1
|
Chakraborty T, Trujillo JT, Kendall T, Mosher RA. Charophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homolog. Genome Biol Evol 2024; 16:evae119. [PMID: 38874416 DOI: 10.1093/gbe/evae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
In flowering plants, euchromatic transposons are transcriptionally silenced by RNA-directed DNA Methylation, a small RNA-guided de novo methylation pathway. RNA-directed DNA Methylation requires the activity of the RNA Polymerases IV and V, which produce small RNA precursors and noncoding targets of small RNAs, respectively. These polymerases are distinguished from Polymerase II by multiple plant-specific paralogous subunits. Most RNA-directed DNA Methylation components are present in all land plants, and some have been found in the charophytic green algae, a paraphyletic group that is sister to land plants. However, the evolutionary origin of key RNA-directed DNA Methylation components, including the two largest subunits of Polymerase IV and Polymerase V, remains unclear. Here, we show that multiple lineages of charophytic green algae encode a single-copy precursor of the largest subunits of Polymerase IV and Polymerase V, resolving the two presumed duplications in this gene family. We further demonstrate the presence of a Polymerase V-like C-terminal domain, suggesting that the earliest form of RNA-directed DNA Methylation utilized a single Polymerase V-like polymerase. Finally, we reveal that charophytic green algae encode a single CLSY/DRD1-type chromatin remodeling protein, further supporting the presence of a single specialized polymerase in charophytic green algae.
Collapse
Affiliation(s)
| | - Joshua T Trujillo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, USA
- Department of Biochemistry, Purdue University, West Lafayette, USA
| | - Timmy Kendall
- The School of Plant Sciences, University of Arizona, Tucson, USA
| | - Rebecca A Mosher
- The School of Plant Sciences, University of Arizona, Tucson, USA
| |
Collapse
|
2
|
Duan B, Qiu C, Sze SH, Kaplan C. Widespread epistasis shapes RNA Polymerase II active site function and evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530048. [PMID: 36909581 PMCID: PMC10002619 DOI: 10.1101/2023.02.27.530048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. At the heart of these msRNAPs is an ultra-conserved active site domain, the trigger loop (TL), coordinating transcription speed and fidelity by critical conformational changes impacting multiple steps in substrate selection, catalysis, and translocation. Previous studies have observed several different types of genetic interactions between eukaryotic RNA polymerase II (Pol II) TL residues, suggesting that the TL's function is shaped by functional interactions of residues within and around the TL. The extent of these interaction networks and how they control msRNAP function and evolution remain to be determined. Here we have dissected the Pol II TL interaction landscape by deep mutational scanning in Saccharomyces cerevisiae Pol II. Through analysis of over 15000 alleles, representing all single mutants, a rationally designed subset of double mutants, and evolutionarily observed TL haplotypes, we identify interaction networks controlling TL function. Substituting residues creates allele-specific networks and propagates epistatic effects across the Pol II active site. Furthermore, the interaction landscape further distinguishes alleles with similar growth phenotypes, suggesting increased resolution over the previously reported single mutant phenotypic landscape. Finally, co-evolutionary analyses reveal groups of co-evolving residues across Pol II converge onto the active site, where evolutionary constraints interface with pervasive epistasis. Our studies provide a powerful system to understand the plasticity of RNA polymerase mechanism and evolution, and provide the first example of pervasive epistatic landscape in a highly conserved and constrained domain within an essential enzyme.
Collapse
Affiliation(s)
- Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843
| | - Craig Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| |
Collapse
|
3
|
Mohamed AA, Vazquez Nunez R, Vos SM. Structural advances in transcription elongation. Curr Opin Struct Biol 2022; 75:102422. [PMID: 35816930 DOI: 10.1016/j.sbi.2022.102422] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/22/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Transcription is the first step of gene expression and involves RNA polymerases. After transcription initiation, RNA polymerase enters elongation followed by transcription termination at the end of the gene. Only recently, structures of transcription elongation complexes bound to key transcription elongation factors have been determined in bacterial and eukaryotic systems. These structures have revealed numerous insights including the basis for transcriptional pausing, RNA polymerase interaction with large complexes such as the ribosome and the spliceosome, and the transition into productive elongation. Here, we review these structures and describe areas for future research.
Collapse
Affiliation(s)
- Abdallah A Mohamed
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/AMohamed_98
| | - Roberto Vazquez Nunez
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/rjareth
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA.
| |
Collapse
|
4
|
Fukudome A, Singh J, Mishra V, Reddem E, Martinez-Marquez F, Wenzel S, Yan R, Shiozaki M, Yu Z, Wang JCY, Takagi Y, Pikaard CS. Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2. Proc Natl Acad Sci U S A 2021; 118:e2115899118. [PMID: 34903670 PMCID: PMC8713982 DOI: 10.1073/pnas.2115899118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/18/2023] Open
Abstract
RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In Arabidopsis, RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 Å, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.
