51
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Long C, E. C, Da LT, Yu J. A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control. Comput Struct Biotechnol J 2019; 17:638-644. [PMID: 31193497 PMCID: PMC6535458 DOI: 10.1016/j.csbj.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022] Open
Abstract
RNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation. Here we summarize our computational work from several recent publications to demonstrate first how T7 RNAP translocates via Brownian alike motions along DNA right after the catalytic product release. Then we show how the backward translocation motions are prevented at post-translocation upon successful nucleotide incorporation, which is also subject to stepwise nucleotide selection and acts as a pawl for "selective ratcheting". The structural dynamics and energetics features revealed from our atomistic molecular dynamics (MD) simulations and related analyses on the single-subunit T7 RNAP thus provided detailed and quantitative characterizations on the Brownian-ratchet working scenario of a prototypical transcription machine with sophisticated nucleotide selectivity for fidelity control. The presented mechanisms can be more or less general for structurally similar viral or mitochondrial RNAPs and some of DNA polymerases, or even for the RNAP engine of the more complicated transcription machinery in higher organisms.
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Affiliation(s)
- Chunhong Long
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Chao E.
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing, 100193, China
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52
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RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing. Mol Cell 2019; 72:369-379.e4. [PMID: 30340024 PMCID: PMC6201815 DOI: 10.1016/j.molcel.2018.09.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 07/23/2018] [Accepted: 08/31/2018] [Indexed: 01/22/2023]
Abstract
The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in footprints of approximately 60 nucleotides. Also, splicing intermediates formed by cleavage at the 5′ splice site are associated with nearly all spliced exons. These spliceosome-bound intermediates are frequently ligated to upstream exons, implying a sequential, constitutive, and U12-dependent splicing process. Finally, lack of detectable spliced products connected to the Pol II active site in human HeLa or murine lymphoid cells suggests that splicing does not occur immediately following 3′ splice site synthesis. Our results imply that most mammalian splicing requires exon definition for completion. S5P CTD Pol II associates with the catalytic spliceosome Elongating Pol II complexes protect about 60 newly synthesized nucleotides Co-transcriptional splicing associated with dominant 5′ ss intermediate U12-dependent introns are sequentially spliced in association with Pol II
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53
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Lin G, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals. Methods 2019; 159-160:23-28. [PMID: 31029767 DOI: 10.1016/j.ymeth.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
Well-diffracting crystals are essential to obtain relevant structural data that will lead to understanding of RNA Polymerase II (Pol II) transcriptional processes at a molecular level. Here we present a strategy to study Pol II crystals using negative stain transmission electron microscopy (TEM) and a methodology to optimize radiation damage free data collection using free electron laser (FEL) at the Linac Coherent Light Source (LCLS). The use of negative stain TEM allowed visualization and optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nano crystals bearing perfect lattices were seeded and used to grow larger crystals for FEL data collection. Moreover, the use of in house designed crystal loops together with ultra-violet (UV) microscopy for crystal detection facilitated data collection. Such strategy permitted collection of multiple crystals of radiation-free-damage data, resulting in the highest resolution of wild type (WT) Pol II crystals ever observed.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Carlos Camacho
- Department of Computanional and Systems Biology, University of Pittsburgh School of Medicine, United States
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States.
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54
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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: 1.3] [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.
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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.
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55
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Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Müller CW. The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. eLife 2019; 8:43204. [PMID: 30913026 PMCID: PMC6435322 DOI: 10.7554/elife.43204] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/09/2019] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-EM structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the Pol I-specific transcription-like factors A49-A34.5 and A12.2. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our structural and biochemical data suggest a mechanism where reversible binding of the A49-A34.5 heterodimer could contribute to the regulation of Pol I transcription initiation and elongation.
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Affiliation(s)
- Lucas Tafur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree, European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Yashar Sadian
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Hanske
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rene Wetzel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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56
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Sanders TJ, Lammers M, Marshall CJ, Walker JE, Lynch ER, Santangelo TJ. TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin. Mol Microbiol 2019; 111:784-797. [PMID: 30592095 PMCID: PMC6417941 DOI: 10.1111/mmi.14191] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA-bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin-remodeling complexes, histone-modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone-based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin-barriers. TFS (TFIIS in Eukarya) and the Spt4-Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone-based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS-enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone-barriers, while Spt4-Spt5 changes to clamp-domain dynamics play a lesser-role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.
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Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Marshall Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Current address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, 80303, USA
| | - Erin R. Lynch
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
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57
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Mishra S, Maraia RJ. RNA polymerase III subunits C37/53 modulate rU:dA hybrid 3' end dynamics during transcription termination. Nucleic Acids Res 2019; 47:310-327. [PMID: 30407541 PMCID: PMC6326807 DOI: 10.1093/nar/gky1109] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/22/2018] [Indexed: 12/18/2022] Open
Abstract
RNA polymerase (RNAP) III synthesizes tRNAs and other transcripts, and mutations to its subunits cause human disorders. The RNAP III subunit-heterodimer C37/53 functions in initiation, elongation and in termination-associated reinitiation with subunit C11. C37/53 is related to heterodimers associated with RNAPs I and II, and C11 is related to TFIIS and Rpa12.2, the active site RNA 3' cleavage factors for RNAPs II and I. Critical to termination is stability of the RNA:DNA hybrid bound in the active center, which is loose for RNAP III relative to other RNAPs. Here, we examined RNAP III lacking C37/53/C11 and various reconstituted forms during termination. First, we established a minimal terminator as 5T and 3A on the non-template and template DNA strands, respectively. We demonstrate that C11 stimulates termination, and does so independently of its RNA cleavage activity. We found that C37/53 sensitizes RNAP III termination to RNA:DNA hybrid strength and promotes RNA 3' end pairing/annealing with the template. The latter counteracts C11-insensitive arrest in the proximal part of the oligo(T)-tract, promoting oligo(rU:dA) extension toward greater hybrid instability and RNA release. The data also indicate that RNA 3' end engagement with the active site is a determinant of termination. Broader implications are also discussed.
