1
|
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023; 382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
Collapse
Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| |
Collapse
|
2
|
Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K. Structures illustrate step-by-step mitochondrial transcription initiation. Nature 2023; 622:872-879. [PMID: 37821701 PMCID: PMC10600007 DOI: 10.1038/s41586-023-06643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Transcription initiation is a key regulatory step in gene expression during which RNA polymerase (RNAP) initiates RNA synthesis de novo, and the synthesized RNA at a specific length triggers the transition to the elongation phase. Mitochondria recruit a single-subunit RNAP and one or two auxiliary factors to initiate transcription. Previous studies have revealed the molecular architectures of yeast1 and human2 mitochondrial RNAP initiation complexes (ICs). Here we provide a comprehensive, stepwise mechanism of transcription initiation by solving high-resolution cryogenic electron microscopy (cryo-EM) structures of yeast mitochondrial RNAP and the transcription factor Mtf1 catalysing two- to eight-nucleotide RNA synthesis at single-nucleotide addition steps. The growing RNA-DNA is accommodated in the polymerase cleft by template scrunching and non-template reorganization, creating stressed intermediates. During early initiation, non-template strand scrunching and unscrunching destabilize the short two- and three-nucleotide RNAs, triggering abortive synthesis. Subsequently, the non-template reorganizes into a base-stacked staircase-like structure supporting processive five- to eight-nucleotide RNA synthesis. The expanded non-template staircase and highly scrunched template in IC8 destabilize the promoter interactions with Mtf1 to facilitate initiation bubble collapse and promoter escape for the transition from initiation to the elongation complex (EC). The series of transcription initiation steps, each guided by the interplay of multiple structural components, reveal a finely tuned mechanism for potential regulatory control.
Collapse
Affiliation(s)
- Quinten Goovaerts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Brent De Wijngaert
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
| | - Kalyan Das
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
| |
Collapse
|
3
|
Dousis A, Ravichandran K, Hobert EM, Moore MJ, Rabideau AE. An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts. Nat Biotechnol 2023; 41:560-568. [PMID: 36357718 PMCID: PMC10110463 DOI: 10.1038/s41587-022-01525-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 09/22/2022] [Indexed: 11/12/2022]
Abstract
In vitro transcription (IVT) is a DNA-templated process for synthesizing long RNA transcripts, including messenger RNA (mRNA). For many research and commercial applications, IVT of mRNA is typically performed using bacteriophage T7 RNA polymerase (T7 RNAP) owing to its ability to produce full-length RNA transcripts with high fidelity; however, T7 RNAP can also produce immunostimulatory byproducts such as double-stranded RNA that can affect protein expression. Such byproducts require complex purification processes, using methods such as reversed-phase high-performance liquid chromatography, to yield safe and effective mRNA-based medicines. To minimize the need for downstream purification processes, we rationally and computationally engineered a double mutant of T7 RNAP that produces substantially less immunostimulatory RNA during IVT compared with wild-type T7 RNAP. The resulting mutant allows for a simplified production process with similar mRNA potency, lower immunostimulatory content and quicker manufacturing time compared with wild-type T7 RNAP. Herein, we describe the computational design and development of this improved T7 RNAP variant.
Collapse
Affiliation(s)
- Athanasios Dousis
- Moderna, Inc., Cambridge, MA, USA
- Tessera Therapeutics, Somerville, MA, USA
| | | | - Elissa M Hobert
- Moderna, Inc., Cambridge, MA, USA
- Laronde, Cambridge, MA, USA
| | | | | |
Collapse
|
4
|
The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021; 203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
Collapse
|
5
|
Petushkov IV, Kulbachinskiy AV. Role of Interactions of the CRE Region of Escherichia coli RNA Polymerase with Nontemplate DNA during Promoter Escape. BIOCHEMISTRY (MOSCOW) 2021; 85:792-800. [PMID: 33040723 DOI: 10.1134/s000629792007007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RNA polymerase (RNAP) recognizes promoter DNA through many interactions that determine specificity of transcription initiation. In addition to the dedicated transcription initiation σ factor in bacteria, the core enzyme of RNAP can also participate in promoter recognition. In particular, guanine residue at the +2 position (+2G) of the nontemplate DNA strand is bound in the CRE pocket formed by the RNAP β subunit. Here, we analyzed the role of these contacts in the process of promoter escape by RNAP by studying point mutations in the β subunit of Escherichia coli RNAP that disrupted these interactions. We found that the presence of +2G in the promoter slowed down the rate of promoter escape and increased proportion of inactive complexes. Amino acid substitutions in the CRE pocket decreased the promoter complex stability and changed the pattern of short RNA products synthesized during initiation, but did not significantly affect the rate of transition to elongation, regardless of the presence of +2G. Thus, the contacts of the CRE pocket with +2G do not make a significant contribution to the kinetics of promoter escape by RNAP, while the observed changes in the efficiency of abortive synthesis are not directly related to the rate of promoter escape.