Collapse
Affiliation(s)
- Akihito Fukudome
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Jasleen Singh
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Vibhor Mishra
- HHMI, Indiana University, Bloomington, IN 47405
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Eswar Reddem
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Francisco Martinez-Marquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405
| | - Rui Yan
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Momoko Shiozaki
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Zhiheng Yu
- CryoEM Facility, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Joseph Che-Yen Wang
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, IN 47405
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 47405;
| | - Craig S Pikaard
- HHMI, Indiana University, Bloomington, IN 47405;
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| |
Collapse
|
5
|
A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models. J Biol Chem 2021; 296:100735. [PMID: 33991521 PMCID: PMC8191312 DOI: 10.1016/j.jbc.2021.100735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/23/2022] Open
Abstract
RNA polymerase II (Pol II) surveils the genome, pausing as it encounters DNA lesions and base modifications and initiating signals for DNA repair among other important regulatory events. Recent work suggests that Pol II pauses at 5-carboxycytosine (5caC), an epigenetic modification of cytosine, because of a specific hydrogen bond between the carboxyl group of 5caC and a specific residue in fork loop 3 of Pol II. This hydrogen bond compromises productive NTP binding and slows down elongation. Apart from this specific interaction, the carboxyl group of 5caC can potentially interact with numerous charged residues in the cleft of Pol II. However, it is not clear how other interactions between Pol II and 5caC contribute to pausing. In this study, we use Markov state models (a type of kinetic network models) built from extensive molecular dynamics simulations to comprehensively study the impact of 5caC on Pol II translocation. We describe two translocation intermediates with specific interactions that prevent the template base from loading into the Pol II active site. In addition to the previously observed state with 5caC constrained by fork loop 3, we discovered a new intermediate state with a hydrogen bond between 5caC and fork loop 2. Surprisingly, we find that 5caC may curb translocation by suppressing kinking of the helix bordering the active site (the bridge helix) because its high flexibility is critical to translocation. Our work provides new insights into how epigenetic modifications of genomic DNA can modulate Pol II translocation, inducing pauses in transcription.
Collapse
|
6
|
Nottebaum S, Weinzierl ROJ. Transcribing Genes the Hard Way: In Vitro Reconstitution of Nanoarchaeal RNA Polymerase Reveals Unusual Active Site Properties. Front Mol Biosci 2021; 8:669314. [PMID: 34141723 PMCID: PMC8204694 DOI: 10.3389/fmolb.2021.669314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Nanoarchaea represent a highly diverged archaeal phylum that displays many unusual biological features. The Nanoarchaeum equitans genome encodes a complete set of RNA polymerase (RNAP) subunits and basal factors. Several of the standard motifs in the active center contain radical substitutions that are normally expected to render the polymerase catalytically inactive. Here we show that, despite these unusual features, a RNAP reconstituted from recombinant Nanoarchaeum subunits is transcriptionally active. Using a sparse-matrix high-throughput screening method we identified an atypical stringent requirement for fluoride ions to maximize its activity under in vitro transcription conditions.
Collapse
Affiliation(s)
- Sven Nottebaum
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Orthomol Pharmazeutische Vertriebs GmbH, Langenfeld, Germany
| | | |
Collapse
|
7
|
Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Nat Struct Mol Biol 2020; 27:668-677. [PMID: 32541898 DOI: 10.1038/s41594-020-0437-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/22/2020] [Indexed: 12/20/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.
Collapse
|
8
|
POLR1B and neural crest cell anomalies in Treacher Collins syndrome type 4. Genet Med 2019; 22:547-556. [PMID: 31649276 PMCID: PMC7056642 DOI: 10.1038/s41436-019-0669-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/23/2019] [Indexed: 11/11/2022] Open
Abstract
Purpose Treacher Collins syndrome (TCS) is a rare autosomal dominant mandibulofacial dysostosis, with a prevalence of 0.2–1/10,000. Features include bilateral and symmetrical malar and mandibular hypoplasia and facial abnormalities due to abnormal neural crest cell (NCC) migration and differentiation. To date, three genes have been identified: TCOF1, POLR1C, and POLR1D. Despite a large number of patients with a molecular diagnosis, some remain without a known genetic anomaly. Methods We performed exome sequencing for four individuals with TCS but who were negative for pathogenic variants in the known causative genes. The effect of the pathogenic variants was investigated in zebrafish. Results We identified three novel pathogenic variants in POLR1B. Knockdown of polr1b in zebrafish induced an abnormal craniofacial phenotype mimicking TCS that was associated with altered ribosomal gene expression, massive p53-associated cellular apoptosis in the neuroepithelium, and reduced number of NCC derivatives. Conclusion Pathogenic variants in the RNA polymerase I subunit POLR1B might induce massive p53-dependent apoptosis in a restricted neuroepithelium area, altering NCC migration and causing cranioskeletal malformations. We identify POLR1B as a new causative gene responsible for a novel TCS syndrome (TCS4) and establish a novel experimental model in zebrafish to study POLR1B-related TCS.
Collapse
|
9
|
Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
Collapse
|
10
|
Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
Collapse
Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
11
|
Shi J, Feng Y. [New inhibitors targeting bacterial RNA polymerase]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2019; 48:44-49. [PMID: 31102357 PMCID: PMC8800650 DOI: 10.3785/j.issn.1008-9292.2019.02.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/05/2018] [Indexed: 06/09/2023]
Abstract
Rifamycins, a group of bacterial RNA polymerase inhibitors, are the firstline antimicrobial drugs to treat tuberculosis. In light of the emergence of rifamycinresistant bacteria, development of new RNA polymerase inhibitors that kill rifamycinresistant bacteria with high bioavailability is urgent. Structural analysis of bacterial RNA polymerase in complex with inhibitors by crystallography and cryo-EM indicates that RNA polymerase inhibitors function through five distinct molecular mechanisms:inhibition of the extension of short RNA; competition with substrates; inhibition of the conformational change of the'bridge helix'; inhibition of clamp opening;inhibition of clamp closure. This article reviews the research progress of these five groups of RNA polymerase inhibitors to provide references for the modification of existing RNA polymerase inhibitors and the discovery of new RNA polymerase inhibitors.
