1
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Deal C, De Wannemaeker L, De Mey M. Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes. FEMS Microbiol Rev 2024; 48:fuae004. [PMID: 38383636 PMCID: PMC10911233 DOI: 10.1093/femsre/fuae004] [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: 08/31/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. Consequently, they can be targeted as elements to control predictability and tuneability of a genetic circuit, which is essential in applications such as the development of robust microbial cell factories. This review considers the promoter elements implicated in the three stages of transcription initiation, detailing the complex interplay of sequence-specific interactions that are involved, and highlighting that DNA sequence features beyond the core promoter elements work in a combinatorial manner to determine transcriptional strength. In particular, we emphasize that, aside from promoter recognition, transcription initiation is also defined by the kinetics of open complex formation and promoter escape, which are also known to be highly sequence specific. Significantly, we focus on how insights into these interactions can be manipulated to lay the foundation for a more rational approach to promoter engineering.
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Affiliation(s)
- Cara Deal
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
| | - Lien De Wannemaeker
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
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2
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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.
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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
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3
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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex. J Mol Biol 2023; 435:167990. [PMID: 36736885 DOI: 10.1016/j.jmb.2023.167990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Stable 37 °C open complexes (OC) of E. coli RNA polymerase (RNAP) at λPR and T7A1 promoters form at similar rates but have very different lifetimes. To understand the downstream interactions responsible for OC lifetime, how promoter sequence directs them and when they form, we report lifetimes of stable OC and unstable late (I2) intermediates for promoters with different combinations of λPR (L) and T7A1 (T) discriminators, core promoters and UP elements. I2 lifetimes are similarly short, while stable OC lifetimes differ greatly, determined largely by the discriminator and modulated by core-promoter and UP elements. The free energy change ΔG3o for I2 → stable OC is approximately -4 kcal more favorable for L-discriminator than for T-discriminator promoters. Downstream-truncation at +6 (DT+6) greatly destabilizes OC at L-discriminator but not T-discriminator promoters, making all ΔG3o values similar (approximately -4 kcal). Urea reduces OC lifetime greatly by affecting ΔG3o. We deduce that urea acts by disfavoring coupled folding of key elements of the β'-clamp, that I2 is an open-clamp OC, and that clamp-closing in I2 → stable OC involves coupled folding. Differences in ΔG3o between downstream-truncated and full-length promoters yield contributions to ΔG3o from interactions with downstream mobile elements (DME) including β-lobe and β'-jaw, more favorable for L-discriminator than for T-discriminator promoters. We deduce how competition between far-downstream DNA and σ70 region 1.1 affects ΔG3o values. We discuss variant-specific ΔG3o contributions in terms of the allosteric network by which differences in discriminator and -10 sequence are sensed and transmitted downstream to affect DME-duplex interactions in I2 → stable OC.
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4
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Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE. Structural and mechanistic basis of σ-dependent transcriptional pausing. Proc Natl Acad Sci U S A 2022; 119:e2201301119. [PMID: 35653571 PMCID: PMC9191641 DOI: 10.1073/pnas.2201301119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/26/2022] [Indexed: 12/20/2022] Open
Abstract
In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein–DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR′ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2–4 bp, and σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2–3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2–3 bp—and only that state—is associated with the consensus sequence, T−3N−2Y−1G+1, (where −1 corresponds to the position of the RNA 3′ end), which is identical to the consensus for pausing in initial transcription and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T−3 resides in the DNA nontemplate strand. A cryoelectron microscopy structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T−3 of the consensus sequence exerts its effects by facilitating scrunching.