Collapse
Affiliation(s)
- I V Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | - A V Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| |
Collapse
|
6
|
Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
Collapse
Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
| |
Collapse
|
7
|
Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol 2020; 19:95-109. [PMID: 33122819 DOI: 10.1038/s41579-020-00450-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. Diverse mechanisms are used among and within the different branches to regulate transcription initiation. Mechanistic studies of transcription initiation in bacteria are especially amenable because the promoter recognition and melting steps are much less complicated than in eukaryotes or archaea. Also, bacteria have critical roles in human health as pathogens and commensals, and the bacterial RNA polymerase is a proven target for antibiotics. Recent biophysical studies of RNA polymerases and their inhibition, as well as transcription initiation and transcription factors, have detailed the mechanisms of transcription initiation in phylogenetically diverse bacteria, inspiring this Review to examine unifying and diverse themes in this process.
Collapse
|
8
|
Imashimizu M, Tokunaga Y, Afek A, Takahashi H, Shimamoto N, Lukatsky DB. Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences. Biomolecules 2020; 10:biom10091299. [PMID: 32916947 PMCID: PMC7564750 DOI: 10.3390/biom10091299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/23/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.
Collapse
Affiliation(s)
- Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
| | - Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
| | - Ariel Afek
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA;
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan;
- Molecular Chirality Research Center, Chiba University, Chiba 263-8522, Japan
- Plant Molecular Science Center, Chiba University, Chiba 260-8675, Japan
| | - Nobuo Shimamoto
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;
| | - David B. Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
| |
Collapse
|
9
|
Basu U, Lee SW, Deshpande A, Shen J, Sohn BK, Cho H, Kim H, Patel SS. The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation. Nucleic Acids Res 2020; 48:2604-2620. [PMID: 31980825 PMCID: PMC7049685 DOI: 10.1093/nar/gkaa040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial RNA polymerases depend on initiation factors, such as TFB2M in humans and Mtf1 in yeast Saccharomyces cerevisiae, for promoter-specific transcription. These factors drive the melting of promoter DNA, but how they support RNA priming and growth was not understood. We show that the flexible C-terminal tails of Mtf1 and TFB2M play a crucial role in RNA priming by aiding template strand alignment in the active site for high-affinity binding of the initiating nucleotides. Using single-molecule fluorescence approaches, we show that the Mtf1 C-tail promotes RNA growth during initiation by stabilizing the scrunched DNA conformation. Additionally, due to its location in the path of the nascent RNA, the C-tail of Mtf1 serves as a sensor of the RNA-DNA hybrid length. Initially, steric clashes of the Mtf1 C-tail with short RNA-DNA hybrids cause abortive synthesis but clashes with longer RNA-DNA trigger conformational changes for the timely release of the promoter DNA to commence the transition into elongation. The remarkable similarities in the functions of the C-tail and σ3.2 finger of the bacterial factor suggest mechanistic convergence of a flexible element in the transcription initiation factor that engages the DNA template for RNA priming and growth and disengages when needed to generate the elongation complex.
Collapse
Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at Robert Wood Johnson Medical School of the Rutgers University, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at Robert Wood Johnson Medical School of the Rutgers University, USA
| | - Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| |
Collapse
|
10
|
Chung S, Lerner E, Jin Y, Kim S, Alhadid Y, Grimaud LW, Zhang IX, Knobler CM, Gelbart WM, Weiss S. The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase. Nucleic Acids Res 2019; 47:1440-1450. [PMID: 30590739 PMCID: PMC6379708 DOI: 10.1093/nar/gky1277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/01/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement's dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.