Collapse
Affiliation(s)
- Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| |
Collapse
|
12
|
Qiu C, Kaplan CD. Functional assays for transcription mechanisms in high-throughput. Methods 2019; 159-160:115-123. [PMID: 30797033 PMCID: PMC6589137 DOI: 10.1016/j.ymeth.2019.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/18/2019] [Indexed: 01/12/2023] Open
Abstract
Dramatic increases in the scale of programmed synthesis of nucleic acid libraries coupled with deep sequencing have powered advances in understanding nucleic acid and protein biology. Biological systems centering on nucleic acids or encoded proteins greatly benefit from such high-throughput studies, given that large DNA variant pools can be synthesized and DNA, or RNA products of transcription, can be easily analyzed by deep sequencing. Here we review the scope of various high-throughput functional assays for studies of nucleic acids and proteins in general, followed by discussion of how these types of study have yielded insights into the RNA Polymerase II (Pol II) active site as an example. We discuss methodological considerations in the design and execution of these experiments that should be valuable to studies in any system.
Collapse
Affiliation(s)
- Chenxi Qiu
- Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
13
|
Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. Hinge action versus grip in translocation by RNA polymerase. Transcription 2017; 9:1-16. [PMID: 28853995 PMCID: PMC5791816 DOI: 10.1080/21541264.2017.1330179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ-β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA-DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K+ and Mg2+ and also an RNA 3'-OH or a 3'-H2 affect RNAP sliding. Because RNAP grip to template suggests a sticky translocation mechanism, and because grip is enhanced by increasing K+ and Mg2+concentration, biochemical assays are consistent with a conformational change that drives forward translocation as observed in simulations. Mutational analysis of the bridge helix indicates that 778-GARKGL-783 (Escherichia coli numbering) is a homeostatic hinge that undergoes multiple bends to compensate for complex conformational dynamics during phosphodiester bond formation and translocation.
Collapse
Affiliation(s)
- Yuri A Nedialkov
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.,b Department of Microbiology , The Ohio State University , Columbus , OH , USA
| | - Kristopher Opron
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.,c Department of Mathematics , Michigan State University , E. Lansing , MI , USA.,d Bioinformatics Core , North Campus Research Complex (NCRC) , Ann Arbor , MI , USA
| | - Hailey L Caudill
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Fadi Assaf
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Amanda J Anderson
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Robert I Cukier
- e Department of Chemistry , Michigan State University , E. Lansing , MI , USA
| | - Guowei Wei
- c Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - Zachary F Burton
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| |
Collapse
|
14
|
Maffioli SI, 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. Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Cell 2017. [PMID: 28622509 DOI: 10.1016/j.cell.2017.05.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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.
Collapse
Affiliation(s)
- Sonia I Maffioli
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Yu Zhang
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Thomas Carzaniga
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | | | - Stefania Serina
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | - Paolo Monciardini
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy
| | | | | | | | - Alina Iulia Chiriac
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | | | | | - Hans-Georg Sahl
- Institute of Medical Microbiology, Immunology, and Parasitology, University of Bonn, D-53012 Bonn, Germany
| | - Gianni Dehò
- Department of Bioscience, University of Milan, 20122 Milan, Italy
| | - Stefano Donadio
- NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy.
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
15
|
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. Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Mol Cell 2017; 66:169-179.e8. [PMID: 28392175 DOI: 10.1016/j.molcel.2017.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023]
Abstract
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.
Collapse
Affiliation(s)
- Wei Lin
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Soma Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shengjian Li
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Sukhendu Mandal
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yi Jiang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
16
|
Wang ZF, Fu YB, Wang PY, Xie P. Dynamics of bridge helix bending in RNA polymerase II. Proteins 2017; 85:614-629. [DOI: 10.1002/prot.25239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Zhan-Feng Wang
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics; Institute of Physics, Chinese Academy of Sciences; Beijing 100190 China
| | - Yi-Ben Fu
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics; Institute of Physics, Chinese Academy of Sciences; Beijing 100190 China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics; Institute of Physics, Chinese Academy of Sciences; Beijing 100190 China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics; Institute of Physics, Chinese Academy of Sciences; Beijing 100190 China
| |
Collapse
|
17
|
High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 2016; 12:e1006321. [PMID: 27898685 PMCID: PMC5127505 DOI: 10.1371/journal.pgen.1006321] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/24/2016] [Indexed: 11/30/2022] Open
Abstract
The active sites of multisubunit RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins. Proper regulation of Pol II transcription, the first step of gene expression, is essential for life. Extensive evidence has revealed a widely conserved and dynamic polymerase active site component, termed the Trigger Loop (TL), in balancing transcription rate and fidelity while possibly allowing control of transcription elongation. Coupling high-throughput sequencing with our previously established genetic system, we are able to assess the in vivo phenotypes for almost all possible single substitution Pol II TL mutants in the budding yeast Saccharomyces cerevisiae. We show that mutants in the TL nucleotide interacting and linker regions widely confer dominant and severe growth defects. Clustering of TL mutants’ transcription-related and general stress phenotypes reveals three main classes of TL mutants, including previously identified fast and slow elongating mutants. Comprehensive analyses of the distribution of fast and slow elongation mutants in light of existing Pol II crystal structures reveal critical regions contributing to proper TL dynamics and function. Evidence is presented linking a previously observed hydrophobic pocket to NTP substrate-induced TL closing, the mechanism critical for correct substrates selection and transcription fidelity. Finally, we assess the functional interplay between TL and its proximal domains, and their presumptive roles in the function and evolution of the TL. Utilizing the Pol II TL as a case study, we present a structural genetics approach that reveals insights into a complex, multi-functional, and essential domain in yeast.