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Affiliation(s)
- Saurabh Mishra
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J Maraia
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD 20852, USA
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58
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Farnung L, Vos SM, Cramer P. Structure of transcribing RNA polymerase II-nucleosome complex. Nat Commun 2018; 9:5432. [PMID: 30575770 PMCID: PMC6303367 DOI: 10.1038/s41467-018-07870-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/05/2018] [Indexed: 01/08/2023] Open
Abstract
Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription. Eukaryotic transcription requires passage of RNA polymerase II (Pol II) through chromatin, which is impaired by nucleosomes. Here the authors report the cryo-EM structure of transcribing Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å, providing insights into the mechanism of chromatin transcription.
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Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany.
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59
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Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate. Mol Cell 2018; 73:107-118.e4. [PMID: 30503775 DOI: 10.1016/j.molcel.2018.10.031] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 10/17/2018] [Indexed: 10/27/2022]
Abstract
In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. How TFIIS affects transcription under normal conditions is poorly understood. We identified backtracking sites in human cells using a dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3' flanking regions where termination is enhanced by TFIISDN, suggesting that backtracked pol II is a favorable substrate for termination. Rescue from backtracking by RNA cleavage also promotes escape from 5' pause sites, prevents premature termination of long transcripts, and enhances activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half, suggesting that rescue of backtracked pol II by TFIIS is a major stimulus of elongation under normal conditions.
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60
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Sýkora M, Pospíšek M, Novák J, Mrvová S, Krásný L, Vopálenský V. Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin. PLoS Pathog 2018; 14:e1007377. [PMID: 30346988 PMCID: PMC6211774 DOI: 10.1371/journal.ppat.1007377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/01/2018] [Accepted: 10/03/2018] [Indexed: 11/19/2022] Open
Abstract
Extrachromosomal hereditary elements such as organelles, viruses, and plasmids are important for the cell fitness and survival. Their transcription is dependent on host cellular RNA polymerase (RNAP) or intrinsic RNAP encoded by these elements. The yeast Kluyveromyces lactis contains linear cytoplasmic DNA virus-like elements (VLEs, also known as linear plasmids) that bear genes encoding putative non-canonical two-subunit RNAP. Here, we describe the architecture and identify the evolutionary origin of this transcription machinery. We show that the two RNAP subunits interact in vivo, and this complex interacts with another two VLE-encoded proteins, namely the mRNA capping enzyme and a putative helicase. RNAP, mRNA capping enzyme and the helicase also interact with VLE-specific DNA in vivo. Further, we identify a promoter sequence element that causes 5' mRNA polyadenylation of VLE-specific transcripts via RNAP slippage at the transcription initiation site, and structural elements that precede the termination sites. As a result, we present a first model of the yeast virus-like element transcription initiation and intrinsic termination. Finally, we demonstrate that VLE RNAP and its promoters display high similarity to poxviral RNAP and promoters of early poxviral genes, respectively, thereby pointing to their evolutionary origin.
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Affiliation(s)
- Michal Sýkora
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Pospíšek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
| | - Josef Novák
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Silvia Mrvová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Václav Vopálenský
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
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61
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Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernández-Tornero C. Structural basis of RNA polymerase I stalling at UV light-induced DNA damage. Proc Natl Acad Sci U S A 2018; 115:8972-8977. [PMID: 30127008 PMCID: PMC6130403 DOI: 10.1073/pnas.1802626115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase I (Pol I) transcribes ribosomal DNA (rDNA) to produce the ribosomal RNA (rRNA) precursor, which accounts for up to 60% of the total transcriptional activity in growing cells. Pol I monitors rDNA integrity and influences cell survival, but little is known about how this enzyme processes UV-induced lesions. We report the electron cryomicroscopy structure of Pol I in an elongation complex containing a cyclobutane pyrimidine dimer (CPD) at a resolution of 3.6 Å. The structure shows that the lesion induces an early translocation intermediate exhibiting unique features. The bridge helix residue Arg1015 plays a major role in CPD-induced Pol I stalling, as confirmed by mutational analysis. These results, together with biochemical data presented here, reveal the molecular mechanism of Pol I stalling by CPD lesions, which is distinct from Pol II arrest by CPD lesions. Our findings open the avenue to unravel the molecular mechanisms underlying cell endurance to lesions on rDNA.
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Affiliation(s)
- Marta Sanz-Murillo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain
| | - Jun Xu
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0625
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093-0625
| | | | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain
| | - David Gil-Carton
- Structural Biology Unit, Cooperative Center for Research in Biosciences (CIC bioGUNE), 48160 Derio, Spain
| | - María Moreno-Morcillo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC, 28049 Madrid, Spain
| | - Dong Wang
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093-0625;
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093-0625
| | - Carlos Fernández-Tornero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas (CSIC), 28040 Madrid, Spain;
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62
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Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β' Subunit. Antimicrob Agents Chemother 2018; 62:AAC.00164-18. [PMID: 29661864 DOI: 10.1128/aac.00164-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is a critical threat to human health due to the increased prevalence of rifampin resistance (RMPr). Fitness defects have been observed in RMPr mutants with amino acid substitutions in the β subunit of RNA polymerase (RNAP). In clinical isolates, this fitness defect can be ameliorated by the presence of secondary mutations in the double-psi β-barrel (DPBB) domain of the β' subunit of RNAP. To identify factors contributing to the fitness defects observed in vivo, several in vitro RNA transcription assays were utilized to probe initiation, elongation, termination, and 3'-RNA hydrolysis with the wild-type and RMPrM. tuberculosis RNAPs. We found that the less prevalent RMPr mutants exhibit significantly poorer termination efficiencies relative to the wild type, an important factor for proper gene expression. We also found that several mechanistic aspects of transcription of the RMPr mutant RNAPs are impacted relative to the wild type. For the clinically most prevalent mutant, the βS450L mutant, these defects are mitigated by the presence of secondary/compensatory mutations in the DPBB domain of the β' subunit.