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Affiliation(s)
- Chirangini Pukhrambam
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Vadim Molodtsov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Mahdi Kooshkbaghi
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ammar Tareen
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Hoa Vu
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Kyle S. Skalenko
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Zhou Yin
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Jared T. Winkelman
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Justin B. Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Richard H. Ebright
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Bryce E. Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
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5
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Plaskon D, Evensen C, Henderson K, Palatnik B, Ishikuri T, Wang HC, Doughty S, Thomas Record M. Step-by-Step Regulation of Productive and Abortive Transcription Initiation by Pyrophosphorolysis. J Mol Biol 2022; 434:167621. [DOI: 10.1016/j.jmb.2022.167621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
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6
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Structural and mechanistic basis of reiterative transcription initiation. Proc Natl Acad Sci U S A 2022; 119:2115746119. [PMID: 35082149 PMCID: PMC8812562 DOI: 10.1073/pnas.2115746119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 02/02/2023] Open
Abstract
Reiterative transcription initiation, observed at promoters that contain homopolymeric sequences at the transcription start site, generates RNA products having 5' sequences noncomplementary to the DNA template. Here, using crystallography and cryoelectron microscopy to define structures, protein-DNA photocrosslinking to map positions of RNAP leading and trailing edges relative to DNA, and single-molecule DNA nanomanipulation to assess RNA polymerase (RNAP)-dependent DNA unwinding, we show that RNA extension in reiterative transcription initiation 1) occurs without DNA scrunching; 2) involves a short, 2- to 3-bp, RNA-DNA hybrid; and 3) generates RNA that exits RNAP through the portal by which scrunched nontemplate-strand DNA exits RNAP in standard transcription initiation. The results establish that, whereas RNA extension in standard transcription initiation proceeds through a scrunching mechanism, RNA extension in reiterative transcription initiation proceeds through a slippage mechanism, with slipping of RNA relative to DNA within a short RNA-DNA hybrid, and with extrusion of RNA from RNAP through an alternative RNA exit.
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7
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Duckworth AT, Keck JL. Use of an unnatural amino acid to map helicase/DNA interfaces via photoactivated crosslinking. Methods Enzymol 2022; 672:55-74. [PMID: 35934485 PMCID: PMC10037347 DOI: 10.1016/bs.mie.2022.02.019] [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] [Indexed: 11/21/2022]
Abstract
Formation of protein/nucleic acid complexes is essential for life. From DNA replication and repair to transcription and translation, myriad different proteins bind nucleic acids to execute their essential cellular functions. Our understanding of the mechanisms underlying recognition and processing of nucleic acids can be greatly informed by mapping protein domains and residues that form interfaces with their DNA or RNA targets. Here we describe a crosslinking protocol in which the unnatural amino acid p-benzoyl-l-phenylalanine (Bpa) integrated at selected sites within the PriA DNA helicase is used to map surfaces of the protein that interact with specific positions in a synthetic DNA replication fork in vitro.
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Affiliation(s)
- Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States.
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8
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Pukhrambam C, Vvedenskaya IO, Nickels BE. XACT-seq: A photocrosslinking-based technique for detection of the RNA polymerase active-center position relative to DNA in Escherichia coli. STAR Protoc 2021; 2:100858. [PMID: 34693360 PMCID: PMC8517213 DOI: 10.1016/j.xpro.2021.100858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
XACT-seq ("crosslink between active-center and template sequencing") is a technique for high-throughput, single-nucleotide resolution mapping of RNA polymerase (RNAP) active-center positions relative to the DNA template. XACT-seq overcomes limitations of approaches that rely on analysis of the RNA 3' end (e.g., native elongating transcript sequencing) or that report RNAP positions with low resolution (e.g., ChIP-seq and ChIP-exo). XACT-seq can be used to map RNAP active-center positions in transcription initiation complexes, initially transcribing complexes, and transcription elongation complexes. For complete details on the use and execution of this protocol, please refer to Winkelman et al. (2020).
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Affiliation(s)
- Chirangini Pukhrambam
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
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9
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Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Proc Natl Acad Sci U S A 2021; 118:2112877118. [PMID: 34599106 DOI: 10.1073/pnas.2112877118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
The first step in gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms "open" complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo, but their structural origins remain largely unknown. Here, we use cryoelectron microscopy to determine the structures of RPo formed de novo at three promoters with widely differing lifetimes at 37 °C: λPR (t1/2 ∼10 h), T7A1 (t1/2 ∼4 min), and a point mutant in λPR (λPR-5C) (t1/2 ∼2 h). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate strand "scrunches" inside the active site cleft; the template strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and affect the subsequent steps of the transcription cycle.