Collapse
|
18
|
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst 2016; 2:260-71. [PMID: 27135538 DOI: 10.1016/j.cels.2016.04.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/10/2015] [Accepted: 04/06/2016] [Indexed: 11/20/2022]
Abstract
Pleiotropic regulatory mutations affect diverse cellular processes, posing a challenge to our understanding of genotype-phenotype relationships across multiple biological scales. Adaptive laboratory evolution (ALE) allows for such mutations to be found and characterized in the context of clear selection pressures. Here, several ALE-selected single-mutation variants in RNA polymerase (RNAP) of Escherichia coli are detailed using an integrated multi-scale experimental and computational approach. While these mutations increase cellular growth rates in steady environments, they reduce tolerance to stress and environmental fluctuations. We detail structural changes in the RNAP that rewire the transcriptional machinery to rebalance proteome and energy allocation toward growth and away from several hedging and stress functions. We find that while these mutations occur in diverse locations in the RNAP, they share a common adaptive mechanism. In turn, these findings highlight the resource allocation trade-offs organisms face and suggest how the structure of the regulatory network enhances evolvability.
Collapse
Affiliation(s)
- Jose Utrilla
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, México
| | - Edward J O'Brien
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ke Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Douglas McCloskey
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jacky Cheung
- Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Harris Wang
- Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Dagoberto Armenta-Medina
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, 62210 Cuernavaca, Morelos, Mexico
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
19
|
CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. Proc Natl Acad Sci U S A 2015; 112:E4178-87. [PMID: 26195788 PMCID: PMC4534225 DOI: 10.1073/pnas.1502368112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg(2+) ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. We report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.
Collapse
|
20
|
Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure 2015; 23:1470-1481. [PMID: 26190576 DOI: 10.1016/j.str.2015.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/30/2022]
Abstract
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.
Collapse
Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Xinyue Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Deepankar Das
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Trevor Michalchuk
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
21
|
Smollett K, Blombach F, Werner F. Transcription in Archaea: preparation of Methanocaldococcus jannaschii transcription machinery. Methods Mol Biol 2015; 1276:291-303. [PMID: 25665571 DOI: 10.1007/978-1-4939-2392-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Archaeal RNA polymerase and general transcription factors are more closely related to those of eukaryotes than of bacteria. As such the study of transcription of archaea is important both in terms of examination of the evolution of the transcriptional machinery and as a simplified tool for eukaryotic transcription. In particular, the hyperthermophilic Methanocaldococcus jannaschii provides us with a fully recombinant RNA polymerase system allowing for much more detailed in vitro examination of the roles of different components during the transcription cycle than otherwise possible. The individual subunits of M. jannaschii enzyme are easily expressed and purified from heterologous expression systems. Forming functional RNA polymerase involves simply combining the different subunits under denaturing conditions and slowly removing the denaturant.
Collapse
Affiliation(s)
- Katherine Smollett
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London, WC1E 6BT, UK,
| | | | | |
Collapse
|
22
|
Windgassen TA, Mooney RA, Nayak D, Palangat M, Zhang J, Landick R. Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase. Nucleic Acids Res 2014; 42:12707-21. [PMID: 25336618 PMCID: PMC4227799 DOI: 10.1093/nar/gku997] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The conformational dynamics of the polymorphous trigger loop (TL) in RNA polymerase (RNAP) underlie multiple steps in the nucleotide addition cycle and diverse regulatory mechanisms. These mechanisms include nascent RNA hairpin-stabilized pausing, which inhibits TL folding into the trigger helices (TH) required for rapid nucleotide addition. The nascent RNA pause hairpin forms in the RNA exit channel and promotes opening of the RNAP clamp domain, which in turn stabilizes a partially folded, paused TL conformation that disfavors TH formation. We report that inhibiting TH unfolding with a disulfide crosslink slowed multiround nucleotide addition only modestly but eliminated hairpin-stabilized pausing. Conversely, a substitution that disrupts the TH folding pathway and uncouples establishment of key TH–NTP contacts from complete TH formation and clamp movement allowed rapid catalysis and eliminated hairpin-stabilized pausing. We also report that the active-site distal arm of the TH aids TL folding, but that a 188-aa insertion in the Escherichia coli TL (sequence insertion 3; SI3) disfavors TH formation and stimulates pausing. The effect of SI3 depends on the jaw domain, but not on downstream duplex DNA. Our results support the view that both SI3 and the pause hairpin modulate TL folding in a constrained pathway of intermediate states.