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63
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Engel C, Neyer S, Cramer P. Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II. Annu Rev Biophys 2018; 47:425-446. [DOI: 10.1146/annurev-biophys-070317-033058] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.
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Affiliation(s)
- Christoph Engel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Current affiliation: Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Simon Neyer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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64
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Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev 2018; 32:682-694. [PMID: 29759984 PMCID: PMC6004073 DOI: 10.1101/gad.313973.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome-destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Haruhiko Ishii
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Franz Meitinger
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Center for Epigenomics, Institute of Genome Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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65
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Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife 2018; 7:34823. [PMID: 29480804 PMCID: PMC5837556 DOI: 10.7554/elife.34823] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/13/2018] [Indexed: 01/22/2023] Open
Abstract
Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket. Tuberculosis (TB) is an infectious disease that affects over ten million people every year. The Mycobacterium tuberculosis bacteria that cause the disease spread through the air from one person to another and mainly infect the lungs. Although curable, TB is difficult to eradicate because it is remarkably widespread, with one third of the world’s population estimated to carry the bacteria. Treatment for TB involves a mix of antibiotics that should be taken for several months to a year. The number of multidrug-resistant TB cases, where the infection is not treatable by the common cocktail of antibiotics, is rapidly increasing. There is therefore a need to discover new drugs that can kill the M. tuberculosis bacteria. An antibiotic called fidaxomicin is used to treat intestinal infections. Although it can kill Mycobacterium tuberculosis cells in culture, it is not absorbed from the intestines to the blood and thus cannot reach the lungs to kill the bacteria. It may be possible to change the structure of the drug so that it can enter the bloodstream. Before this can be done, researchers need to understand exactly how fidaxomicin kills the bacteria so that they know which parts of the drug they can alter without making it less effective. Fidaxomicin kills bacterial cells by binding to an enzyme called RNA polymerase. The antibiotic prevents the enzyme from reading and ‘transcribing’ DNA to form molecules that are essential for life. To learn more about how fidaxomicin has this effect, Boyaci, Chen et al. used cryo-electron microscopy to look at structures of the M. tuberculosis RNA polymerase in different states, including when it was bound to fidaxomicin. The structures reveal the chemical details of the interactions between the RNA polymerase and the antibiotic. The two molecules bind to each other through a region of the RNA polymerase that is unique to M. tuberculosis and closely related bacteria. Fidaxomicin acts like a doorstop to jam the RNA polymerase in an open state that cannot bind to DNA and transcribe genes. Medicinal chemists could now build on these findings to develop new drugs that might treat TB, either by modifying fidaxomicin or designing new antibiotics that bind to the same region of the RNA polymerase. Because the fidaxomicin-binding region of the RNA polymerase is specific to M. tuberculosis new antibiotics could be tailored towards the bacteria that have a minimal effect on a patient’s normal gut bacteria.
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Affiliation(s)
- Hande Boyaci
- The Rockefeller University, New York, United States
| | - James Chen
- The Rockefeller University, New York, United States
| | | | - Margaret Palka
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- The Rockefeller University, New York, United States
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66
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Unarta IC, Zhu L, Tse CKM, Cheung PPH, Yu J, Huang X. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Curr Opin Struct Biol 2018; 49:54-62. [PMID: 29414512 DOI: 10.1016/j.sbi.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Transcription elongation cycle (TEC) of RNA polymerase II (Pol II) is a process of adding a nucleoside triphosphate to the growing messenger RNA chain. Due to the long timescale events in Pol II TEC, an advanced computational technique, such as Markov State Model (MSM), is needed to provide atomistic mechanism and reaction rates. The combination of MSM and experimental results can be used to build a kinetic network model (KNM) of the whole TEC. This review provides a brief protocol to build MSM and KNM of the whole TEC, along with the latest findings of MSM and other computational studies of Pol II TEC. Lastly, we offer a perspective on potentially using a sequence dependent KNM to predict genome-wide transcription error.
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Affiliation(s)
- Ilona Christy Unarta
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong
| | - Lizhe Zhu
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Carmen Ka Man Tse
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peter Pak-Hang Cheung
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100084, China
| | - Xuhui Huang
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, Hong Kong; Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.
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67
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Martínez-Fernández V, Garrido-Godino AI, Mirón-García MC, Begley V, Fernández-Pévida A, de la Cruz J, Chávez S, Navarro F. Rpb5 modulates the RNA polymerase II transition from initiation to elongation by influencing Spt5 association and backtracking. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1-13. [DOI: 10.1016/j.bbagrm.2017.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/13/2022]
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68
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Fouqueau T, Blombach F, Hartman R, Cheung ACM, Young MJ, Werner F. The transcript cleavage factor paralogue TFS4 is a potent RNA polymerase inhibitor. Nat Commun 2017; 8:1914. [PMID: 29203770 PMCID: PMC5715097 DOI: 10.1038/s41467-017-02081-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/05/2017] [Indexed: 12/03/2022] Open
Abstract
TFIIS-like transcript cleavage factors enhance the processivity and fidelity of archaeal and eukaryotic RNA polymerases. Sulfolobus solfataricus TFS1 functions as a bona fide cleavage factor, while the paralogous TFS4 evolved into a potent RNA polymerase inhibitor. TFS4 destabilises the TBP–TFB–RNAP pre-initiation complex and inhibits transcription initiation and elongation. All inhibitory activities are dependent on three lysine residues at the tip of the C-terminal zinc ribbon of TFS4; the inhibition likely involves an allosteric component and is mitigated by the basal transcription factor TFEα/β. A chimeric variant of yeast TFIIS and TFS4 inhibits RNAPII transcription, suggesting that the molecular basis of inhibition is conserved between archaea and eukaryotes. TFS4 expression in S. solfataricus is induced in response to infection with the Sulfolobus turreted icosahedral virus. Our results reveal a compelling functional diversification of cleavage factors in archaea, and provide novel insights into transcription inhibition in the context of the host–virus relationship. Transcript cleavage factors such as eukaryotic TFIIS assist the resumption of transcription following RNA pol II backtracking. Here the authors find that one of the Sulfolobus solfataricus TFIIS homolog—TFS4—has evolved into a potent RNA polymerase inhibitor potentially involved in antiviral defense.