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10
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Lee K, Ziegelhoffer T, Delewski W, Berger SE, Sabat G, Craig EA. Pathway of Hsp70 interactions at the ribosome. Nat Commun 2021; 12:5666. [PMID: 34580293 PMCID: PMC8476630 DOI: 10.1038/s41467-021-25930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, an Hsp70 molecular chaperone triad assists folding of nascent chains emerging from the ribosome tunnel. In fungi, the triad consists of canonical Hsp70 Ssb, atypical Hsp70 Ssz1 and J-domain protein cochaperone Zuo1. Zuo1 binds the ribosome at the tunnel exit. Zuo1 also binds Ssz1, tethering it to the ribosome, while its J-domain stimulates Ssb’s ATPase activity to drive efficient nascent chain interaction. But the function of Ssz1 and how Ssb engages at the ribosome are not well understood. Employing in vivo site-specific crosslinking, we found that Ssb(ATP) heterodimerizes with Ssz1. Ssb, in a manner consistent with the ADP conformation, also crosslinks to ribosomal proteins across the tunnel exit from Zuo1. These two modes of Hsp70 Ssb interaction at the ribosome suggest a functionally efficient interaction pathway: first, Ssb(ATP) with Ssz1, allowing optimal J-domain and nascent chain engagement; then, after ATP hydrolysis, Ssb(ADP) directly with the ribosome. Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | - Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Scott E Berger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Chemistry, Lafayette College, Easton, PA, 18042, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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11
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Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise. Proc Natl Acad Sci U S A 2021; 118:2021941118. [PMID: 34290140 DOI: 10.1073/pnas.2021941118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcription initiation is highly regulated by promoter sequence, transcription factors, and ligands. All known transcription inhibitors, an important class of antibiotics, act in initiation. To understand regulation and inhibition, the biophysical mechanisms of formation and stabilization of the "open" promoter complex (OC), of synthesis of a short RNA-DNA hybrid upon nucleotide addition, and of escape of RNA polymerase (RNAP) from the promoter must be understood. We previously found that RNAP forms three different OC with λPR promoter DNA. The 37 °C RNAP-λPR OC (RPO) is very stable. At lower temperatures, RPO is less stable and in equilibrium with an intermediate OC (I3). Here, we report step-by-step rapid quench-flow kinetic data for initiation and growth of the RNA-DNA hybrid at 25 and 37 °C that yield rate constants for each step of productive nucleotide addition. Analyzed together, with previously published data at 19 °C, our results reveal that I3 and not RPO is the productive initiation complex at all temperatures. From the strong variations of rate constants and activation energies and entropies for individual steps of hybrid extension, we deduce that contacts of RNAP with the bubble strands are disrupted stepwise as the hybrid grows and translocates. Stepwise disruption of RNAP-strand contacts is accompanied by stepwise bubble collapse, base stacking, and duplex formation, as the hybrid extends to a 9-mer prior to disruption of upstream DNA-RNAP contacts and escape of RNAP from the promoter.
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12
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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.
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13
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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.
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14
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Zuo Y, De S, Feng Y, Steitz TA. Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. iScience 2020; 23:101445. [PMID: 32829286 PMCID: PMC7452309 DOI: 10.1016/j.isci.2020.101445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ3.2 loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the σ3 domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and σ-RNAP core separation to transition transcription from initiation to elongation.
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Affiliation(s)
- Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Swastik De
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, New Haven, CT 06510, USA
| | - Yingang Feng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, Shandong 266101, China
| | - 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
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15
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XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing. Mol Cell 2020; 79:797-811.e8. [PMID: 32750314 DOI: 10.1016/j.molcel.2020.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a "stepping" mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a "scrunching" mechanism, has not. We report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolution (XACT-seq; "crosslink-between-active-center-and-template sequencing"). We apply this method to detect and quantify pausing in initial transcription at 411 (∼4,000,000) promoter sequences in vivo in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4 to 5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard coded by sequence elements similar to those for transcription-elongation pausing.
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16
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Stepwise Promoter Melting by Bacterial RNA Polymerase. Mol Cell 2020; 78:275-288.e6. [PMID: 32160514 DOI: 10.1016/j.molcel.2020.02.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 01/22/2023]
Abstract
Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.
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17
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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.
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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
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18
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Pupov D, Petushkov I, Esyunina D, Murakami KS, Kulbachinskiy A. Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA. Nucleic Acids Res 2019; 46:11477-11487. [PMID: 30321408 PMCID: PMC6265461 DOI: 10.1093/nar/gky919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023] Open
Abstract
The σ factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary σ factor (‘σ finger’) directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources. In Escherichia coli, the silencing mainly results from the action of the secondary channel factor DksA, which together with ppGpp binds RNAP and dramatically decreases the stability of intrinsically unstable rRNA promoter complexes. We demonstrate that this switch depends on the σ finger that destabilizes RNAP–promoter interactions. Mutations in the σ finger moderately decrease initiating NTP binding but significantly increase promoter complex stability and reduce DksA affinity to the RNAP–rRNA promoter complex, thus making rRNA transcription less sensitive to DksA/ppGpp both in vitro and in vivo. Thus, destabilization of rRNA promoter complexes by the σ finger makes them a target for robust regulation by the stringent response factors under stress conditions.