Collapse
Affiliation(s)
- Tricia A Windgassen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dhananjaya Nayak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Murali Palangat
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jinwei Zhang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
23
|
Diaz C, Corentin H, Thierry V, Chantal A, Tanguy B, David S, Jean-Marc H, Pascual F, Françoise B, Edgardo F. Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators. Proteins 2014; 82:2982-97. [PMID: 25082719 DOI: 10.1002/prot.24657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/15/2022]
Abstract
The secondary structure of some protein segments may vary between α-helix and β-strand. To predict these switchable segments, we have developed an algorithm, Switch-P, based solely on the protein sequence. This algorithm was used on the extracellular parts of FGF receptors. For FGFR2, it predicted that β4 and β5 strands of the third Ig-like domain were highly switchable. These two strands possess a high number of somatic mutations associated with cancer. Analysis of PDB structures of FGF receptors confirmed the switchability prediction for β5. We thus evaluated if compound-driven α-helix/β-strand switching of β5 could modulate FGFR2 signaling. We performed the virtual screening of a library containing 1.4 million of chemical compounds with two models of the third Ig-like domain of FGFR2 showing different secondary structures for β5, and we selected 32 compounds. Experimental testing using proliferation assays with FGF7-stimulated SNU-16 cells and a FGFR2-dependent Erk1/2 phosphorylation assay with FGFR2-transfected L6 cells, revealed activators and inhibitors of FGFR2. Our method for the identification of switchable proteinic regions, associated with our virtual screening approach, provides an opportunity to discover new generation of drugs with under-explored mechanism of action.
Collapse
Affiliation(s)
- Constantino Diaz
- Exploratory Unit, Sanofi-Aventis Research and Development, 195 Route d'Espagne, 31036, Toulouse, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. eLife 2014; 3:e02451. [PMID: 24843001 PMCID: PMC4029172 DOI: 10.7554/elife.02451] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
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. DOI:http://dx.doi.org/10.7554/eLife.02451.001 The need for new antibiotics is becoming increasingly critical, as more and more bacteria become resistant to existing drugs. To develop new treatments, researchers need to understand how antibiotics work. One way antibiotics can kill bacteria is by targeting an enzyme called bacterial RNA polymerase. This enzyme builds chains of RNA that bacteria need to survive. Sal is an antibiotic produced by a marine bacterium found on the surface of a species of jellyfish. Degen, Feng et al. show that Sal kills bacteria by inhibiting bacterial RNA polymerase and explain how Sal inhibits RNA polymerase. Sal binds to a rod-like structural element within RNA polymerase known as the ‘bridge helix’. The bridge helix has been proposed by others to contain two ‘hinges’ that open and close—allowing the bridge helix to bend and unbend—at specific steps in the cycle through which RNA polymerase builds an RNA chain. Degen, Feng et al. show that Sal binds directly to one of the two hinges and show that Sal binds to the hinge in the unbent state. Therefore, Degen, Feng et al. propose that Sal inhibits the enzyme by preventing the hinge from bending. The binding site on RNA polymerase for Sal is different from, and does not overlap, the binding sites of current antibacterial drugs. As a result, Sal is able to kill bacteria that are resistant to current antibacterial drugs. When Degen, Feng et al. administered Sal in combination with a current antibacterial drug that targets RNA polymerase, bacteria did not detectably develop resistance to either Sal or the current antibacterial drug. The structure of the complex between Sal and RNA polymerase suggests several ways that Sal could be modified to improve its ability to interact with RNA polymerase, thereby potentially increasing Sal's antibacterial activity. Future research could develop a range of new drugs based on Sal that could kill bacteria more effectively. DOI:http://dx.doi.org/10.7554/eLife.02451.002
Collapse
Affiliation(s)
- David Degen
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Feng
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | - Yon W Ebright
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | | | - Sukhendu Mandal
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, United States
| | | |
Collapse
|
25
|
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. eLife 2014; 3:e02450. [PMID: 24755292 PMCID: PMC3994528 DOI: 10.7554/elife.02450] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
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. DOI:http://dx.doi.org/10.7554/eLife.02450.001 As increasing numbers of bacteria become resistant to antibiotics, new drugs are needed to fight bacterial infections. To develop new antibacterial drugs, researchers need to understand how existing antibiotics work. There are many ways to kill bacteria, but one of the most effective is to target an enzyme called bacterial RNA polymerase. If bacterial RNA polymerase is prevented from working, bacteria cannot synthesize RNA and cannot survive. GE23077 (GE for short) is an antibiotic produced by bacteria found in soil. Although GE stops bacterial RNA polymerase from working, and thereby kills bacteria, it does not affect mammalian RNA polymerases, and so does not kill mammalian cells. Understanding how GE works could help with the development of new antibacterial drugs. Zhang et al. present results gathered from a range of techniques to show how GE inhibits bacterial RNA polymerase. These show that GE works by binding to a site on RNA polymerase that is different from the binding sites of previously characterized antibacterial drugs. The mechanism used to inhibit the RNA polymerase is also different. The newly identified binding site has several features that make it an unusually attractive target for development of antibacterial compounds. Bacteria can become resistant to an antibiotic if genetic mutations lead to changes in the site the antibiotic binds to. However, the site that GE binds to on RNA polymerase is essential for RNA polymerase to function and so cannot readily be changed without crippling the enzyme. Therefore, this type of antibiotic resistance is less likely to develop. In addition, the newly identified binding site for GE on RNA polymerase is located next to the binding site for a current antibacterial drug, rifampin. Zhang et al. therefore linked GE and rifampin to form a two-part (‘bipartite’) compound designed to bind simultaneously to the GE and the rifampin binding sites. This compound was able to inhibit drug-resistant RNA polymerases tens to thousands of times more potently than GE or rifampin alone. DOI:http://dx.doi.org/10.7554/eLife.02450.002