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Affiliation(s)
- Thomas Fouqueau
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Fabian Blombach
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Ross Hartman
- Department of Microbiology, Montana State University, 173520, Bozeman, MT, MT 59717, USA
| | - Alan C M Cheung
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Mark J Young
- Department of Microbiology, Montana State University, 173520, Bozeman, MT, MT 59717, USA.,Department of Plant Sciences, Montana State University, 173150, Bozeman, MT, MT 59717, USA
| | - Finn Werner
- Institute of Structural & Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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69
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Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Nature 2017; 551:653-657. [PMID: 29168508 PMCID: PMC5907806 DOI: 10.1038/nature24658] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022]
Abstract
Eukaryotic transcription-coupled repair (TCR), or transcription-coupled nucleotide excision repair (TC-NER), is an important and well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking RNA polymerase II (Pol II) translocation1,2. Cockayne syndrome group B protein in humans (CSB, or ERCC6), or its yeast orthologs (Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe), is among the first proteins to be recruited to the lesion-arrested Pol II during initiation of eukaryotic TCR1,3–10. Mutations in CSB are associated with Cockayne syndrome, an autosomal-recessive neurologic disorder characterized by progeriod features, growth failure, and photosensitivity1. The molecular mechanism of eukaryotic TCR initiation remains elusive, with several long-standing questions unanswered: How do cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II? How does CSB interact with the arrested Pol II complex? What is the role of CSB in TCR initiation? The lack of structures of CSB or the Pol II-CSB complex have hindered our ability to answer those questions. Here we report the first structure of S. cerevisiae Pol II-Rad26 complex solved by cryo-electron microscopy (cryo-EM). The structure reveals that Rad26 binds to the DNA upstream of Pol II where it dramatically alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes forward movement of Pol II and elucidate key roles for Rad26/CSB in both TCR and transcription elongation.
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70
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Mullen NJ, Price DH. Hydrogen peroxide yields mechanistic insights into human mRNA capping enzyme function. PLoS One 2017; 12:e0186423. [PMID: 29028835 PMCID: PMC5640233 DOI: 10.1371/journal.pone.0186423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Capping of nascent RNA polymerase II (Pol II) transcripts is required for gene expression and the first two steps are catalyzed by separate 5' triphosphatase and guanylyltransferase activities of the human capping enzyme (HCE). The cap is added co-transcriptionally, but how the two activities are coordinated is unclear. Our previous in vitro work has suggested that an unidentified factor modulates the minimum length at which nascent transcripts can be capped. Using the same well-established in vitro system with hydrogen peroxide as a capping inhibitor, we show that this unidentified factor targets the guanylyltransferase activity of HCE. We also uncover the mechanism of HCE inhibition by hydrogen peroxide, and by using mass spectrometry demonstrate that the active site cysteine residue of the HCE triphosphatase domain becomes oxidized. Using recombinant proteins for the two separated HCE domains, we provide evidence that the triphosphatase normally acts on transcripts shorter than can be acted upon by the guanylyltransferase. Our further characterization of the capping reaction dependence on transcript length and its interaction with the unidentified modulator of capping raises the interesting possibility that the capping reaction could be regulated.
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Affiliation(s)
- Nicholas J. Mullen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - David H. Price
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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71
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Gressel S, Schwalb B, Decker TM, Qin W, Leonhardt H, Eick D, Cramer P. CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife 2017; 6:29736. [PMID: 28994650 PMCID: PMC5669633 DOI: 10.7554/elife.29736] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/06/2017] [Indexed: 12/11/2022] Open
Abstract
Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.
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Affiliation(s)
- Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Michael Decker
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Weihua Qin
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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72
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Cramer P. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday. J Mol Biol 2017; 429:2603-2610. [PMID: 28501586 DOI: 10.1016/j.jmb.2017.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective.
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Affiliation(s)
- Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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73
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Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure. Microbiol Mol Biol Rev 2017; 81:81/3/e00010-17. [PMID: 28701329 DOI: 10.1128/mmbr.00010-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The past 17 years have been marked by a revolution in our understanding of cellular multisubunit DNA-dependent RNA polymerases (MSDDRPs) at the structural level. A parallel development over the past 15 years has been the emerging story of the giant viruses, which encode MSDDRPs. Here we link the two in an attempt to understand the specialization of multisubunit RNA polymerases in the domain of life encompassing the large nucleocytoplasmic DNA viruses (NCLDV), a superclade that includes the giant viruses and the biochemically well-characterized poxvirus vaccinia virus. The first half of this review surveys the recently determined structural biology of cellular RNA polymerases for a microbiology readership. The second half discusses a reannotation of MSDDRP subunits from NCLDV families and the apparent specialization of these enzymes by virus family and by subunit with regard to subunit or domain loss, subunit dissociability, endogenous control of polymerase arrest, and the elimination/customization of regulatory interactions that would confer higher-order cellular control. Some themes are apparent in linking subunit function to structure in the viral world: as with cellular RNA polymerases I and III and unlike cellular RNA polymerase II, the viral enzymes seem to opt for speed and processivity and seem to have eliminated domains associated with higher-order regulation. The adoption/loss of viral RNA polymerase proofreading functions may have played a part in matching intrinsic mutability to genome size.
