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Le TT, Yang Y, Tan C, Suhanovsky MM, Fulbright RM, Inman JT, Li M, Lee J, Perelman S, Roberts JW, Deaconescu AM, Wang MD. Mfd Dynamically Regulates Transcription via a Release and Catch-Up Mechanism. Cell 2017; 172:344-357.e15. [PMID: 29224782 DOI: 10.1016/j.cell.2017.11.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/21/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022]
Abstract
The bacterial Mfd ATPase is increasingly recognized as a general transcription factor that participates in the resolution of transcription conflicts with other processes/roadblocks. This function stems from Mfd's ability to preferentially act on stalled RNA polymerases (RNAPs). However, the mechanism underlying this preference and the subsequent coordination between Mfd and RNAP have remained elusive. Here, using a novel real-time translocase assay, we unexpectedly discovered that Mfd translocates autonomously on DNA. The speed and processivity of Mfd dictate a "release and catch-up" mechanism to efficiently patrol DNA for frequently stalled RNAPs. Furthermore, we showed that Mfd prevents RNAP backtracking or rescues a severely backtracked RNAP, allowing RNAP to overcome stronger obstacles. However, if an obstacle's resistance is excessive, Mfd dissociates the RNAP, clearing the DNA for other processes. These findings demonstrate a remarkably delicate coordination between Mfd and RNAP, allowing efficient targeting and recycling of Mfd and expedient conflict resolution.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Yi Yang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Chuang Tan
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Margaret M Suhanovsky
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | | | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ming Li
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Sarah Perelman
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexandra M Deaconescu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
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Mustaev A, Roberts J, Gottesman M. Transcription elongation. Transcription 2017; 8:150-161. [PMID: 28301288 PMCID: PMC5501382 DOI: 10.1080/21541264.2017.1289294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/23/2022] Open
Abstract
This review is focused on recent progress in understanding how Escherichia coli RNAP polymerase translocates along the DNA template and the factors that affect this movement. We discuss the fundamental aspects of RNAP translocation, template signals that influence forward or backward movement, and host or phage factors that modulate translocation.
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Affiliation(s)
- Arkady Mustaev
- PHRI Center, NJMS, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Jeffrey Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Max Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA
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Kang JY, Olinares PDB, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. eLife 2017; 6. [PMID: 28318486 PMCID: PMC5386594 DOI: 10.7554/elife.25478] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/19/2017] [Indexed: 01/24/2023] Open
Abstract
Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β’ subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs. DOI:http://dx.doi.org/10.7554/eLife.25478.001
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Affiliation(s)
- Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York City, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
| | - Arkady Mustaev
- Public Health Research Institute, Newark, United States.,Department of Microbiology and Molecular Genetics, Rutgers Biomedical and Health Sciences, Newark, United States.,Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York City, United States
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University Medical Center, New York City, United States
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States
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