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Functional single-cell genomics of human cytomegalovirus infection. Nat Biotechnol 2022; 40:391-401. [PMID: 34697476 DOI: 10.1038/s41587-021-01059-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022]
Abstract
Understanding how viral and host factors interact and how perturbations impact infection is the basis for designing antiviral interventions. Here we define the functional contribution of each viral and host factor involved in human cytomegalovirus infection in primary human fibroblasts through pooled CRISPR interference and nuclease screening. To determine how genetic perturbation of critical host and viral factors alters the timing, course and progression of infection, we applied Perturb-seq to record the transcriptomes of tens of thousands of CRISPR-modified single cells and found that, normally, most cells follow a stereotypical transcriptional trajectory. Perturbing critical host factors does not change the stereotypical transcriptional trajectory per se but can stall, delay or accelerate progression along the trajectory, allowing one to pinpoint the stage of infection at which host factors act. Conversely, perturbation of viral factors can create distinct, abortive trajectories. Our results reveal the roles of host and viral factors and provide a roadmap for the dissection of host-pathogen interactions.
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Abstract
The endoplasmic reticulum (ER) is the site of membrane protein insertion, folding, and assembly in eukaryotes. Over the past few years, a combination of genetic and biochemical studies have implicated an abundant factor termed the ER membrane protein complex (EMC) in several aspects of membrane protein biogenesis. This large nine-protein complex is built around a deeply conserved core formed by the EMC3-EMC6 subcomplex. EMC3 belongs to the universally conserved Oxa1 superfamily of membrane protein transporters, whereas EMC6 is an ancient, widely conserved obligate partner. EMC has an established role in the insertion of transmembrane domains (TMDs) and less understood roles during the later steps of membrane protein folding and assembly. Several recent structures suggest hypotheses about the mechanism(s) of TMD insertion by EMC, with various biochemical and proteomics studies beginning to reveal the range of EMC's membrane protein substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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3
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Rice SA. Release of HSV-1 Cell-Free Virions: Mechanisms, Regulation, and Likely Role in Human-Human Transmission. Viruses 2021; 13:v13122395. [PMID: 34960664 PMCID: PMC8704881 DOI: 10.3390/v13122395] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/17/2022] Open
Abstract
Herpes simplex virus type 1, or HSV-1, is a widespread human pathogen that replicates in epithelial cells of the body surface and then establishes latent infection in peripheral neurons. When HSV-1 replicates, viral progeny must be efficiently released to spread infection to new target cells. Viral spread occurs via two major routes. In cell-cell spread, progeny virions are delivered directly to cellular junctions, where they infect adjacent cells. In cell-free release, progeny virions are released into the extracellular milieu, potentially allowing the infection of distant cells. Cell-cell spread of HSV-1 has been well studied and is known to be important for in vivo infection and pathogenesis. In contrast, HSV-1 cell-free release has received less attention, and its significance to viral biology is unclear. Here, I review the mechanisms and regulation of HSV-1 cell-free virion release. Based on knowledge accrued in other herpesviral systems, I argue that HSV-1 cell-free release is likely to be tightly regulated in vivo. Specifically, I hypothesize that this process is generally suppressed as the virus replicates within the body, but activated to high levels at sites of viral reactivation, such as the oral mucosa and skin, in order to promote efficient transmission of HSV-1 to new human hosts.