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74
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Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS Genet 2017; 13:e1006863. [PMID: 28665995 PMCID: PMC5513554 DOI: 10.1371/journal.pgen.1006863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/17/2017] [Accepted: 06/10/2017] [Indexed: 01/04/2023] Open
Abstract
Transcriptome studies on eukaryotic cells have revealed an unexpected abundance and diversity of noncoding RNAs synthesized by RNA polymerase II (Pol II), some of which influence the expression of protein-coding genes. Yet, much less is known about biogenesis of Pol II non-coding RNA than mRNAs. In the budding yeast Saccharomyces cerevisiae, initiation of non-coding transcripts by Pol II appears to be similar to that of mRNAs, but a distinct pathway is utilized for termination of most non-coding RNAs: the Sen1-dependent or “NNS” pathway. Here, we examine the effect on the S. cerevisiae transcriptome of conditional mutations in the genes encoding six different essential proteins that influence Sen1-dependent termination: Sen1, Nrd1, Nab3, Ssu72, Rpb11, and Hrp1. We observe surprisingly diverse effects on transcript abundance for the different proteins that cannot be explained simply by differing severity of the mutations. Rather, we infer from our results that termination of Pol II transcription of non-coding RNA genes is subject to complex combinatorial control that likely involves proteins beyond those studied here. Furthermore, we identify new targets and functions of Sen1-dependent termination, including a role in repression of meiotic genes in vegetative cells. In combination with other recent whole-genome studies on termination of non-coding RNAs, our results provide promising directions for further investigation. The information stored in the DNA of a cell’s chromosomes is transmitted to the rest of the cell by transcribing the DNA into RNA copies or “transcripts”. The fidelity of this process, and thus the health of the cell, depends critically on the proper function of proteins that direct transcription. Since hundreds of genes, each specifying a unique RNA transcript, are arranged in tandem along each chromosome, the beginning and end of each gene must be marked in the DNA sequence. Although encoded in DNA, the signal for terminating an RNA transcript is usually recognized in the transcript itself. We examined the genome-wide functional targets of six proteins implicated in transcription termination by identifying transcripts whose structure or abundance is altered by a mutation that compromises the activity of each protein. For a small minority of transcripts, a mutation in any of the six proteins disrupts termination. Much more commonly, a transcript is affected by a mutation in only one or a few of the six proteins, revealing the varying extent to which the proteins cooperate with one another. We discovered affected transcripts that were not known to be controlled by any of the six proteins, including a cohort of genes required for meiosis.
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Affiliation(s)
- Xin Chen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Melissa N. Carver
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Ulrika Müller
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (DAB); (DTA)
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail: (DAB); (DTA)
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75
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Abstract
Transcription elongation is not uniform and transcription is often hindered by protein-bound factors or DNA lesions that limit translocation and impair catalysis. Despite the high degree of sequence and structural homology of the multi-subunit RNA polymerases (RNAP), substantial differences in response to DNA lesions have been reported. Archaea encode only a single RNAP with striking structural conservation with eukaryotic RNAP II (Pol II). Here, we demonstrate that the archaeal RNAP from Thermococcus kodakarensis is sensitive to a variety of DNA lesions that pause and arrest RNAP at or adjacent to the site of DNA damage. DNA damage only halts elongation when present in the template strand, and the damage often results in RNAP arresting such that the lesion would be encapsulated with the transcription elongation complex. The strand-specific halt to archaeal transcription elongation on modified templates is supportive of RNAP recognizing DNA damage and potentially initiating DNA repair through a process akin to the well-described transcription-coupled DNA repair (TCR) pathways in Bacteria and Eukarya.
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Affiliation(s)
- Alexandra M Gehring
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA.,b Institute for Genome Architecture and Function, Colorado State University , Fort Collins , CO , USA
| | - Thomas J Santangelo
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA.,b Institute for Genome Architecture and Function, Colorado State University , Fort Collins , CO , USA
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76
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Portz B, Lu F, Gibbs EB, Mayfield JE, Rachel Mehaffey M, Zhang YJ, Brodbelt JS, Showalter SA, Gilmour DS. Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain. Nat Commun 2017; 8:15231. [PMID: 28497792 PMCID: PMC5437306 DOI: 10.1038/ncomms15231] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 03/09/2017] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase II contains a repetitive, intrinsically disordered, C-terminal domain (CTD) composed of heptads of the consensus sequence YSPTSPS. The CTD is heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation and termination, RNA processing and chromatin modification. Despite being a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of phosphorylation are poorly understood. Here we present a biophysical and biochemical interrogation of the structure of the full length CTD of Drosophila melanogaster, which we conclude is a compact random coil. Surprisingly, we find that the repetitive CTD is structurally heterogeneous. Phosphorylation causes increases in radius, protein accessibility and stiffness, without disrupting local structural heterogeneity. Additionally, we show the human CTD is also structurally heterogeneous and able to substitute for the D. melanogaster CTD in supporting fly development to adulthood. This finding implicates conserved structural organization, not a precise array of heptad motifs, as important to CTD function.