Collapse
Affiliation(s)
- SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yan Jin
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Soohong Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
| | - Logan Wilson Grimaud
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - Irina X Zhang
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Present address: Irina X. Zhang, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Correspondence may also be addressed to William M. Gelbart. Tel: +1 310 825 2005; Fax: +1 310 206 4038;
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute (MBI), University of California Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, CA 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
- To whom correspondence should be addressed. Tel: +1 310 794 0093; Fax: +1 310 267 4672;
| |
Collapse
|
11
|
Heyduk E, Heyduk T. DNA template sequence control of bacterial RNA polymerase escape from the promoter. Nucleic Acids Res 2019; 46:4469-4486. [PMID: 29546317 PMCID: PMC5961368 DOI: 10.1093/nar/gky172] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/28/2018] [Indexed: 01/09/2023] Open
Abstract
Promoter escape involves breaking of the favourable contacts between RNA polymerase (RNAP) and the promoter to allow transition to an elongation complex. The sequence of DNA template that is transcribed during promoter escape (ITS; Initially Transcribed Sequence) can affect promoter escape by mechanisms that are not yet fully understood. We employed a highly parallel strategy utilizing Next Generation Sequencing (NGS) to collect data on escape properties of thousands of ITS variants. We show that ITS controls promoter escape through a combination of position-dependent effects (most prominently, sequence-directed RNAP pausing), and position-independent effects derived from sequence encoded physical properties of the template (for example, RNA/DNA duplex stability). ITS often functions as an independent unit affecting escape in the same manner regardless of the promoter from which transcription initiates. However, in some cases, a strong dependence of ITS effects on promoter context was observed suggesting that promoters may have 'allosteric' abilities to modulate ITS effects. Large effects of ITS on promoter output and the observed interplay between promoter sequence and ITS effects suggests that the definition of bacterial promoter should include ITS sequence.
Collapse
Affiliation(s)
- Ewa Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| |
Collapse
|
12
|
Henderson KL, Evensen CE, Molzahn CM, Felth LC, Dyke S, Liao G, Shkel IA, Record MT. RNA Polymerase: Step-by-Step Kinetics and Mechanism of Transcription Initiation. Biochemistry 2019; 58:2339-2352. [PMID: 30950601 DOI: 10.1021/acs.biochem.9b00049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To determine the step-by-step kinetics and mechanism of transcription initiation and escape by E. coli RNA polymerase from the λPR promoter, we quantify the accumulation and decay of transient short RNA intermediates on the pathway to promoter escape and full-length (FL) RNA synthesis over a wide range of NTP concentrations by rapid-quench mixing and phosphorimager analysis of gel separations. Experiments are performed at 19 °C, where almost all short RNAs detected are intermediates in FL-RNA synthesis by productive complexes or end-products in nonproductive (stalled) initiation complexes and not from abortive initiation. Analysis of productive-initiation kinetic data yields composite second-order rate constants for all steps of NTP binding and hybrid extension up to the escape point (11-mer). The largest of these rate constants is for incorporation of UTP into the dinucleotide pppApU in a step which does not involve DNA opening or translocation. Subsequent steps, each of which begins with reversible translocation and DNA opening, are slower with rate constants that vary more than 10-fold, interpreted as effects of translocation stress on the translocation equilibrium constant. Rate constants for synthesis of 4- and 5-mer, 7-mer to 9-mer, and 11-mer are particularly small, indicating that RNAP-promoter interactions are disrupted in these steps. These reductions in rate constants are consistent with the previously determined ∼9 kcal cost of escape from λPR. Structural modeling and previous results indicate that the three groups of small rate constants correspond to sequential disruption of in-cleft, -10, and -35 interactions. Parallels to escape by T7 RNAP are discussed.
