Structure of RNA polymerase bound to ribosomal 30S subunit

Abstract
Data availability
Article and author information
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Abstract

In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of E. coli RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation.

Data availability

The following data sets were generated

1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) Structure of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
6AWB.

https://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=FC26A7B1
1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) cryo-EM map of 30S ribosomal subunit and RNA polymerase complex in non-rotated state
EMD-7014.

https://www.ebi.ac.uk/pdbe/emdb/
1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state
6AWC.

https://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=41138448
1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) cryo-EM map of 30S ribosomal subunit and RNA polymerase complex in rotated state
EMD-7015.

https://www.ebi.ac.uk/pdbe/emdb/
1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) Structure of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex
6AWD.

https://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=D1A165EB
1. Demo
2. G.
3. Rasouly
4. A.
5. Vasilyev
6. N.
7. Svetlov
8. V.
9. Loveland
10. A.B.
11. Diaz-Avalos
12. R.
13. Grigorieff
14. N.
15. Nudler
16. E.
17. Korostelev
18. A.A.
(2017) cryo-EM map of 30S (S1 depleted) ribosomal subunit and RNA polymerase complex
EMD-7016.

https://www.ebi.ac.uk/pdbe/emdb/

Article and author information

Author details

Gabriel Demo

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
No competing interests declared.
Aviram Rasouly

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States

Competing interests
No competing interests declared.
Nikita Vasilyev

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States

Competing interests
No competing interests declared.
Vladimir Svetlov

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States

Competing interests
No competing interests declared.
Anna B Loveland

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
No competing interests declared.
Ruben Diaz-Avalos

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States

Competing interests
No competing interests declared.
Nikolaus Grigorieff

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States

Competing interests
Nikolaus Grigorieff, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-1506-909X
Evgeny Nudler

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States

For correspondence
evgeny.nudler@nyumc.org

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-8811-3071
Andrei A Korostelev

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

For correspondence
andrei.korostelev@umassmed.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-1588-717X

Funding

National Institutes of Health (GM106105)

Andrei A Korostelev

National Institutes of Health (GM107465)

Andrei A Korostelev

National Institutes of Health (GM107329)

Evgeny Nudler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

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.