-Targeted Rifamycin-AAP Conjugates").
His research focusses on the structure, mechanism, and regulation of bacterial transcription complexes, and on the development of inhibitors of bacterial transcription as antituberculosis agents and broad-spectrum antibacterial agents. His research employs tools of structural biology, biophysics, and drug-discovery.
He received his A.B. (Biology, summa cum laude) and Ph.D. (Microbiology and Molecular Genetics) degrees from Harvard University. He performed graduate research at Harvard and the Institut Pasteur and was a Junior Fellow of the Harvard University Society of Fellows. In 1987, he was appointed as a Laboratory Director at the Waksman Institute and a faculty member at Rutgers University. From 1997 to 2013, he was co-appointed as an Investigator of the Howard Hughes Medical Institute.
He has received the Searle Scholar Award, the Walter J. Johnson Prize, the Schering-Plough Award of the American Society for Biochemistry and Molecular Biology, the Waksman Award of the Theobold Smith Society, the MERIT Award of the National Institutes of Health, and the Chancellor's Award for Excellence in Research of Rutgers University. He is a Member of the American Academy of Arts and Sciences and a Fellow of the American Association for Advancement of Science, the American Academy of Microbiology, and the Infectious Diseases Society of America.
He has more than one hundred seventy-five publications and more than forty issued and pending patents.
He served for sixteen years as editor of the Journal of Molecular Biology. He has served on the National Institutes of Health Molecular Biology Study Section and on National Institutes of Health special emphasis panels. He is a member of the Institutional Biosafety Committee of Rutgers University, and he has been a member of the Antimicrobial Resistance Committee of the Infectious Diseases Society of America, the Working Group on Pathogen Security of the state of New Jersey, and the Controlling Dangerous Pathogens Project of the Center for International Security Studies. He has testified at US House and US Senate hearings on biosafety, biosecurity, and biorisk management.