Collapse
Affiliation(s)
- Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Malinen AM, NandyMazumdar M, Turtola M, Malmi H, Grocholski T, Artsimovitch I, Belogurov GA. CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase. Nat Commun 2014; 5:3408. [PMID: 24598909 PMCID: PMC3959191 DOI: 10.1038/ncomms4408] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/06/2014] [Indexed: 01/17/2023] Open
Abstract
Bacterial RNA polymerase (RNAP) is a validated target for antibacterial drugs. CBR703 series antimicrobials allosterically inhibit transcription by binding to a conserved α helix (β' bridge helix, BH) that interconnects the two largest RNAP subunits. Here we show that disruption of the BH-β subunit contacts by amino-acid substitutions invariably results in accelerated catalysis, slowed-down forward translocation and insensitivity to regulatory pauses. CBR703 partially reverses these effects in CBR-resistant RNAPs while inhibiting catalysis and promoting pausing in CBR-sensitive RNAPs. The differential response of variant RNAPs to CBR703 suggests that the inhibitor binds in a cavity walled by the BH, the β' F-loop and the β fork loop. Collectively, our data are consistent with a model in which the β subunit fine tunes RNAP elongation activities by altering the BH conformation, whereas CBRs deregulate transcription by increasing coupling between the BH and the β subunit.
Collapse
Affiliation(s)
- Anssi M. Malinen
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Monali NandyMazumdar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Matti Turtola
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Henri Malmi
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Thadee Grocholski
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | | |
Collapse
|
27
|
Wang B, Feig M, Cukier RI, Burton ZF. Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev 2013; 113:8546-66. [PMID: 23987500 PMCID: PMC3829680 DOI: 10.1021/cr400046x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Beibei Wang
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
| | - Michael Feig
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Robert I. Cukier
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zachary F. Burton
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824-1319, United States
| |
Collapse
|
28
|
Affiliation(s)
- Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London , Darwin Building, Gower Street, London WC1E 6BT, U.K
| |
Collapse
|
29
|
Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
| |
Collapse
|
30
|
Nayak D, Voss M, Windgassen T, Mooney RA, Landick R. Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase. Mol Cell 2013; 50:882-93. [PMID: 23769674 DOI: 10.1016/j.molcel.2013.05.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/10/2013] [Accepted: 05/07/2013] [Indexed: 01/22/2023]
Abstract
Transcriptional pausing, which regulates transcript elongation in both prokaryotes and eukaryotes, is thought to involve formation of alternative RNA polymerase conformations in which nucleotide addition is inhibited in part by restriction of trigger loop (TL) folding. The polymorphous TL must convert from a random coil to a helical hairpin that contacts the nucleotide triphosphate (NTP) substrate to allow rapid nucleotide addition. Understanding the distribution of TL conformations in different enzyme states is made difficult by the TL's small size and sensitive energetics. Here, we report a Cys-pair reporter strategy to elucidate the relative occupancies of different TL conformations in E. coli RNA polymerase based on the ability of Cys residues engineered into the TL and surrounding regions to form disulfide bonds. Our results indicate that a paused complex stabilized by a nascent RNA hairpin favors nonproductive TL conformations that persist after NTP binding but can be reversed by the elongation factor RfaH.
Collapse
Affiliation(s)
- Dhananjaya Nayak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | | | | | | |
Collapse
|
31
|
Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF. The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:187-98. [PMID: 23202476 PMCID: PMC3619131 DOI: 10.1016/j.bbagrm.2012.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/14/2012] [Accepted: 11/17/2012] [Indexed: 01/22/2023]
Abstract
The bridge α-helix in the β' subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation. In Escherichia coli RNAP, a bulky hydrophobic segment near the N-terminal end of the bridge helix is identified (β' 772-YFI-774; the YFI motif). YFI is located at a distance from the active center and adjacent to a glycine hinge (β' 778-GARKG-782) involved in dynamic bending of the bridge helix. Remarkably, amino acid substitutions in YFI significantly alter intrinsic termination, pausing, fidelity and translocation of RNAP. F773V RNAP largely ignores the λ tR2 terminator at 200μM NTPs and is strongly reduced in λ tR2 recognition at 1μM NTPs. F773V alters RNAP pausing and backtracking and favors misincorporation. By contrast, the adjacent Y772A substitution increases fidelity and exhibits other transcriptional defects generally opposite to those of F773V. All atom molecular dynamics simulation revealed two separate functional connections emanating from YFI explaining the distinct effects of substitutions: Y772 communicates with the active site through the link domain in the β subunit, whereas F773 communicates through the fork domain in the β subunit. I774 interacts with the F-loop, which also contacts the glycine hinge of the bridge helix. These results identified negative and positive circuits coupled at YFI and employed for regulation of catalysis, elongation, termination and translocation.