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Affiliation(s)
- Stephen A Rice
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
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Kumar T, Maitra S, Rahman A, Bhattacharjee S. A conserved guided entry of tail-anchored pathway is involved in the trafficking of a subset of membrane proteins in Plasmodium falciparum. PLoS Pathog 2021; 17:e1009595. [PMID: 34780541 PMCID: PMC8629386 DOI: 10.1371/journal.ppat.1009595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/29/2021] [Accepted: 10/19/2021] [Indexed: 01/22/2023] Open
Abstract
Tail-anchored (TA) proteins are defined by the absence of N-terminus signal sequence and the presence of a single transmembrane domain (TMD) proximal to their C-terminus. They play fundamental roles in cellular processes including vesicular trafficking, protein translocation and quality control. Some of the TA proteins are post-translationally integrated by the Guided Entry of TA (GET) pathway to the cellular membranes; with their N-terminus oriented towards the cytosol and C-terminus facing the organellar lumen. The TA repertoire and the GET machinery have been extensively characterized in the yeast and mammalian systems, however, they remain elusive in the human malaria parasite Plasmodium falciparum. In this study, we bioinformatically predicted a total of 63 TA proteins in the P. falciparum proteome and revealed the association of a subset with the P. falciparum homolog of Get3 (PfGet3). In addition, our proximity labelling studies either definitively identified or shortlisted the other eligible GET constituents, and our in vitro association studies validated associations between PfGet3 and the corresponding homologs of Get4 and Get2 in P. falciparum. Collectively, this study reveals the presence of proteins with hallmark TA signatures and the involvement of evolutionary conserved GET trafficking pathway for their targeted delivery within the parasite. Tail-anchored (TA) membrane proteins are known to play essential cellular functions in the eukaryotes. These proteins are trafficked to their respective destinations by post-translational translocation pathways that are evolutionarily conserved from yeast to human. However, they remain unidentified in the malaria parasite Plasmodium falciparum. We have used bioinformatic prediction algorithms in conjunction with functional validation studies to identify the candidate TA repertoire and some of the homologs of the trafficking machinery in P. falciparum. Initially, we predicted the presence of 63 putative TA proteins localized to distinct compartments within this parasite, including a few confirmed TA homologs in other eukaryotic systems. We then identified and characterized PfGet3 as a central component in the Guided-Entry of TA (GET) translocation machinery, and our bacterial co-expression and pulldown assays with two selected recombinant TA proteins, PfBOS1 and PfUSE1, showed co-association with PfGet3. We also identified PfGet2 and PfGet4 as the other two components of the GET machinery in P. falciparum using proximity biotinylation followed by mass spectrometry. Interestingly, we also found six TA proteins in the parasite enriched in this fraction. We further validated the direct interactions between a few TA candidates, PfGet4 and PfGet2 with PfGet3 using recombinant-based pulldown studies. In conclusion, this study classified a subset of membrane proteins with the TA nomenclature and implicated a previously unidentified GET pathway for their translocation in this apicomplexan parasite.
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Affiliation(s)
- Tarkeshwar Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Satarupa Maitra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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Inhibitors of the Sec61 Complex and Novel High Throughput Screening Strategies to Target the Protein Translocation Pathway. Int J Mol Sci 2021; 22:ijms222112007. [PMID: 34769437 PMCID: PMC8585047 DOI: 10.3390/ijms222112007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
Proteins targeted to the secretory pathway start their intracellular journey by being transported across biological membranes such as the endoplasmic reticulum (ER). A central component in this protein translocation process across the ER is the Sec61 translocon complex, which is only intracellularly expressed and does not have any enzymatic activity. In addition, Sec61 translocon complexes are difficult to purify and to reconstitute. Screening for small molecule inhibitors impairing its function has thus been notoriously difficult. However, such translocation inhibitors may not only be valuable tools for cell biology, but may also represent novel anticancer drugs, given that cancer cells heavily depend on efficient protein translocation into the ER to support their fast growth. In this review, different inhibitors of protein translocation will be discussed, and their specific mode of action will be compared. In addition, recently published screening strategies for small molecule inhibitors targeting the whole SRP-Sec61 targeting/translocation pathway will be summarized. Of note, slightly modified assays may be used in the future to screen for substances affecting SecYEG, the bacterial ortholog of the Sec61 complex, in order to identify novel antibiotic drugs.