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Affiliation(s)
- Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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19
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Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK. The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Mol Microbiol 2019; 112:992-1009. [PMID: 31254296 DOI: 10.1111/mmi.14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Abstract
Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α-helix with unstructured N- and C-terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70 ) and the stress sigma factor holoenzyme (EσS ) in vitro, but has a greater impact on EσS . In both cases, SutA appears to affect intermediates in the open complex formation and its N-terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.
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Affiliation(s)
- Megan Bergkessel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett M Babin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Roxana Eggleston-Rangel
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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20
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Mazumder A, Kapanidis AN. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. J Mol Biol 2019; 431:3947-3959. [PMID: 31082441 PMCID: PMC7057261 DOI: 10.1016/j.jmb.2019.04.046] [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: 03/20/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
Abstract
Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge methodologies. Here, we discuss recent structural, biochemical, and single-molecule biophysical studies targeting the mechanisms of transcription initiation in bacteria, including the formation of the open complex, the reaction of initial transcription, and the promoter escape step that leads to elongation. We specifically focus on the mechanisms employed by the RNA polymerase holoenzyme with the housekeeping sigma factor σ70. The recent progress provides answers to long-held questions, identifies intriguing new behaviours, and opens up fresh questions for the field of transcription.
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Affiliation(s)
- Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
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21
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Windgassen TA, Leroux M, Sandler SJ, Keck JL. Function of a strand-separation pin element in the PriA DNA replication restart helicase. J Biol Chem 2018; 294:2801-2814. [PMID: 30593500 DOI: 10.1074/jbc.ra118.006870] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/26/2018] [Indexed: 11/06/2022] Open
Abstract
DNA helicases are motor proteins that couple the chemical energy of nucleoside triphosphate hydrolysis to the mechanical functions required for DNA unwinding. Studies of several helicases have identified strand-separating "pin" structures that are positioned to intercept incoming dsDNA and promote strand separation during helicase translocation. However, pin structures vary among helicases and it remains unclear whether they confer a conserved unwinding mechanism. Here, we tested the biochemical and cellular roles of a putative pin element within the Escherichia coli PriA DNA helicase. PriA orchestrates replication restart in bacteria by unwinding the lagging-strand arm of abandoned DNA replication forks and reloading the replicative helicase with the help of protein partners that combine with PriA to form what is referred to as a primosome complex. Using in vitro protein-DNA cross-linking, we localized the putative pin (a β-hairpin within a zinc-binding domain in PriA) near the ssDNA-dsDNA junction of the lagging strand in a PriA-DNA replication fork complex. Removal of residues at the tip of the β-hairpin eliminated PriA DNA unwinding, interaction with the primosome protein PriB, and cellular function. We isolated a spontaneous intragenic suppressor mutant of the priA β-hairpin deletion mutant in which 22 codons around the deletion site were duplicated. This suppressor variant and an Ala-substituted β-hairpin PriA variant displayed wildtype levels of DNA unwinding and PriB binding in vitro These results suggest essential but sequence nonspecific roles for the PriA pin element and coupling of PriA DNA unwinding to its interaction with PriB.
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Affiliation(s)
- Tricia A Windgassen
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Maxime Leroux
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Steven J Sandler
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - James L Keck
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
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22
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Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Proc Natl Acad Sci U S A 2018; 115:E9075-E9084. [PMID: 30201718 DOI: 10.1073/pnas.1809842115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3'-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-linking studies reveal a surface on the winged-helix domain of PriA that binds to parental duplex DNA. Deleting the winged-helix domain alters PriA's structure-specific DNA unwinding properties and impairs its activity in vivo. Our observations lead to a model in which coordinated parental-, leading-, and lagging-strand DNA binding provide PriA with the structural specificity needed to act on abandoned DNA replication forks.
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23
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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.
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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.
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24
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Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell 2018; 69:828-839.e5. [PMID: 29478808 DOI: 10.1016/j.molcel.2018.01.035] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/05/2017] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes by DksA. This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.
