1
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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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2
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Birkholz EA, Morgan CJ, Laughlin TG, Lau RK, Prichard A, Rangarajan S, Meza GN, Lee J, Armbruster EG, Suslov S, Pogliano K, Meyer JR, Villa E, Corbett KD, Pogliano J. A mobile intron facilitates interference competition between co-infecting viruses. bioRxiv 2023:2023.09.30.560319. [PMID: 37808663 PMCID: PMC10557746 DOI: 10.1101/2023.09.30.560319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Mobile introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. Here we studied a mobile intron in bacteriophage ΦPA3 and found its homing endonuclease gp210 contributes to viral competition by interfering with the virogenesis of co-infecting phage ΦKZ. We show that gp210 targets a specific sequence in its competitor ΦKZ, preventing the assembly of progeny viruses. This work reports the first demonstration of how a mobile intron can be deployed to engage in interference competition and provide a reproductive advantage. Given the ubiquity of introns, this selective advantage likely has widespread evolutionary implications in nature.
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3
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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4
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy A, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett K, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. bioRxiv 2023:2023.02.24.529968. [PMID: 36865095 PMCID: PMC9980170 DOI: 10.1101/2023.02.24.529968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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5
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Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, Amaro RE, Pogliano J, Corbett KD, Villa E. Architecture and self-assembly of the jumbo phage nucleus-like compartment. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, McCammon JA, Amaro RE, Pogliano J, Corbett KD, Villa E. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 2022; 608:429-435. [PMID: 35922510 PMCID: PMC9365700 DOI: 10.1038/s41586-022-05013-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 01/31/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022]
Abstract
Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2-4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
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Affiliation(s)
- Thomas G. Laughlin
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Amar Deep
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Amy M. Prichard
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Christian Seitz
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Yajie Gu
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Eray Enustun
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Sergey Suslov
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Kanika Khanna
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA ,grid.47840.3f0000 0001 2181 7878Present Address: Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Erica A. Birkholz
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Emily Armbruster
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - J. Andrew McCammon
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Rommie E. Amaro
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Joe Pogliano
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D. Corbett
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA. .,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA.
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7
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Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nat Commun 2021; 12:5664. [PMID: 34580310 PMCID: PMC8476515 DOI: 10.1038/s41467-021-25992-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 09/10/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
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Affiliation(s)
- Arik Shams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sean A Higgins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, 92093, USA
| | - Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Rachel Lew
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Shin Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Maria Lukarska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Madeline Arnold
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brett T Staahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
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8
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Laughlin TG, Savage DF, Davies KM. Recent advances on the structure and function of NDH-1: The complex I of oxygenic photosynthesis. Biochim Biophys Acta Bioenerg 2020; 1861:148254. [PMID: 32645407 DOI: 10.1016/j.bbabio.2020.148254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/07/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022]
Abstract
Photosynthetic NADH dehydrogenase-like complex type-1 (a.k.a, NDH, NDH-1, or NDH-1L) is a multi-subunit, membrane-bound oxidoreductase related to the respiratory complex I. Although originally discovered 30 years ago, a number of recent advances have revealed significant insight into the structure, function, and physiology of NDH-1. Here, we highlight progress in understanding the function of NDH-1 in the photosynthetic light reactions of both cyanobacteria and chloroplasts from biochemical and structural perspectives. We further examine the cyanobacterial-specific forms of NDH-1 that possess vectorial carbonic anhydrase (vCA) activity and function in the CO2-concentrating mechanism (CCM). We compare the proposed mechanism for the cyanobacterial NDH-1 vCA-activity to that of the DAB (DABs accumulates bicarbonate) complex, another putative vCA. Finally, we discuss both new and remaining questions pertaining to the mechanisms of NDH-1 complexes in light of these recent advances.
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Affiliation(s)
- Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Karen M Davies
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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9
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Laughlin TG, Bayne A, Trempe JF, Savage D, Davies K. Structure of the Cyanobacterial NAD(P)H Dehydrogenase-Like Complex of Oxygenic Photosynthesis. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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10
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Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol 2019; 4:2204-2215. [PMID: 31406332 PMCID: PMC10184468 DOI: 10.1038/s41564-019-0520-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/30/2022]
Abstract
Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of the components of CCMs is lacking. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins-which we name DabA and DabB, for DABs accumulate bicarbonate-assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. Interestingly, DAB operons are found in a diverse range of bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. On the basis of these results, we propose that DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.
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Affiliation(s)
- John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Allen W Chen
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Kelly Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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Sutter M, Laughlin TG, Sloan NB, Serwas D, Davies KM, Kerfeld CA. Structure of a Synthetic β-Carboxysome Shell. Plant Physiol 2019; 181:1050-1058. [PMID: 31501298 PMCID: PMC6836842 DOI: 10.1104/pp.19.00885] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/24/2019] [Indexed: 05/30/2023]
Abstract
Carboxysomes are capsid-like, CO2-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO2-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO2 and the prevention of CO2 escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO2 concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells.