Collapse
Affiliation(s)
- Kate L Henderson
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Claire E Evensen
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Cristen M Molzahn
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lindsey C Felth
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Sarah Dyke
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Guanyu Liao
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Irina A Shkel
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - M Thomas Record
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| |
Collapse
|
13
|
Li L, Fang C, Zhuang N, Wang T, Zhang Y. Structural basis for transcription initiation by bacterial ECF σ factors. Nat Commun 2019; 10:1153. [PMID: 30858373 PMCID: PMC6411747 DOI: 10.1038/s41467-019-09096-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
Collapse
Affiliation(s)
- Lingting Li
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chengli Fang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ningning Zhuang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Tiantian Wang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Zhang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| |
Collapse
|
14
|
Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
Collapse
|
15
|
Nedialkov Y, Svetlov D, Belogurov GA, Artsimovitch I. Locking the nontemplate DNA to control transcription. Mol Microbiol 2018; 109:445-457. [PMID: 29758107 PMCID: PMC6173972 DOI: 10.1111/mmi.13983] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 12/31/2022]
Abstract
Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest. We used Escherichia coli RfaH, whose interactions with DNA are best characterized, to test this idea. We report that RfaH stabilizes the upstream edge of the transcription bubble, favoring forward translocation, and protects the upstream duplex DNA from exonuclease cleavage. Modeling suggests that RfaH loops the nontemplate DNA around its surface and restricts the upstream DNA duplex mobility. Strikingly, we show that RfaH-induced DNA protection and antipausing activity can be mimicked by shortening the nontemplate strand in elongation complexes assembled on synthetic scaffolds. We propose that remodeling of the nontemplate DNA controls recruitment of regulatory factors and R-loop formation during transcription elongation across all life.
Collapse
Affiliation(s)
- Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
| | - Dmitri Svetlov
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
16
|
Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nat Commun 2018; 9:1478. [PMID: 29662062 PMCID: PMC5902446 DOI: 10.1038/s41467-018-03902-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 03/20/2018] [Indexed: 01/25/2023] Open
Abstract
Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.
Collapse
Affiliation(s)
- David Dulin
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052, Erlangen, Germany.
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Anssi M Malinen
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
- Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Jacob J W Bakermans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Martin Kaller
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
| |
Collapse
|
17
|
Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase. Biochem J 2017; 474:4053-4064. [DOI: 10.1042/bcj20170436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/29/2022]
Abstract
In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5′-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ70 subunit of Escherichia coli RNAP. We show that substitutions and deletions in σ region 3.2 decrease the rate of promoter escape and lead to accumulation of inactive complexes during transcription initiation. Secondary channel factors differentially regulate this process depending on the promoter and mutations in σ region 3.2. GreA generally increase the rate of promoter escape; DksA also stimulates promoter escape on certain templates, while GreB either stimulates or inhibits this process depending on the template. When observed, the stimulation of promoter escape correlates with the accumulation of stressed transcription complexes with scrunched DNA, while changes in the RNA 5′-end structure modulate promoter clearance. Thus, the initiation-to-elongation transition is controlled by a complex interplay between RNAP-binding protein factors and the growing RNA chain.
Collapse
|
18
|
Alhadid Y, Chung S, Lerner E, Taatjes DJ, Borukhov S, Weiss S. Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence. Protein Sci 2017; 26:1278-1290. [PMID: 28370550 PMCID: PMC5477543 DOI: 10.1002/pro.3160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 01/30/2023]
Abstract
Over the past decade, fluorescence-based single-molecule studies significantly contributed to characterizing the mechanism of RNA polymerase at different steps in transcription, especially in transcription initiation. Transcription by bacterial DNA-dependent RNA polymerase is a multistep process that uses genomic DNA to synthesize complementary RNA molecules. Transcription initiation is a highly regulated step in E. coli, but it has been challenging to study its mechanism because of its stochasticity and complexity. In this review, we describe how single-molecule approaches have contributed to our understanding of transcription and have uncovered mechanistic details that were not observed in conventional assays because of ensemble averaging.