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Affiliation(s)
- Bede Portz
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Feiyue Lu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.,The Huck Institutes of Life Sciences. The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua E Mayfield
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, USA
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
| | | | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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77
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Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Bürger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC. Structural basis for λN-dependent processive transcription antitermination. Nat Microbiol 2017; 2:17062. [DOI: 10.1038/nmicrobiol.2017.62] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/24/2017] [Indexed: 11/09/2022]
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78
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E C, Duan B, Yu J. Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation. J Phys Chem B 2017; 121:3777-3786. [PMID: 28199109 DOI: 10.1021/acs.jpcb.6b11668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 kBT) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.
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Affiliation(s)
- Chao E
- Beijing Computational Science Research Center , Beijing 100193, China
| | - Baogen Duan
- Beijing Computational Science Research Center , Beijing 100193, China
| | - Jin Yu
- Beijing Computational Science Research Center , Beijing 100193, China
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79
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Abstract
During transcriptional elongation, RNA polymerases (RNAP) employ a stepping mechanism to translocate along the DNA template while synthesizing RNA. Optical trapping assays permit the progress of single molecules of RNA polymerase to be monitored in real time, at resolutions down to the level of individual base pairs. Additionally, optical trapping assays permit the application of exquisitely controlled, external forces on RNAP. Responses to such forces can reveal details of the load-dependent kinetics of transcriptional elongation and pausing. Traditionally, the bacterial form of RNAP from E. coli has served as a model for the study of transcriptional elongation using optical traps. However, it is now feasible to perform optical trapping experiments using the eukaryotic polymerase, RNAPII, as well. In this report, we describe the methods to perform optical trapping transcriptional elongation assays with both prokaryotic RNAP and eukaryotic RNAPII. We provide detailed instructions on how to reconstitute transcription elongation complexes, derivatize beads used in the assays, and perform optical trapping measurements.
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80
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Hantsche M, Cramer P. Strukturelle Grundlage der Transkription: 10 Jahre nach dem Chemie-Nobelpreis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
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81
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Lahmy S, Pontier D, Bies-Etheve N, Laudié M, Feng S, Jobet E, Hale CJ, Cooke R, Hakimi MA, Angelov D, Jacobsen SE, Lagrange T. Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes Dev 2016; 30:2565-2570. [PMID: 27986858 PMCID: PMC5204349 DOI: 10.1101/gad.289553.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/17/2016] [Indexed: 12/29/2022]
Abstract
RNA polymerase V (Pol V) long noncoding RNAs (lncRNAs) have been proposed to guide ARGONAUTE4 (AGO4) to chromatin in RNA-directed DNA methylation (RdDM) in plants. Here, we provide evidence, based on laser UV-assisted zero-length cross-linking, for functionally relevant AGO4-DNA interaction at RdDM targets. We further demonstrate that Pol V lncRNAs or the act of their transcription are required to lock Pol V holoenzyme into a stable DNA-bound state that allows AGO4 recruitment via redundant glycine-tryptophan/tryptophan-glycine AGO hook motifs present on both Pol V and its associated factor, SPT5L. We propose a model in which AGO4-DNA interaction could be responsible for the unique specificities of RdDM.
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Affiliation(s)
- Sylvie Lahmy
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Michèle Laudié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Christopher J Hale
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Pathology, Center for Precision Diagnostics, University of Washington, Seattle, Washington 98195, USA
| | - Richard Cooke
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), UMR5309, CNRS, U1209, Institut National de la Santé et de la Recherche Médicale (INSERM), Grenoble Alpes University, 38000 Grenoble, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC), UMR 5239, CNRS/École Normale Supérieure de Lyon (ENSL)/Université Claude Bernard Lyon 1 (UCBL), 69007 Lyon, France.,Institut NeuroMyogène (INMG), UMR 5310, CNRS/UCBL/ENSL, 69007 Lyon, France
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
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82
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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: 25] [Impact Index Per Article: 2.8] [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.
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83
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Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJH, Sachse C, Müller CW. Molecular Structures of Transcribing RNA Polymerase I. Mol Cell 2016; 64:1135-1143. [PMID: 27867008 PMCID: PMC5179497 DOI: 10.1016/j.molcel.2016.11.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/26/2016] [Accepted: 11/04/2016] [Indexed: 01/22/2023]
Abstract
RNA polymerase I (Pol I) is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA. Recently, the crystal structure of apo Pol I gave unprecedented insight into its molecular architecture. Here, we present three cryo-EM structures of elongating Pol I, two at 4.0 Å and one at 4.6 Å resolution, and a Pol I open complex at 3.8 Å resolution. Two modules in Pol I mediate the narrowing of the DNA-binding cleft by closing the clamp domain. The DNA is bound by the clamp head and by the protrusion domain, allowing visualization of the upstream and downstream DNA duplexes in one of the elongation complexes. During formation of the Pol I elongation complex, the bridge helix progressively folds, while the A12.2 C-terminal domain is displaced from the active site. Our results reveal the conformational changes associated with elongation complex formation and provide additional insight into the Pol I transcription cycle. Pol I gradually closes its DNA-binding cleft during elongation complex formation Pol I bridge helix folds into a conformation similar to that in other RNA polymerases During elongation, the Pol I A12.2 C-terminal domain is excluded from the cleft A49 tandem winged helix domain contacts upstream DNA, similar to TFIIE
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Affiliation(s)
- Lucas Tafur
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Yashar Sadian
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Niklas A Hoffmann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Rene Wetzel
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wim J H Hagen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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84
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Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature 2016; 540:607-610. [PMID: 27842382 DOI: 10.1038/nature20561] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/25/2016] [Indexed: 11/08/2022]
Abstract
RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.
