1
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun 2023; 14:2308. [PMID: 37085489 PMCID: PMC10120482 DOI: 10.1038/s41467-023-37787-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (~30 kb). Here, we present a plasmid-based viral genome assembly and rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA, USA.
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Hannah S Martin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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2
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Kumar GR, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. bioRxiv 2023:2023.01.31.525914. [PMID: 36798416 PMCID: PMC9934579 DOI: 10.1101/2023.01.31.525914] [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: 02/11/2023]
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (30kb). Here, we designed a plasmid-based viral genome assembly and resc ue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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3
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Soveg FW, Gross JD, Krogan NJ, Jerome KR, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. PLoS Pathog 2022; 18:e1010811. [PMID: 36095012 PMCID: PMC9499238 DOI: 10.1371/journal.ppat.1010811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/22/2022] [Accepted: 08/18/2022] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response, independently of the Mitochondrial Antiviral Signaling Protein MAVS. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Victor L. Lam
- University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer M. Hayashi
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Frank W. Soveg
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - John D. Gross
- University of California San Francisco, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States of America
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4
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Simoneau CR, Chen PY, Xing GK, Khalid MM, Meyers NL, Hayashi JM, Taha TY, Leon KE, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose J, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M. NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids. bioRxiv 2022:2022.08.02.502100. [PMID: 35982664 PMCID: PMC9387123 DOI: 10.1101/2022.08.02.502100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that accurately recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. NF-κB inhibitor alpha was consistently upregulated in infected epithelial cells, and its mRNA expression positively correlated with infection levels. Confocal microscopy showed more IκBα expression in infected than bystander cells, but found concurrent nuclear translocation of NF-κB that IκBα usually prevents. Overexpressing a nondegradable IκBα mutant reduced NF-κB translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and identify an incomplete NF-κB feedback loop as a rheostat of viral infection that may promote inflammation and severe disease.
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Affiliation(s)
- Camille R. Simoneau
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Galen K. Xing
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | | | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Kristoffer E. Leon
- Gladstone Institute of Virology, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Tal Ashuach
- Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA
| | | | - Lauren Rodriguez
- ImmunoX CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Xiaohui Fang
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mazharul Maishan
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shawn Schultz
- Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA
| | - Jeroen Roose
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Michael A. Matthay
- Department of Medicine and Department of Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mehrdad Arjomandi
- Medical Service, San Francisco VA Healthcare System, San Francisco, CA, USA
- Division of Pulmonary and Critical Care, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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5
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Matsui Y, Li L, Prahl M, Cassidy AG, Ozarslan N, Golan Y, Gonzalez VJ, Lin CY, Jigmeddagva U, Chidboy MA, Montano M, Taha TY, Khalid MM, Sreekumar B, Hayashi JM, Chen PY, Kumar GR, Warrier L, Wu AH, Song D, Jegatheesan P, Rai DS, Govindaswami B, Needens J, Rincon M, Myatt L, Asiodu IV, Flaherman VJ, Afshar Y, Jacoby VL, Murtha AP, Robinson JF, Ott M, Greene WC, Gaw SL. Neutralizing antibody activity against SARS-CoV-2 variants in gestational age-matched mother-infant dyads after infection or vaccination. JCI Insight 2022; 7:e157354. [PMID: 35579965 PMCID: PMC9309042 DOI: 10.1172/jci.insight.157354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/07/2021] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
Pregnancy confers unique immune responses to infection and vaccination across gestation. To date, there are limited data comparing vaccine- and infection-induced neutralizing Abs (nAbs) against COVID-19 variants in mothers during pregnancy. We analyzed paired maternal and cord plasma samples from 60 pregnant individuals. Thirty women vaccinated with mRNA vaccines (from December 2020 through August 2021) were matched with 30 naturally infected women (from March 2020 through January 2021) by gestational age of exposure. Neutralization activity against the 5 SARS-CoV-2 spike sequences was measured by a SARS-CoV-2-pseudotyped spike virion assay. Effective nAbs against SARS-CoV-2 were present in maternal and cord plasma after both infection and vaccination. Compared with WT spike protein, these nAbs were less effective against the Delta and Mu spike variants. Vaccination during the third trimester induced higher cord-nAb levels at delivery than did infection during the third trimester. In contrast, vaccine-induced nAb levels were lower at the time of delivery compared with infection during the first trimester. The transfer ratio (cord nAb level divided by maternal nAb level) was greatest in mothers vaccinated in the second trimester. SARS-CoV-2 vaccination or infection in pregnancy elicits effective nAbs with differing neutralization kinetics that are influenced by gestational time of exposure.