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Affiliation(s)
- Vadim Molodtsov
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elena Sineva
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Michael Cashel
- Intramural Research Program, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah E Ades
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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25
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Barvík I, Rejman D, Panova N, Šanderová H, Krásný L. Non-canonical transcription initiation: the expanding universe of transcription initiating substrates. FEMS Microbiol Rev 2017; 41:131-138. [PMID: 27799279 DOI: 10.1093/femsre/fuw041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.
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Affiliation(s)
- Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Natalya Panova
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Šanderová
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
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26
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Yu L, Winkelman JT, Pukhrambam C, Strick TR, Nickels BE, Ebright RH. The mechanism of variability in transcription start site selection. eLife 2017; 6:32038. [PMID: 29168694 PMCID: PMC5730371 DOI: 10.7554/elife.32038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/22/2017] [Indexed: 01/24/2023] Open
Abstract
During transcription initiation, RNA polymerase (RNAP) binds to promoter DNA, unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing a single-stranded ‘transcription bubble,’ and selects a transcription start site (TSS). TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. Variability in TSS selection has been proposed to involve DNA ‘scrunching’ and ‘anti-scrunching,’ the hallmarks of which are: (i) forward and reverse movement of the RNAP leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble. Here, using in vitro and in vivo protein-DNA photocrosslinking and single-molecule nanomanipulation, we show bacterial TSS selection exhibits both hallmarks of scrunching and anti-scrunching, and we define energetics of scrunching and anti-scrunching. The results establish the mechanism of TSS selection by bacterial RNAP and suggest a general mechanism for TSS selection by bacterial, archaeal, and eukaryotic RNAP. Genes store the information needed to build and repair cells. This information is written in a chemical code within the structure of DNA molecules. To make use of the information, cells copy sections of a gene into a DNA-like molecule called RNA. An enzyme called RNA polymerase makes RNA molecules from DNA templates in a process called transcription. RNA polymerase can only make RNA by attaching to DNA and separating the two strands of the DNA double helix. This creates a short region of single-stranded DNA known as a “transcription bubble”. RNA polymerase can start transcription at different distances from the sites where it initially attaches to DNA, depending on the DNA sequence and the cell’s environment. It had not been known how RNA polymerase selects different transcription start sites in different cases. One hypothesis had been that differences in the size of the transcription bubble – the amount of unwound single-stranded DNA – could be responsible for differences in transcription start sites. For example, RNA polymerase could increase the size of the bubble through a process called “DNA scrunching”, in which RNA polymerase pulls in and unwinds extra DNA from further along the gene. Yu, Winkelman et al. looked for indicators of DNA scrunching to see whether it contributes to the selection of transcription start sites. By mapping the positions of the two edges of RNA polymerase relative to DNA, they saw that RNA polymerase pulls in extra DNA when selecting a transcription start site further from its initial attachment site. Next, by measuring the amount of DNA unwinding, they saw that RNA polymerase unwinds extra DNA when it selects a transcription start site further from its initial attachment site. This was the case for both RNA polymerase in a test tube and RNA polymerase in living bacterial cells. The results showed that DNA scrunching accounts for known patterns of selection of transcription start sites. The findings hint at a common theory for the selection of transcription start sites across all life by DNA scrunching. Understanding these basic principles of biology reveals more about how cells work and how cells adapt to changing conditions. The experimental methods developed for mapping the positions of proteins on DNA and for measuring DNA unwinding will help scientists to learn more about other aspects of how DNA is stored, copied, read, and controlled.
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Affiliation(s)
- Libing Yu
- Department of Chemistry, Rutgers University, Piscataway, United States.,Waksman Institute, Rutgers University, Piscataway, United States
| | - Jared T Winkelman
- Department of Chemistry, Rutgers University, Piscataway, United States.,Waksman Institute, Rutgers University, Piscataway, United States.,Department of Genetics, Rutgers University, Piscataway, United States
| | - Chirangini Pukhrambam
- Waksman Institute, Rutgers University, Piscataway, United States.,Department of Genetics, Rutgers University, Piscataway, United States
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Paris, France
| | - Bryce E Nickels
- Waksman Institute, Rutgers University, Piscataway, United States.,Department of Genetics, Rutgers University, Piscataway, United States
| | - Richard H Ebright
- Department of Chemistry, Rutgers University, Piscataway, United States.,Waksman Institute, Rutgers University, Piscataway, United States
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27
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Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 2017; 68:388-397.e6. [PMID: 28988932 DOI: 10.1016/j.molcel.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023]
Abstract
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ70-holoenzyme (Eσ70) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ70 determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
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Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shili Feng
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Leon
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zongli Li
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
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28
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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.