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85
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Hantsche M, Cramer P. The Structural Basis of Transcription: 10 Years After the Nobel Prize in Chemistry. Angew Chem Int Ed Engl 2016; 55:15972-15981. [DOI: 10.1002/anie.201608066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
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86
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Lai WKM, Pugh BF. Genome-wide uniformity of human 'open' pre-initiation complexes. Genome Res 2016; 27:15-26. [PMID: 27927716 PMCID: PMC5204339 DOI: 10.1101/gr.210955.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5' ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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87
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Zhang Y, Najmi SM, Schneider DA. Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:246-255. [PMID: 27989933 DOI: 10.1016/j.bbagrm.2016.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, nuclear RNA synthesis is accomplished by at least three unique, multisubunit RNA polymerases. The roles of these enzymes are generally partitioned into the synthesis of the three major classes of RNA: rRNA, mRNA, and tRNA for RNA polymerases I, II, and III respectively. Consistent with their unique cellular roles, each enzyme has a complement of specialized transcription factors and enzymatic properties. However, not all transcription factors have evolved to affect only one eukaryotic RNA polymerase. In fact, many factors have been shown to influence the activities of multiple nuclear RNA polymerases. This review focuses on a subset of these factors, specifically addressing the mechanisms by which these proteins influence RNA polymerases I and II.
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Affiliation(s)
- Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Saman M Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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88
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Abstract
The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.
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89
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Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Proc Natl Acad Sci U S A 2016; 113:E4005-14. [PMID: 27339134 DOI: 10.1073/pnas.1602591113] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain-based active site closure mechanism and proposed a six-state NAC model including a hypothetical state representing translocation intermediates. Using the RdRP from another human enterovirus, enterovirus 71, here we report seven RdRP elongation complex structures derived from a crystal lattice that allows three NAC events. These structures suggested a key order of events in initial NTP binding and NTP-induced active site closure and revealed a bona fide translocation intermediate featuring asymmetric movement of the template-product duplex. Our work provides essential missing links in understanding NTP recognition and translocation mechanisms in viral RdRPs and emphasizes the uniqueness of the viral RdRPs compared with other processive polymerases.
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90
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Kaster BC, Knippa KC, Kaplan CD, Peterson DO. RNA Polymerase II Trigger Loop Mobility: INDIRECT EFFECTS OF Rpb9. J Biol Chem 2016; 291:14883-95. [PMID: 27226557 DOI: 10.1074/jbc.m116.714394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Indexed: 01/08/2023] Open
Abstract
Rpb9 is a conserved RNA polymerase II (pol II) subunit, the absence of which confers alterations to pol II enzymatic properties and transcription fidelity. It has been suggested previously that Rpb9 affects mobility of the trigger loop (TL), a structural element of Rpb1 that moves in and out of the active site with each elongation cycle. However, a biochemical mechanism for this effect has not been defined. We find that the mushroom toxin α-amanitin, which inhibits TL mobility, suppresses the effect of Rpb9 on NTP misincorporation, consistent with a role for Rpb9 in this process. Furthermore, we have identified missense alleles of RPB9 in yeast that suppress the severe growth defect caused by rpb1-G730D, a substitution within Rpb1 α-helix 21 (α21). These alleles suggest a model in which Rpb9 indirectly affects TL mobility by anchoring the position of α21, with which the TL directly interacts during opening and closing. Amino acid substitutions in Rpb9 or Rpb1 that disrupt proposed anchoring interactions resulted in phenotypes shared by rpb9Δ strains, including increased elongation rate in vitro Combinations of rpb9Δ with the fast rpb1 alleles that we identified did not result in significantly faster in vitro misincorporation rates than those resulting from rpb9Δ alone, and this epistasis is consistent with the idea that defects caused by the rpb1 alleles are related mechanistically to the defects caused by rpb9Δ. We conclude that Rpb9 supports intra-pol II interactions that modulate TL function and thus pol II enzymatic properties.
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Affiliation(s)
- Benjamin C Kaster
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Kevin C Knippa
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Craig D Kaplan
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - David O Peterson
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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91
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He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature 2016; 533:359-65. [PMID: 27193682 PMCID: PMC4940141 DOI: 10.1038/nature17970] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.
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Affiliation(s)
- Yuan He
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Chunli Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Carla Inouye
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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92
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Automated structure modeling of large protein assemblies using crosslinks as distance restraints. Nat Methods 2016; 13:515-20. [PMID: 27111507 DOI: 10.1038/nmeth.3838] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/19/2016] [Indexed: 11/08/2022]
Abstract
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
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93
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Zhang L, Pardo-Avila F, Unarta IC, Cheung PPH, Wang G, Wang D, Huang X. Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models. Acc Chem Res 2016; 49:687-94. [PMID: 26991064 DOI: 10.1021/acs.accounts.5b00536] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
RNA polymerase II (Pol II) is an essential enzyme that catalyzes transcription with high efficiency and fidelity in eukaryotic cells. During transcription elongation, Pol II catalyzes the nucleotide addition cycle (NAC) to synthesize mRNA using DNA as the template. The transitions between the states of the NAC require conformational changes of both the protein and nucleotides. Although X-ray structures are available for most of these states, the dynamics of the transitions between states are largely unknown. Molecular dynamics (MD) simulations can predict structure-based molecular details and shed light on the mechanisms of these dynamic transitions. However, the employment of MD simulations on a macromolecule (tens to hundreds of nanoseconds) such as Pol II is challenging due to the difficulty of reaching biologically relevant timescales (tens of microseconds or even longer). For this challenge to be overcome, kinetic network models (KNMs), such as Markov State Models (MSMs), have become a popular approach to access long-timescale conformational changes using many short MD simulations. We describe here our application of KNMs to characterize the molecular mechanisms of the NAC of Pol II. First, we introduce the general background of MSMs and further explain procedures for the construction and validation of MSMs by providing some technical details. Next, we review our previous studies in which we applied MSMs to investigate the individual steps of the NAC, including translocation and pyrophosphate ion release. In particular, we describe in detail how we prepared the initial conformations of Pol II elongation complex, performed MD simulations, extracted MD conformations to construct MSMs, and further validated them. We also summarize our major findings on molecular mechanisms of Pol II elongation based on these MSMs. In addition, we have included discussions regarding various key points and challenges for applications of MSMs to systems as large as the Pol II elongation complex. Finally, to study the overall NAC, we combine the individual steps of the NAC into a five-state KNM based on a nonbranched Brownian ratchet scheme to explain the single-molecule optical tweezers experimental data. The studies complement experimental observations and provide molecular mechanisms for the transcription elongation cycle. In the long term, incorporation of sequence-dependent kinetic parameters into KNMs has great potential for identifying error-prone sequences and predicting transcription dynamics in genome-wide transcriptomes.