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Affiliation(s)
- Yusuke Matsui
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
| | - Lin Li
- Division of Maternal-Fetal Medicine and
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Mary Prahl
- Department of Pediatrics
- Division of Pediatric Infectious Diseases and Global Health
| | | | - Nida Ozarslan
- Division of Maternal-Fetal Medicine and
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Yarden Golan
- Department of Bioengineering and Therapeutic Sciences
| | | | | | - Unurzul Jigmeddagva
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Megan A. Chidboy
- Division of Maternal-Fetal Medicine and
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Mauricio Montano
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | - Bharath Sreekumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | - Jennifer M. Hayashi
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | - Pei-Yi Chen
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
| | | | - Alan H.B. Wu
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Dongli Song
- Department of Pediatrics, Division of Neonatology, Santa Clara Valley Medical Center, San Jose, California, USA
| | - Priya Jegatheesan
- Department of Pediatrics, Division of Neonatology, Santa Clara Valley Medical Center, San Jose, California, USA
| | - Daljeet S. Rai
- Stanford-O’Connor Family Medicine Residency Program, Division of Family Medicine, Stanford University, Palo Alto, California, USA
| | | | - Jordan Needens
- Department of Obstetrics and Gynecology, Marshall University Joan C. Edwards School of Medicine, Huntington, West Virginia, USA
| | - Monica Rincon
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Leslie Myatt
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | | | | | - Yalda Afshar
- Department of Obstetrics and Gynecology, UCLA, Los Angeles, California, USA
| | | | | | - Joshua F. Robinson
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Department of Medicine, and
| | - Warner C. Greene
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, California, USA
- Department of Medicine, and
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Stephanie L. Gaw
- Division of Maternal-Fetal Medicine and
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, San Francisco, California, USA
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6
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Khalid MM, Taha TY, Tabata T, Hayashi JM, Soveg FW, Carlson-Stevermer J, Gupta M, Zhang MY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Fujimori DG, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. Cell Rep 2022; 40:111088. [PMID: 35839775 PMCID: PMC9234021 DOI: 10.1016/j.celrep.2022.111088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/27/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Inhibitors of bromodomain and extraterminal domain (BET) proteins are possible anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here we show that BET proteins should not be inactivated therapeutically because they are critical antiviral factors at the post-entry level. Depletion of BRD3 or BRD4 in cells overexpressing ACE2 exacerbates SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible “histone mimetic.” E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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Affiliation(s)
- Irene P Chen
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Longbotham
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Gladstone Institutes, San Francisco, CA 94158, USA
| | | | | | | | | | - Meghna Gupta
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meng Yao Zhang
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Victor L Lam
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yang Li
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zanlin Yu
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erron W Titus
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amy Diallo
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Oki
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Kevin Holden
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Nevan Krogan
- Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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7
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Gross JD, Krogan NJ, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. bioRxiv 2022:2022.01.04.474979. [PMID: 35018374 PMCID: PMC8750649 DOI: 10.1101/2022.01.04.474979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Victor L Lam
- University of California San Francisco, San Francisco, CA, United States
| | - Jennifer M Hayashi
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, United States
| | - John D Gross
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, United States
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, United States
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8
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Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
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Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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9
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Galonić Fujimori D, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. bioRxiv 2021. [PMID: 34816261 DOI: 10.1101/2021.11.14.468537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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10
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021; 184:3426-3437.e8. [PMID: 33991487 PMCID: PMC8057738 DOI: 10.1016/j.cell.2021.04.025] [Citation(s) in RCA: 313] [Impact Index Per Article: 104.3] [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: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023]
Abstract
We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mir M Khalid
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | | | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jing Cheng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Jennifer M Hayashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Camille R Simoneau
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - G Renuka Kumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, CA 94804, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, CA 94804, USA
| | - Monica Haw
- California Department of Public Health, Richmond, CA 94804, USA
| | - John Bell
- California Department of Public Health, Richmond, CA 94804, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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11
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Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano K, Hayashi JM, Carlson-Stevermer J, Oki J, Holden K, Krogan NJ, Ott M, Puschnik AS. Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. bioRxiv 2020:2020.09.24.312298. [PMID: 32995787 PMCID: PMC7523113 DOI: 10.1101/2020.09.24.312298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Coronaviridae are a family of viruses that causes disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors that are common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted parallel genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we discovered phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle as well as the potential development of host-directed therapies.
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Affiliation(s)
- Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | | | | | - Mehdi Bouhaddou
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | | | | | | | | | | | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
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12
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Hayashi JM, Morita YS. Mycobacterial Membrane Domain, or a Primordial Organelle? Yale J Biol Med 2019; 92:549-556. [PMID: 31543716 PMCID: PMC6747930] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mycobacteria, like many other prokaryotic organisms, do not appear to have membrane-bound organelles to organize the subcellular space. Nevertheless, mycobacteria and related bacteria grow their cell envelope in a spatially controlled manner, restricting cell elongation to the polar regions of the rod-shaped cell. This spatial organization demands that de novo synthesized cell envelope components must be supplied to the polar ends of the cell. Because many cell envelope components are either lipids or built as lipid-anchored precursors, the plasma membrane is the major site of the biosynthesis. Thus, there are logistical questions of where in the plasma membrane these lipids and lipid precursors are made and how they are subsequently delivered to the growing poles of the cell. Our discovery of an intracellular membrane domain (IMD) fills in this gap. Currently available data suggest that the IMD is a membrane domain within the plasma membrane of mycobacteria, which mediates key biosynthetic reactions for cell envelope and other lipid biosynthetic reactions. Consistent with its role in polar growth, the IMD is enriched in the polar regions of actively growing cells and becomes less polarized when the cells experience non-growing conditions. We discuss how such membrane compartmentalization may be generated and maintained in a mycobacterial cell and why it has not evolved into a bona fide organelle. In a broader perspective, we suggest that segregation of biosynthetic pathways into different domains of a planar membrane could be more widespread than we currently think.