Collapse
Affiliation(s)
- Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
| | - SangYoon Chung
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Eitan Lerner
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Sergei Borukhov
- Rowan University School of Osteopathic Medicine, Stratford, New Jersey, 08084
| | - Shimon Weiss
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
- Molecular Biology Institute (MBI), University of California, Los Angeles, California, 90095
- California NanoSystems Institute, University of California, Los Angeles, California, 90095
- Department of Physiology, University of California, Los Angeles, California, 90095
| |
Collapse
|
19
|
Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase. Proc Natl Acad Sci U S A 2017; 114:E3032-E3040. [PMID: 28348246 DOI: 10.1073/pnas.1618675114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To investigate roles of the discriminator and open complex (OC) lifetime in transcription initiation by Escherichia coli RNA polymerase (RNAP; α2ββ'ωσ70), we compare productive and abortive initiation rates, short RNA distributions, and OC lifetime for the λPR and T7A1 promoters and variants with exchanged discriminators, all with the same transcribed region. The discriminator determines the OC lifetime of these promoters. Permanganate reactivity of thymines reveals that strand backbones in open regions of long-lived λPR-discriminator OCs are much more tightly held than for shorter-lived T7A1-discriminator OCs. Initiation from these OCs exhibits two kinetic phases and at least two subpopulations of ternary complexes. Long RNA synthesis (constrained to be single round) occurs only in the initial phase (<10 s), at similar rates for all promoters. Less than half of OCs synthesize a full-length RNA; the majority stall after synthesizing a short RNA. Most abortive cycling occurs in the slower phase (>10 s), when stalled complexes release their short RNA and make another without escaping. In both kinetic phases, significant amounts of 8-nt and 10-nt transcripts are produced by longer-lived, λPR-discriminator OCs, whereas no RNA longer than 7 nt is produced by shorter-lived T7A1-discriminator OCs. These observations and the lack of abortive RNA in initiation from short-lived ribosomal promoter OCs are well described by a quantitative model in which ∼1.0 kcal/mol of scrunching free energy is generated per translocation step of RNA synthesis to overcome OC stability and drive escape. The different length-distributions of abortive RNAs released from OCs with different lifetimes likely play regulatory roles.
Collapse
|
20
|
Lerner E, Ingargiola A, Lee JJ, Borukhov S, Michalet X, Weiss S. Different types of pausing modes during transcription initiation. Transcription 2017; 8:242-253. [PMID: 28332923 DOI: 10.1080/21541264.2017.1308853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.
Collapse
Affiliation(s)
- Eitan Lerner
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Antonino Ingargiola
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Jookyung J Lee
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Sergei Borukhov
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Xavier Michalet
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Shimon Weiss
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.,c Molecular Biology Institute , University of California , Los Angeles , CA , USA.,d Department of Physiology , University of California , Los Angeles , CA , USA
| |
Collapse
|
21
|
Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci 2016; 3:73. [PMID: 27882317 PMCID: PMC5101437 DOI: 10.3389/fmolb.2016.00073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
Collapse
Affiliation(s)
- Jookyung Lee
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| |
Collapse
|
22
|
Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 2016; 113:E6562-E6571. [PMID: 27729537 DOI: 10.1073/pnas.1605038113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g., from a 7-base transcript) were markedly slower than from earlier stages (e.g., from a 2- or 4-base transcript). In addition, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states. Further examination with magnetic tweezers transcription experiments showed that RNAP adopted a long-lived backtracked state during initiation and that the paused-backtracked initiation intermediate was populated abundantly at physiologically relevant nucleoside triphosphate (NTP) concentrations. The paused intermediate population was further increased when the NTP concentration was decreased and/or when an imbalance in NTP concentration was introduced (situations that mimic stress). Our results confirm the existence of a previously hypothesized paused and backtracked RNAP initiation intermediate and suggest it is biologically relevant; furthermore, such intermediates could be exploited for therapeutic purposes and may reflect a conserved state among paused, initiating eukaryotic RNA polymerase II enzymes.
Collapse
|
23
|
Winkelman JT, Winkelman BT, Boyce J, Maloney MF, Chen AY, Ross W, Gourse RL. Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes. Mol Cell 2015; 59:768-80. [PMID: 26257284 DOI: 10.1016/j.molcel.2015.06.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/25/2015] [Accepted: 06/30/2015] [Indexed: 12/21/2022]
Abstract
RNA polymerase binds tightly to DNA to recognize promoters with high specificity but then releases these contacts during the initial stage of transcription. We report a site-specific crosslinking approach to map the DNA path in bacterial transcription intermediates at amino acid and nucleotide resolution. After validating the approach by showing that the DNA path in open complexes (RPO) is the same as in high-resolution X-ray structures, we define the path following substrate addition in "scrunched" complexes (RPITC). The DNA bulges that form within the transcription bubble in RPITC are positioned differently on the two strands. Our data suggest that the non-template strand bulge is extruded into solvent in complexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand tunnel, exerting stress on interactions between the β flap, β' clamp, and σ3.2. We propose that this stress contributes to σ3.2 displacement from the RNA exit channel, facilitating promoter escape.