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Affiliation(s)
- Lu Zhang
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Fátima Pardo-Avila
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ilona Christy Unarta
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Peter Pak-Hang Cheung
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Guo Wang
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Dong Wang
- Department
of Cellular and Molecular Medicine, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Xuhui Huang
- Department
of Chemistry and State Key Laboratory of Molecular Neuroscience, Center
for System Biology and Human Health, School of Science, and IAS, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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94
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Liu B, Zuo Y, Steitz TA. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 2016; 113:4051-6. [PMID: 27035955 PMCID: PMC4839411 DOI: 10.1073/pnas.1520555113] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520
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95
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Schulz S, Gietl A, Smollett K, Tinnefeld P, Werner F, Grohmann D. TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proc Natl Acad Sci U S A 2016; 113:E1816-25. [PMID: 26979960 PMCID: PMC4822635 DOI: 10.1073/pnas.1515817113] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription is an intrinsically dynamic process and requires the coordinated interplay of RNA polymerases (RNAPs) with nucleic acids and transcription factors. Classical structural biology techniques have revealed detailed snapshots of a subset of conformational states of the RNAP as they exist in crystals. A detailed view of the conformational space sampled by the RNAP and the molecular mechanisms of the basal transcription factors E (TFE) and Spt4/5 through conformational constraints has remained elusive. We monitored the conformational changes of the flexible clamp of the RNAP by combining a fluorescently labeled recombinant 12-subunit RNAP system with single-molecule FRET measurements. We measured and compared the distances across the DNA binding channel of the archaeal RNAP. Our results show that the transition of the closed to the open initiation complex, which occurs concomitant with DNA melting, is coordinated with an opening of the RNAP clamp that is stimulated by TFE. We show that the clamp in elongation complexes is modulated by the nontemplate strand and by the processivity factor Spt4/5, both of which stimulate transcription processivity. Taken together, our results reveal an intricate network of interactions within transcription complexes between RNAP, transcription factors, and nucleic acids that allosterically modulate the RNAP during the transcription cycle.
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Affiliation(s)
- Sarah Schulz
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Katherine Smollett
- RNA Polymerase Laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany; Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Finn Werner
- RNA Polymerase Laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom;
| | - Dina Grohmann
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany;
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96
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Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P. Structure of transcribing mammalian RNA polymerase II. Nature 2016; 529:551-4. [DOI: 10.1038/nature16482] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/24/2015] [Indexed: 12/12/2022]
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97
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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98
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Yakhnin AV, Murakami KS, Babitzke P. NusG Is a Sequence-specific RNA Polymerase Pause Factor That Binds to the Non-template DNA within the Paused Transcription Bubble. J Biol Chem 2016; 291:5299-308. [PMID: 26742846 DOI: 10.1074/jbc.m115.704189] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/06/2022] Open
Abstract
NusG, referred to as Spt5 in archaeal and eukaryotic organisms, is the only transcription factor conserved in all three domains of life. This general transcription elongation factor binds to RNA polymerase (RNAP) soon after transcription initiation and dissociation of the RNA polymerase σ factor. Escherichia coli NusG increases transcription processivity by suppressing RNAP pausing, whereas Bacillus subtilis NusG dramatically stimulates pausing at two sites in the untranslated leader of the trpEDCFBA operon. These two regulatory pause sites participate in transcription attenuation and translational control mechanisms, respectively. Here we report that B. subtilis NusG makes sequence-specific contacts with a T-rich sequence in the non-template DNA (ntDNA) strand within the paused transcription bubble. NusG protects T residues of the recognition sequence from permanganate oxidation, and these T residues increase the affinity of NusG to the elongation complex. Binding of NusG to RNAP does not require interaction with RNA. These results indicate that bound NusG prevents forward movement of RNA polymerase by simultaneously contacting RNAP and the ntDNA strand. Mutational studies indicate that amino acid residues of two short regions within the NusG N-terminal domain are primarily responsible for recognition of the trp operon pause signals. Structural modeling indicates that these two regions are adjacent to each another in the protein. We propose that recognition of specific sequences in the ntDNA and stimulation of RNAP pausing is a conserved function of NusG-like transcription factors.
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Affiliation(s)
- Alexander V Yakhnin
- From the Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Katsuhiko S Murakami
- From the Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Paul Babitzke
- From the Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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99
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Zhang L, Jiang H, Sheong F, Pardo-Avila F, Cheung PH, Huang X. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands. Methods Enzymol 2016; 578:343-71. [DOI: 10.1016/bs.mie.2016.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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100
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Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJH, Sachse C, Müller CW. Molecular structures of unbound and transcribing RNA polymerase III. Nature 2015; 528:231-6. [PMID: 26605533 PMCID: PMC4681132 DOI: 10.1038/nature16143] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets.
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Affiliation(s)
- Niklas A. Hoffmann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J. Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestr. 85, 22607 Hamburg, Germany
| | - Maria Moreno-Morcillo
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sebastian Glatt
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wim J. H. Hagen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
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