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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
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29
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TraR directly regulates transcription initiation by mimicking the combined effects of the global regulators DksA and ppGpp. Proc Natl Acad Sci U S A 2017; 114:E5539-E5548. [PMID: 28652326 PMCID: PMC5514744 DOI: 10.1073/pnas.1704105114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli F element-encoded protein TraR is a distant homolog of the chromosome-encoded transcription factor DksA. Here we address the mechanism by which TraR acts as a global regulator, inhibiting some promoters and activating others. We show that TraR regulates transcription directly in vitro by binding to the secondary channel of RNA polymerase (RNAP) using interactions similar, but not identical, to those of DksA. Even though it binds to RNAP with only slightly higher affinity than DksA and is only half the size of DksA, TraR by itself inhibits transcription as strongly as DksA and ppGpp combined and much more than DksA alone. Furthermore, unlike DksA, TraR activates transcription even in the absence of ppGpp. TraR lacks the residues that interact with ppGpp in DksA, and TraR binding to RNAP uses the residues in the β' rim helices that contribute to the ppGpp binding site in the DksA-ppGpp-RNAP complex. Thus, unlike DksA, TraR does not bind ppGpp. We propose a model in which TraR mimics the effects of DksA and ppGpp together by binding directly to the region of the RNAP secondary channel that otherwise binds ppGpp, and its N-terminal region, like the coiled-coil tip of DksA, engages the active-site region of the enzyme and affects transcription allosterically. These data provide insights into the function not only of TraR but also of an evolutionarily widespread and diverse family of TraR-like proteins encoded by bacteria, as well as bacteriophages and other extrachromosomal elements.
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30
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Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell 2017; 67:106-116.e4. [PMID: 28579332 PMCID: PMC5505868 DOI: 10.1016/j.molcel.2017.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/05/2017] [Indexed: 01/25/2023]
Abstract
Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. RNA polymerase closed complex (RPc) structure reveals DNA distortions by σ Intermediate complex (RPi) structure reveals the roles of AAA activator DNA distortion and opening are initiated in RPc and RPi before entering the RNAP RNAP conformation in RPi is significantly different from closed or open complex
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31
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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.
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32
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Winkelman JT, Gourse RL. Open complex DNA scrunching: A key to transcription start site selection and promoter escape. Bioessays 2017; 39:10.1002/bies.201600193. [PMID: 28052345 PMCID: PMC5313389 DOI: 10.1002/bies.201600193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacterial RNA polymerase-promoter open complexes can exist in a range of states in which the leading edge of the enzyme moves but the trailing edge does not, a phenomenon we refer to as "open complex scrunching." Here we describe how open complex scrunching can determine the position of the transcription start site for some promoters, modulate the level of expression, and potentially could be targeted by factors to regulate transcription. We suggest that open complex scrunching at the extraordinarily active ribosomal RNA promoters might have evolved to initiate transcription at an unusual position relative to the core promoter elements in order to maximize the rate of promoter escape.
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Affiliation(s)
- Jared T. Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Genetics and Waksman Institute, Rutgers University, NJ, USA
| | - Richard L. Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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33
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RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes. Proc Natl Acad Sci U S A 2016; 113:14994-14999. [PMID: 27956639 DOI: 10.1073/pnas.1613673114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.
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34
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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.
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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
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35
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Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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36
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Windgassen TA, Keck JL. An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase. Nucleic Acids Res 2016; 44:9745-9757. [PMID: 27484483 PMCID: PMC5175346 DOI: 10.1093/nar/gkw690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Helicases couple ATP hydrolysis to nucleic acid binding and unwinding via molecular mechanisms that remain poorly defined for most enzyme subfamilies within the superfamily 2 (SF2) helicase group. A crystal structure of the PriA SF2 DNA helicase, which governs restart of prematurely terminated replication processes in bacteria, revealed the presence of an aromatic-rich loop (ARL) on the presumptive DNA-binding surface of the enzyme. The position and sequence of the ARL was similar to loops known to couple ATP hydrolysis with DNA binding in a subset of other SF2 enzymes, however, the roles of the ARL in PriA had not been investigated. Here, we show that changes within the ARL sequence uncouple PriA ATPase activity from DNA binding. In vitro protein-DNA crosslinking experiments define a residue- and nucleotide-specific interaction map for PriA, showing that the ARL binds replication fork junctions whereas other sites bind the leading or lagging strands. We propose that DNA binding to the ARL allosterically triggers ATP hydrolysis in PriA. Additional SF2 helicases with similarly positioned loops may also couple DNA binding to ATP hydrolysis using related mechanisms.