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Affiliation(s)
- Jennifer M. Hayashi
- Gladstone Institute of Virology and Immunology, University of California San Francisco, CA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA,To whom all correspondence should be addressed: Yasu S. Morita, Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003; Tel: 413-545-4604; Fax: 413-545-1578;
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13
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Toyonaga K, Torigoe S, Motomura Y, Kamichi T, Hayashi JM, Morita YS, Noguchi N, Chuma Y, Kiyohara H, Matsuo K, Tanaka H, Nakagawa Y, Sakuma T, Ohmuraya M, Yamamoto T, Umemura M, Matsuzaki G, Yoshikai Y, Yano I, Miyamoto T, Yamasaki S. C-Type Lectin Receptor DCAR Recognizes Mycobacterial Phosphatidyl-Inositol Mannosides to Promote a Th1 Response during Infection. Immunity 2016; 45:1245-1257. [PMID: 27887882 DOI: 10.1016/j.immuni.2016.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/25/2016] [Accepted: 08/26/2016] [Indexed: 12/21/2022]
Abstract
Phosphatidyl-inositol mannosides (PIM) are glycolipids unique to mycobacteria and other related bacteria that stimulate host immune responses and are implicated in mycobacteria pathogenicity. Here, we found that the FcRγ-coupled C-type lectin receptor DCAR (dendritic cell immunoactivating receptor; gene symbol Clec4b1) is a direct receptor for PIM. Mycobacteria activated reporter cells expressing DCAR, and delipidation of mycobacteria abolished this activity. Acylated PIMs purified from mycobacteria were identified as ligands for DCAR. DCAR was predominantly expressed in small peritoneal macrophages and monocyte-derived inflammatory cells in lungs and spleen. These cells produced monocyte chemoattractant protein-1 (MCP-1) upon PIM treatment, and absence of DCAR or FcRγ abrogated MCP-1 production. Upon mycobacterial infection, Clec4b1-deficient mice showed reduced numbers of monocyte-derived inflammatory cells at the infection site, impaired IFNγ production by T cells, and an increased bacterial load. Thus, DCAR is a critical receptor for PIM that functions to promote T cell responses against mycobacteria.
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Affiliation(s)
- Kenji Toyonaga
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shota Torigoe
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshitomo Motomura
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Takane Kamichi
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences Kyushu University, Fukuoka 812-8582, Japan
| | - Jennifer M Hayashi
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Naoto Noguchi
- Division of Host Defense, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | | | | | | | - Hiroshi Tanaka
- Department of Applied Chemistry, Graduate School of Science and Technology, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Yoshiko Nakagawa
- Center for Animal Resources and Development, Kumamoto University, Kumamoto 860-0811, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
| | - Masaki Ohmuraya
- Center for Animal Resources and Development, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
| | - Masayuki Umemura
- Molecular Microbiology Group, Department of Infectious Diseases, Tropical Biosphere Research Center, and Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Goro Matsuzaki
- Molecular Microbiology Group, Department of Infectious Diseases, Tropical Biosphere Research Center, and Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Yasunobu Yoshikai
- Division of Host Defense, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Ikuya Yano
- Japan BCG Laboratory, Kiyose 204-0022, Japan
| | - Tomofumi Miyamoto
- Department of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Sho Yamasaki
- Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
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14
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Beck JJ, Higbee BS, Light DM, Gee WS, Merrill GB, Hayashi JM. Hull split and damaged almond volatiles attract male and female navel orangeworm moths. J Agric Food Chem 2012; 60:8090-8096. [PMID: 22849631 DOI: 10.1021/jf302658v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A blend of volatiles derived from the emissions of almonds at hull split and mechanically damaged almonds was compared to almond meal, the current monitoring standard for the insect pest navel orangeworm (NOW). Field trapping studies were performed to determine the blend's ability to attract adult NOW. The blend comprised racemic 1-octen-3-ol, ethyl benzoate, methyl salicylate, acetophenone, and racemic (E)-conophthorin. Ethyl acetate was used as a solvent with a blend component concentration of 100 mg/mL. The blend attracted both sexes of NOW when tested in five 2-week intervals spanning the first three flights of NOW in commercial almond orchards in the southern Central Valley of California. The blend demonstrated consistently higher capture rates for female NOW throughout the evaluation period, but unlike almond meal it significantly attracted males. Reported is a survey of the major and minor volatiles emitted from almonds at hull split, the key period of vulnerability to NOW infestation. Also reported is the attractancy of a formulated test blend based on the host plant volatile emissions, electroantennographic screening experiments, and field trapping studies. The results of this test blend highlight progress toward a host-plant-based attractant for NOW, a major insect pest of California tree nuts that presently lacks an adequate monitoring tool.
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Affiliation(s)
- John J Beck
- Plant Mycotoxin Research, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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