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Affiliation(s)
- Markus Sutter
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Thomas G Laughlin
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Nancy B Sloan
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel Serwas
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Karen M Davies
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Puray-Chavez MN, Farghali MH, Yapo V, Huber AD, Liu D, Ndongwe TP, Casey MC, Laughlin TG, Hannink M, Tedbury PR, Sarafianos SG. Effects of Moloney Leukemia Virus 10 Protein on Hepatitis B Virus Infection and Viral Replication. Viruses 2019; 11:v11070651. [PMID: 31319455 PMCID: PMC6669478 DOI: 10.3390/v11070651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022] Open
Abstract
Moloney leukemia virus 10 (MOV10) is an RNA helicase that has been shown to affect the replication of several viruses. The effect of MOV10 on Hepatitis B virus (HBV) infection is not known and its role on the replication of this virus is poorly understood. We investigated the effect of MOV10 down-regulation and MOV10 over-expression on HBV in a variety of cell lines, as well as in an infection system using a replication competent virus. We report that MOV10 down-regulation, using siRNA, shRNA, and CRISPR/Cas9 gene editing technology, resulted in increased levels of HBV DNA, HBV pre-genomic RNA, and HBV core protein. In contrast, MOV10 over-expression reduced HBV DNA, HBV pre-genomic RNA, and HBV core protein. These effects were consistent in all tested cell lines, providing strong evidence for the involvement of MOV10 in the HBV life cycle. We demonstrated that MOV10 does not interact with HBV-core. However, MOV10 binds HBV pgRNA and this interaction does not affect HBV pgRNA decay rate. We conclude that the restriction of HBV by MOV10 is mediated through effects at the level of viral RNA.
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Affiliation(s)
- Maritza N Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mahmoud H Farghali
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta QXXV+C5, Egypt
| | - Vincent Yapo
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Andrew D Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Tanyaradzwa P Ndongwe
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mary C Casey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Thomas G Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mark Hannink
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Philip R Tedbury
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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13
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Huber AD, Pineda DL, Liu D, Boschert KN, Gres AT, Wolf JJ, Coonrod EM, Tang J, Laughlin TG, Yang Q, Puray-Chavez MN, Ji J, Singh K, Kirby KA, Wang Z, Sarafianos SG. Novel Hepatitis B Virus Capsid-Targeting Antiviral That Aggregates Core Particles and Inhibits Nuclear Entry of Viral Cores. ACS Infect Dis 2019; 5:750-758. [PMID: 30582687 DOI: 10.1021/acsinfecdis.8b00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An estimated 240 million are chronically infected with hepatitis B virus (HBV), which can lead to liver disease, cirrhosis, and hepatocellular carcinoma. Currently, HBV treatment options include only nucleoside reverse transcriptase inhibitors and the immunomodulatory agent interferon alpha, and these treatments are generally not curative. New treatments with novel mechanisms of action, therefore, are highly desired for HBV therapy. The viral core protein (Cp) has gained attention as a possible therapeutic target because of its vital roles in the HBV life cycle. Several classes of capsid assembly effectors (CAEs) have been described in detail, and these compounds all increase capsid assembly rate but inhibit HBV replication by different mechanisms. In this study, we have developed a thermal shift-based screening method for CAE discovery and characterization, filling a much-needed gap in high-throughput screening methods for capsid-targeting molecules. Using this approach followed by cell-based screening, we identified the compound HF9C6 as a CAE with low micromolar potency against HBV replication. HF9C6 caused large multicapsid aggregates when capsids were assembled in vitro and analyzed by transmission electron microscopy. Interestingly, when HBV-expressing cells were treated with HF9C6, Cp was excluded from cell nuclei, suggesting that this compound may inhibit nuclear entry of Cp and capsids. Furthermore, mutational scanning of Cp suggested that HF9C6 binds the known CAE binding pocket, indicating that key Cp-compound interactions within this pocket have a role in determining the CAE mechanism of action.
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Affiliation(s)
- Andrew D. Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
| | - Dallas L. Pineda
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kelsey N. Boschert
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, 204 Gwynn Hall, Columbia, Missouri 65211, United States
| | - Anna T. Gres
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Jennifer J. Wolf
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Emily M. Coonrod
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, Missouri 65211, United States
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Thomas G. Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Qiongying Yang
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Maritza N. Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Juan Ji
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Karen A. Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
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Laughlin TG, Savage DF, Davies KM. Revealing the Subunit Architecture of NAD(P)H Dehydrogenase Type-1 from Cyanobacteria through Cryo-EM. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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15
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Kirby KA, Ong YT, Hachiya A, Laughlin TG, Chiang LA, Pan Y, Moran JL, Marchand B, Singh K, Gallazzi F, Quinn TP, Yoshimura K, Murakami T, Matsushita S, Sarafianos SG. Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247. FASEB J 2014; 29:70-80. [PMID: 25351987 DOI: 10.1096/fj.14-252262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 Å) crystal structure of the KD-247 antigen binding fragment and examined the potential interactions with various V3 loop targets. Unlike most antibodies, KD-247 appears to interact with its target primarily through light chain residues. Several of these interactions involve Arg(315) of the V3 loop. To evaluate the role of light chain residues in the recognition of the V3 loop, we generated 20 variants of KD-247 single-chain variable fragments with mutations in the antigen-binding site. Purified proteins were assessed for V3 loop binding using AlphaScreen technology and for HIV-1 neutralization. Our data revealed that recognition of the clade-specificity defining residue Arg(315) of the V3 loop is based on a network of interactions that involve Tyr(L32), Tyr(L92), and Asn(L27d) that directly interact with Arg(315), thus elucidating the molecular interactions of KD-247 with its V3 loop target.
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Affiliation(s)
- Karen A Kirby
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Yee Tsuey Ong
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Atsuko Hachiya
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Thomas G Laughlin
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Leslie A Chiang
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Yun Pan
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Jennifer L Moran
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Bruno Marchand
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine
| | | | - Thomas P Quinn
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Kazuhisa Yoshimura
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshio Murakami
- The Chemo-Sero-Therapeutic Research Institute (Kaketsuken), Kyokushi, Kikuchi, Kumamoto, Japan; and
| | - Shuzo Matsushita
- Division of Clinical Retrovirology and Infectious Diseases, Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, School of Medicine, Department of Biochemistry, University of Missouri, Columbia, Missouri, USA;
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