Structural basis of transcription arrest by coliphage HK022 nun in an Escherichia coli RNA polymerase elongation complex
- The Rockefeller University, United States
- Public Health Research Institute, United States
- Columbia University Medical Center, United States
Abstract
Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λΔNA.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.
Data availability
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CryoEM structure of HK022 Nun - E. coli RNA polymerase elongation complexPublicly available at the RCSB Protein Data Bank (accession no: 5UP6).
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CryoEM structure of HK022 Nun - E. coli RNA polymerase elongation complexPublicly available at the EMBL-EBI Protein Data Bank in Europe (accession no: EMD-8584).
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CryoEM structure of crosslinked E.coli RNA polymerase elongation complexPublicly available at the RCSB Protein Data Bank (accession no: 5UPA).
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CryoEM structure of crosslinked E.coli RNA polymerase elongation complexPublicly available at the EMBL-EBI Protein Data Bank in Europe (accession no: EMD-8585).
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CryoEM structure of E.coli RNA polymerase elongation complexPublicly available at the RCSB Protein Data Bank (accession no: 5UPC).
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CryoEM structure of E.coli RNA polymerase elongation complexPublicly available at the EMBL-EBI Protein Data Bank in Europe (accession no: EMD-8586).
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Crystal Structure Analysis of the E.coli holoenzymePublicly available at the RCSB Protein Data Bank (accession no: 4LJZ).
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Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analogPublicly available at the RCSB Protein Data Bank (accession no: 2O5J).
Article and author information
Author details
Funding
National Institutes of Health (R35 GM118130)
- Seth A Darst
National Institutes of Health (R01 GM037219)
- Max E Gottesman
National Institutes of Health (P41 GM103314)
- Brian T Chait
Public Health Research Institute Research Support grant
- Arkady Mustaev
National Institutes of Health (P41 GM109824)
- Brian T Chait
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nikolaus Grigorieff, Janelia Research Campus, Howard Hughes Medical Institute, United States
Version history
- Received: January 26, 2017
- Accepted: March 19, 2017
- Accepted Manuscript published: March 20, 2017 (version 1)
- Version of Record published: April 10, 2017 (version 2)
Copyright
© 2017, Kang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structural basis of transcription arrest by coliphage HK022 nun in an Escherichia coli RNA polymerase elongation complex
eLife 6:e25478.
https://doi.org/10.7554/eLife.25478
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