Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism

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Abstract

Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartments in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.

Data availability

Cryo-EM maps of holo and apo-SrpI have been deposited at the EM Data Resource with accession codes EMD-22094 and EMD-22095 respectively. The refined coordinate model has been deposited at the Protein Data Bank (PDB) with accession code 6X8M and 6X8T.

The following data sets were generated

1. LaFrance
2. B.J.
3. Nichols
4. R.J.
5. Phillips
6. N.R.
7. Oltrogge
8. L.M.
9. Valentin-Alvarado
10. L.E.
11. Bischoff
12. A.J.
13. Savage
14. D.F.
15. Nogales
16. E
(2020) CryoEM structure of the holo-SrpI encapsulin complex from Synechococcus elongatus PCC 7942
PDB, 6X8M.

https://www.rcsb.org/structure/6X8M
1. LaFrance
2. B.J.
3. Nichols
4. R.J.
5. Phillips
6. N.R.
7. Oltrogge
8. L.M.
9. Valentin-Alvarado
10. L.E.
11. Bischoff
12. A.J.
13. Savage
14. D.F.
15. Nogales
16. E
(2020) CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942
PDB, 6X8T.

https://www.rcsb.org/structure/6X8T
(2020) CryoEM structure of the holo-SrpI encapsulin complex from Synechococcus elongatus PCC 7942
EMD-22094.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22094
(2020) CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942
EMD-22095.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-22095
(2020) CryoEM SPA of Holo-SrpI Encapsulin Complex (Raw Frames)
EMPIAR-10506.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10506/
(2020) CryoEM SPA of Apo-SrpI Encapsulin Complex (Raw Frames)
EMPIAR-10510.

https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10510/

Article and author information

Author details

Robert J Nichols

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Benjamin LaFrance

Department of Molecular and Cell Biology,, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Naiya R Phillips

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Devon R Radford

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Luke M Oltrogge

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5716-9980
Luis E Valentin-Alvarado

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Amanda J Bischoff

Department of Chemistry,, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.
Eva Nogales

Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States

For correspondence
enogales@lbl.gov

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9816-3681
David F Savage

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States

For correspondence
savage@berkeley.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0042-2257

Funding

U.S. Department of Energy (Grant DE-SC00016240 (to D.F.S))

Robert J Nichols
Naiya R Phillips
Luke M Oltrogge
David F Savage

National Science Foundation (GRFP-1106400)

Benjamin LaFrance

Howard Hughes Medical Institute

Eva Nogales

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.