Collapse
Affiliation(s)
- Yuri A. Nedialkov
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
| | - Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Fadi Assaf
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio USA
| | - Maria L. Kireeva
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Mikhail Kashlev
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert I. Cukier
- Department of Chemistry, Michigan State University, E. Lansing, MI 48824-1319, USA
| | - Evgeny Nudler
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
| | - Zachary F. Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
| |
Collapse
|
32
|
Wiesler SC, Werner F, Weinzierl ROJ. Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase. Methods Mol Biol 2013; 977:217-227. [PMID: 23436365 DOI: 10.1007/978-1-62703-284-1_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
TFIIB-like general transcription factors are required for transcription initiation by all eukaryotic and archaeal RNA polymerases (RNAPs). TFIIB facilitates both recruitment and post-recruitment steps of initiation; in particular, TFIIB stimulates abortive initiation. X-ray crystallography of TFIIB-RNAP II complexes shows that the TFIIB linker region penetrates the RNAP active center, yet the impact of this arrangement on RNAP activity and underlying mechanisms remains elusive. Promoter-independent abortive initiation assays exploit the intrinsic ability of RNAP enzymes to initiate transcription from nicked DNA templates and record the formation of the first phosphodiester bonds. These assays can be used to measure the effect of transcription factors such as TFIIB and RNAP mutations on abortive transcription.
Collapse
Affiliation(s)
- Simone C Wiesler
- Department of Life Sciences, Imperial College London, London, UK
| | | | | |
Collapse
|
33
|
Kaplan CD. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:39-54. [PMID: 23022618 DOI: 10.1016/j.bbagrm.2012.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 01/12/2023]
Abstract
Transcription by RNA polymerase II (Pol II), and all RNA polymerases for that matter, may be understood as comprising two cycles. The first cycle relates to the basic mechanism of the transcription process wherein Pol II must select the appropriate nucleoside triphosphate (NTP) substrate complementary to the DNA template, catalyze phosphodiester bond formation, and translocate to the next position on the DNA template. Performing this cycle in an iterative fashion allows the synthesis of RNA chains that can be over one million nucleotides in length in some larger eukaryotes. Overlaid upon this enzymatic cycle, transcription may be divided into another cycle of three phases: initiation, elongation, and termination. Each of these phases has a large number of associated transcription factors that function to promote or regulate the gene expression process. Complicating matters, each phase of the latter transcription cycle are coincident with cotranscriptional RNA processing events. Additionally, transcription takes place within a highly dynamic and regulated chromatin environment. This chromatin environment is radically impacted by active transcription and associated chromatin modifications and remodeling, while also functioning as a major platform for Pol II regulation. This review will focus on our basic knowledge of the Pol II transcription mechanism, and how altered Pol II activity impacts gene expression in vivo in the model eukaryote Saccharomyces cerevisiae. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
| |
Collapse
|
34
|
Nedialkov YA, Nudler E, Burton ZF. RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription 2012; 3:260-9. [PMID: 23132506 PMCID: PMC3632624 DOI: 10.4161/trns.22307] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Exonuclease (Exo) III was used to probe translocation states of RNA polymerase (RNAP) ternary elongation complexes (TECs). Escherichia coli RNAP stalls primarily in a post-translocation register that makes relatively slow excursions to a hyper-translocated state or to a pre-translocated state. Tagetitoxin (TGT) strongly inhibits hyper-translocation and inhibits backtracking, so, as indicated by Exo III mapping, TGT appears to stabilize both the pre- and probably a partially post-translocation state of RNAP. Because the pre-translocated to post-translocated transition is slow at many template positions, these studies appear inconsistent with a model in which RNAP makes frequent and rapid (i.e., millisecond phase) oscillations between pre- and post-translocation states. Nine nucleotides (9-nt) and 10-nt TECs, and TECs with longer nascent RNAs, have distinct translocation properties consistent with a 9–10 nt RNA/DNA hybrid. RNAP mutant proteins in the bridge helix and trigger loop are identified that inhibit or stimulate forward and backward translocation.
Collapse
Affiliation(s)
- Yuri A Nedialkov
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | | |
Collapse
|
35
|
Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF. Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC BIOPHYSICS 2012; 5:11. [PMID: 22676913 PMCID: PMC3533926 DOI: 10.1186/2046-1682-5-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/07/2012] [Indexed: 11/10/2022]
Abstract
UNLABELLED BACKGROUND During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile "trigger loop" of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the "bridge helix" that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. RESULTS All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as "switch" residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop. CONCLUSIONS Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation.
