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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG. Author Correction: Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. Nat Struct Mol Biol 2021; 28:702. [PMID: 34285420 PMCID: PMC8294294 DOI: 10.1038/s41594-021-00642-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- David M Kern
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Ben Sorum
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Sonali S Mali
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Christopher M Hoel
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Savitha Sridharan
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan P Remis
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Daniel B Toso
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Abhay Kotecha
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Diana M Bautista
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA.
| | - Stephen G Brohawn
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
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Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG. Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs. bioRxiv 2021. [PMID: 32587976 PMCID: PMC7310636 DOI: 10.1101/2020.06.17.156554] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3–6. 3a has been implicated in viral release7, inhibition of autophagy8, inflammasome activation9, and cell death10,11 and its deletion reduces viral titer and morbidity in mice1, raising the possibility that 3a could be an effective vaccine or therapeutic target3,12. Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 Å resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca2+-permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multiple Alphacoronavirus and Betacoronavirus lineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases.
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Affiliation(s)
- David M Kern
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Ben Sorum
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Sonali S Mali
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Christopher M Hoel
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Savitha Sridharan
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Jonathan P Remis
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Daniel B Toso
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Diana M Bautista
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Stephen G Brohawn
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
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Abstract
A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.
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Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M. The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol 2014; 5:474. [PMID: 25250022 PMCID: PMC4158809 DOI: 10.3389/fmicb.2014.00474] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/22/2014] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus.
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Affiliation(s)
- James E Berleman
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA ; School of Biology, St. Mary's College Moraga, CA, USA
| | - Simon Allen
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Megan A Danielewicz
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Amita Gorur
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jack Cunha
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Masood Z Hadi
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Space Biosciences Division, Synthetic Biology Program, NASA Ames Research Center Moffett Field, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - David R Zusman
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol 2013; 16:598-610. [PMID: 23848955 DOI: 10.1111/1462-2920.12187] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022]
Abstract
The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.
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Affiliation(s)
- Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94025, USA
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Lunde CS, Rouhani S, Remis JP, Glaeser RM. Microcrystal screening with a novel design for beamline-mountable crystallization wells. J Appl Crystallogr 2008. [DOI: 10.1107/s0021889808000952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A simple and flexible system is described forin situscreening of microcrystals of membrane proteins that are grown within a connected-bilayer matrix formed by hydrated lipids. Using sheets of appropriate polymer materials to create a thin multiwell cassette, crystals can be evaluated by UV microscopy as well as by more conventional forms of light microscopy. Crystallization wells can be individually excised and mounted for diffraction screening on a synchrotron X-ray source. In addition, crystallization hit rates were significantly improved by employing a vapor diffusion approach rather than the batch crystallization method that is normally used with hydrated-lipid gels.
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Lunde CS, Rouhani S, Remis JP, Ruzin SE, Ernst JA, Glaeser RM. UV microscopy at 280 nm is effective in screening for the growth of protein microcrystals. J Appl Crystallogr 2005. [DOI: 10.1107/s0021889805028888] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This paper describes the relatively simple modification of a light microscope to operate with ultraviolet-based optics. Using a 280 nm UV illumination source, protein microcrystals are readily visualized in gels made from hydrated bilayers of phospholipids. Non-colored proteins stand out as clearly as colored proteins in this system, the imaging of which is based on UV absorption by tryptophan residues. In addition, protein crystals are easily distinguished from salt crystals. Artifacts from the lipid-based crystallization medium, which are frequently seen in brightfield microscopy, are greatly reduced when viewed in this UV-based microscope.
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