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Affiliation(s)
- Tricia A Windgassen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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37
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Winkelman JT, Chandrangsu P, Ross W, Gourse RL. Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters. Proc Natl Acad Sci U S A 2016; 113:E1787-95. [PMID: 26976590 PMCID: PMC4822585 DOI: 10.1073/pnas.1522159113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most Escherichia coli promoters initiate transcription with a purine 7 or 8 nt downstream from the -10 hexamer, but some promoters, including the ribosomal RNA promoter rrnB P1, start 9 nt from the -10 element. We identified promoter and RNA polymerase determinants of this noncanonical rrnB P1 start site using biochemical and genetic approaches including mutational analysis of the promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa cross-linking to map the path of open complex DNA at amino acid and nucleotide resolution. We find that mutations in several promoter regions affect transcription start site (TSS) selection. In particular, we show that the absence of strong interactions between the discriminator region and σ region 1.2 and between the extended -10 element and σ region 3.0, identified previously as a determinant of proper regulation of rRNA promoters, is also required for the unusual TSS. We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex expands and is "scrunched" into the active site channel of RNA polymerase, similar to the situation in initial transcribing complexes. However, in the rrnB P1 open complex, scrunching occurs before RNA synthesis begins. We find that the scrunched open complex exhibits reduced abortive product synthesis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcriptional activity of rRNA promoters by increasing promoter escape, helping to offset the reduction in promoter activity that would result from the weak interactions with σ.
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Affiliation(s)
- Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Pete Chandrangsu
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
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38
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Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science 2016; 351:1090-3. [PMID: 26941320 DOI: 10.1126/science.aad6881] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.
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Affiliation(s)
- Jared T Winkelman
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Irina O Vvedenskaya
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuanchao Zhang
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yu Zhang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Jeremy G Bird
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Deanne M Taylor
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Richard H Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
| | - Bryce E Nickels
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA. Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
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39
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Chander M, Lee A, Vallery TK, Thandar M, Jiang Y, Hsu LM. Mechanisms of Very Long Abortive Transcript Release during Promoter Escape. Biochemistry 2015; 54:7393-408. [PMID: 26610896 DOI: 10.1021/acs.biochem.5b00712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A phage T5 N25 promoter variant, DG203, undergoes the escape transition at the +16 to +19 positions after transcription initiation. By specifically examining the abortive activity of the initial transcribing complex at position +19 (ITC19), we observe the production of both GreB-sensitive and GreB-resistant VLAT19. This suggests that ITC19, which is perched on the brink of escape, is highly unstable and can achieve stabilization through either backtracking or forward translocation. Of the forward-tracked fraction, only a small percentage escapes normally (followed by stepwise elongation) to produce full-length RNA; the rest presumably hypertranslocates to release GreB-resistant VLATs. VLAT formation is dependent not only on consensus -35/-10 promoters with 17 bp spacing but also on sequence characteristics of the spacer DNA. Analysis of DG203 promoter variants containing different spacer sequences reveals that AT-rich spacers intrinsically elevate the level of VLAT formation. The AT-rich spacer of DG203 joined to the -10 box presents an UP element sequence capable of interacting with the polymerase α subunit C-terminal domain (αCTD) during the escape transition, which in turn enhances VLAT release. Utilization of the spacer/-10 region UP element by αCTD subunits requires a 10-15 bp hypertranslocation. We document the physical occurrence of hyper forward translocation using ExoIII footprinting analysis.
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Affiliation(s)
- Monica Chander
- Biology Department, Bryn Mawr College , Bryn Mawr, Pennsylvania 19010, United States
| | - Ahri Lee
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Tenaya K Vallery
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Mya Thandar
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Yunnan Jiang
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Lilian M Hsu
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
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