Collapse
Affiliation(s)
- Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Bradford T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Julian Boyce
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Michael F Maloney
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Albert Y Chen
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.
| |
Collapse
|
24
|
Skancke J, Bar N, Kuiper M, Hsu LM. Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry 2015; 54:4267-75. [PMID: 26083830 DOI: 10.1021/acs.biochem.5b00272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abortive transcription initiation can be rate-limiting for promoter escape and therefore represents a barrier to productive gene expression. The mechanism for abortive initiation is unknown, but the amount of abortive transcript is known to vary with the composition of the initial transcribed sequence (ITS). Here, we used a thermodynamic model of translocation combined with experimental validation to investigate the relationship between ITS and promoter escape on a set of phage T5 N25 promoters. We found a strong, negative correlation between RNAP's propensity to occupy the pretranslocated state during initial transcription and the efficiency of promoter escape (r = -0.67; p < 10(-6)). This correlation was almost entirely caused by free energy changes due to variation in the RNA 3' dinucleotide sequence at each step, implying that this sequence element controls the disposition of initial transcribing complexes. We tested our model experimentally by constructing a set of novel N25-ITS promoter variants; quantitative transcription analysis again showed a strong correlation (r = -0.81; p < 10(-6)). Our results support a model in which sequence-directed bias for the pretranslocated state during scrunching results in increased backtracking, which limits the efficiency of promoter escape. This provides an answer to the long-standing issue of how sequence composition of the ITS affects promoter escape efficiency.
Collapse
Affiliation(s)
- Jørgen Skancke
- †Department of Chemical Engineering, Norwegian University of Science and Technology, Sem Sælandsvei 4, 7491 Trondheim, Norway
| | - Nadav Bar
- †Department of Chemical Engineering, Norwegian University of Science and Technology, Sem Sælandsvei 4, 7491 Trondheim, Norway
| | - Martin Kuiper
- ‡Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Lilian M Hsu
- §Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, United States
| |
Collapse
|
25
|
Zuo Y, Steitz TA. Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 2015; 58:534-40. [PMID: 25866247 DOI: 10.1016/j.molcel.2015.03.010] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/12/2015] [Accepted: 03/06/2015] [Indexed: 11/15/2022]
Abstract
During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.
Collapse
Affiliation(s)
- Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
26
|
Kinetics of promoter escape by bacterial RNA polymerase: effects of promoter contacts and transcription bubble collapse. Biochem J 2014; 463:135-44. [PMID: 24995916 DOI: 10.1042/bj20140179] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Promoter escape by RNA polymerase, the transition between the initiation and elongation, is a critical step that defines transcription output at many promoters. In the present study we used a real-time fluorescence assay for promoter melting and escape to study the determinants of the escape. Perturbation of core promoter-polymerase contacts had opposing effects on the rates of melting and escape, demonstrating a direct role of core promoter elements sequence in setting not only the kinetics of promoter melting, but also the kinetics of promoter escape. The start of RNA synthesis is accompanied by an enlargement of the transcription bubble and pulling in of the downstream DNA into the enzyme, resulting in DNA scrunching. Promoter escape results in collapse of the enlarged bubble. To test whether the energy that could be potentially released by the collapse of the bubble plays a role in determining escape kinetics, we measured the rates of promoter escape in promoter constructs, in which the amount of this energy was perturbed by introducing sequence mismatches. We found no significant changes in the rate of promoter escape with these promoter constructs suggesting that the energy released upon bubble collapse does not play a critical role in determining the kinetics of promoter escape.
Collapse
|
27
|
Strobel EJ, Roberts JW. Regulation of promoter-proximal transcription elongation: enhanced DNA scrunching drives λQ antiterminator-dependent escape from a σ70-dependent pause. Nucleic Acids Res 2014; 42:5097-108. [PMID: 24550164 PMCID: PMC4005639 DOI: 10.1093/nar/gku147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During initial transcription, RNA polymerase remains bound at the promoter and synthesizes RNA without movement along the DNA template, drawing downstream DNA into itself in a process called scrunching and thereby storing energy to sever the bonds that hold the enzyme at the promoter. We show that DNA scrunching also is the driving force behind the escape of RNA polymerase from a regulatory pause of the late gene operon of bacteriophage λ, and that this process is enhanced by the activity of the Q(λ) antiterminator. Furthermore, we show that failure of transcription complexes to escape the pause results in backtracking and arrest in a process analogous to abortive initiation. We identify a sequence element that modulates both abortive synthesis and the formation of arrested elongation complexes.
Collapse
Affiliation(s)
- Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | | |
Collapse
|