Collapse
Affiliation(s)
- Maria L Kireeva
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
| | - Steve A Seibold
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
- Department of Chemistry, Michigan State University, E. Lansing, MI, 48824, USA
- Department of Chemistry, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Céline Domecq
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), 110, Avenue des Pins Ouest, Montréal, Québec, H2W 1R7, CANADA
| | - Robert I Cukier
- Department of Chemistry, Michigan State University, E. Lansing, MI, 48824, USA
| | - Benoit Coulombe
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), 110, Avenue des Pins Ouest, Montréal, Québec, H2W 1R7, CANADA
- Department of Biochemistry, Université de Montréal, Montréal, Québec, H3C 3J7, CANADA
| | - Mikhail Kashlev
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, 21702-1201, USA
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, 48824-1319, USA
| |
Collapse
|
36
|
The Bridge Helix of RNA polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2011:608385. [PMID: 22312317 PMCID: PMC3270539 DOI: 10.1155/2011/608385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/25/2011] [Indexed: 11/17/2022]
Abstract
The availability of in vitro assembly systems to produce recombinant archaeal RNA polymerases (RNAPs) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying RNAP function. Over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. The Bridge Helix domain, which appears in numerous X-ray structures as a 35-amino-acid-long alpha helix, coordinates the concerted movement of several other domains during catalysis through kinking of two discrete molecular hinges. Mutations affecting these kinking mechanisms have a direct effect on the specific catalytic activity of RNAP and can in some instances more than double it. Molecular dynamics simulations have established themselves as exceptionally useful for providing additional insights and detailed models to explain the underlying structural motions.
Collapse
|
37
|
Sevostyanova A, Belogurov GA, Mooney RA, Landick R, Artsimovitch I. The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol Cell 2012; 43:253-62. [PMID: 21777814 DOI: 10.1016/j.molcel.2011.05.026] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/25/2011] [Accepted: 05/16/2011] [Indexed: 10/18/2022]
Abstract
In all organisms, RNA polymerase (RNAP) relies on accessory factors to complete synthesis of long RNAs. These factors increase RNAP processivity by reducing pausing and termination, but their molecular mechanisms remain incompletely understood. We identify the β gate loop as an RNAP element required for antipausing activity of a bacterial virulence factor RfaH, a member of the universally conserved NusG family. Interactions with the gate loop are necessary for suppression of pausing and termination by RfaH, but are dispensable for RfaH binding to RNAP mediated by the β' clamp helices. We hypothesize that upon binding to the clamp helices and the gate loop RfaH bridges the gap across the DNA channel, stabilizing RNAP contacts with nucleic acid and disfavoring isomerization into a paused state. We show that contacts with the gate loop are also required for antipausing by NusG and propose that most NusG homologs use similar mechanisms to increase RNAP processivity.
Collapse
Affiliation(s)
- Anastasia Sevostyanova
- Department of Microbiology and the RNA Group, Ohio State University, Columbus, OH 43210, USA
| | | | | | | | | |
Collapse
|
38
|
Danchin A, Binder PM, Noria S. Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk. Genes (Basel) 2011; 2:998-1016. [PMID: 24710302 PMCID: PMC3927596 DOI: 10.3390/genes2040998] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/25/2011] [Accepted: 11/16/2011] [Indexed: 12/25/2022] Open
Abstract
The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to 'tinker', i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles.
Collapse
Affiliation(s)
- Antoine Danchin
- AMAbiotics SAS, CEA/Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.
| | - Philippe M Binder
- Natural Sciences Division, University of Hawaii, Hilo, HI 96720-4091, USA.
| | - Stanislas Noria
- Fondation Fourmentin-Guilbert, 2 avenue du Pavé Neuf, 93160 Noisy-le-Grand, France.
| |
Collapse
|
39
|
Jovanovic M, Burrows PC, Bose D, Cámara B, Wiesler S, Zhang X, Wigneshweraraj S, Weinzierl ROJ, Buck M. Activity map of the Escherichia coli RNA polymerase bridge helix. J Biol Chem 2011; 286:14469-79. [PMID: 21357417 PMCID: PMC3077646 DOI: 10.1074/jbc.m110.212902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Transcription, the synthesis of RNA from a DNA template, is performed by multisubunit RNA polymerases (RNAPs) in all cellular organisms. The bridge helix (BH) is a distinct feature of all multisubunit RNAPs and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and RNA and DNA binding. Because the BH has been captured in both kinked and straight conformations in different crystals structures of RNAP, recently supported by molecular dynamics studies, it has been proposed that cycling between these conformations is an integral part of the nucleotide addition cycle. To further evaluate the role of the BH, we conducted systematic alanine scanning mutagenesis of the Escherichia coli RNAP BH to determine its contributions to activities required for transcription. Combining our data with an atomic model of E. coli RNAP, we suggest that alterations in the interactions between the BH and (i) the trigger loop, (ii) fork loop 2, and (iii) switch 2 can help explain the observed changes in RNAP functionality associated with some of the BH variants. Additionally, we show that extensive defects in E. coli RNAP functionality depend upon a single previously not studied lysine residue (Lys-781) that is strictly conserved in all bacteria. It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality.
Collapse
Affiliation(s)
- Milija Jovanovic
- Division of Biology, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kindgom
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Hein PP, Landick R. The bridge helix coordinates movements of modules in RNA polymerase. BMC Biol 2010; 8:141. [PMID: 21114873 PMCID: PMC2993669 DOI: 10.1186/1741-7007-8-141] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 11/25/2010] [Indexed: 02/07/2023] Open
Abstract
The RNA polymerase 'bridge helix' is a metastable α-helix that spans the leading edge of the enzyme active-site cleft. A new study published in BMC Biology reveals surprising tolerance to helix-disrupting changes in a region previously thought crucial for translocation, and suggests roles for two hinge-like segments of the bridge helix in coordinating modules that move during the nucleotide-addition cycle. See Research article: http://www.biomedcentral.com/1741-7007/8/134
Collapse
Affiliation(s)
- Pyae P Hein
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | |
Collapse
|