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Funk C, Marques da Silveira e Santos D, Ott M, Raschbichler V, Bailer SM. The HSV1 Tail-Anchored Membrane Protein pUL34 Contains a Basic Motif That Supports Active Transport to the Inner Nuclear Membrane Prior to Formation of the Nuclear Egress Complex. Viruses 2021; 13:v13081544. [PMID: 34452409 PMCID: PMC8402719 DOI: 10.3390/v13081544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 11/23/2022] Open
Abstract
Herpes simplex virus type 1 nucleocapsids are released from the host nucleus by a budding process through the nuclear envelope called nuclear egress. Two viral proteins, the integral membrane proteins pUL34 and pUL31, form the nuclear egress complex at the inner nuclear membrane, which is critical for this process. The nuclear import of both proteins ensues separately from each other: pUL31 is actively imported through the central pore channel, while pUL34 is transported along the peripheral pore membrane. With this study, we identified a functional bipartite NLS between residues 178 and 194 of pUL34. pUL34 lacking its NLS is mislocalized to the TGN but retargeted to the ER upon insertion of the authentic NLS or a mimic NLS, independent of the insertion site. If co-expressed with pUL31, either of the pUL34-NLS variants is efficiently, although not completely, targeted to the nuclear rim where co-localization with pUL31 and membrane budding seem to occur, comparable to the wild-type. The viral mutant HSV1(17+)Lox-UL34-NLS mt is modestly attenuated but viable and associated with localization of pUL34-NLS mt to both the nuclear periphery and cytoplasm. We propose that targeting of pUL34 to the INM is facilitated by, but not dependent on, the presence of an NLS, thereby supporting NEC formation and viral replication.
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Affiliation(s)
- Christina Funk
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany; (C.F.); (D.M.d.S.eS.)
| | - Débora Marques da Silveira e Santos
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany; (C.F.); (D.M.d.S.eS.)
- Institute for Interfacial Engineering and Plasma Technology IGVP, University of Stuttgart, 70174 Stuttgart, Germany
| | - Melanie Ott
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, 80539 Munich, Germany; (M.O.); (V.R.)
| | - Verena Raschbichler
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, 80539 Munich, Germany; (M.O.); (V.R.)
| | - Susanne M. Bailer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany; (C.F.); (D.M.d.S.eS.)
- Institute for Interfacial Engineering and Plasma Technology IGVP, University of Stuttgart, 70174 Stuttgart, Germany
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, 80539 Munich, Germany; (M.O.); (V.R.)
- Correspondence: ; Tel.: +49-711-970-4180
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Dearborn AD, Marcotrigiano J. Hepatitis C Virus Structure: Defined by What It Is Not. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036822. [PMID: 31501263 DOI: 10.1101/cshperspect.a036822] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) represents an important and growing public health problem, chronically infecting an estimated 70 million people worldwide. This blood-borne pathogen is generating a new wave of infections in the United States, associated with increasing intravenous drug use over the last decade. In most cases, HCV establishes a chronic infection, sometimes causing cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Although a curative therapy exists, it is extremely expensive and provides no barrier to reinfection; therefore, a vaccine is urgently needed. The virion is asymmetric and heterogeneous with the buoyancy and protein content similar to low-density lipoparticles. Core protein is unstructured, and of the two envelope glycoproteins, E1 and E2, the function of E1 remains enigmatic. E2 is responsible for specifically binding host receptors CD81 and scavenger receptor class B type I (SR-BI). This review will focus on structural progress on HCV virion, core protein, envelope glycoproteins, and specific host receptors.
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Affiliation(s)
- Altaira D Dearborn
- The Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joseph Marcotrigiano
- The Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Morgens DW, Chan C, Kane AJ, Weir NR, Li A, Dubreuil MM, Tsui CK, Hess GT, Lavertu A, Han K, Polyakov N, Zhou J, Handy EL, Alabi P, Dombroski A, Yao D, Altman RB, Sello JK, Denic V, Bassik MC. Retro-2 protects cells from ricin toxicity by inhibiting ASNA1-mediated ER targeting and insertion of tail-anchored proteins. eLife 2019; 8:48434. [PMID: 31674906 PMCID: PMC6858068 DOI: 10.7554/elife.48434] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
The small molecule Retro-2 prevents ricin toxicity through a poorly-defined mechanism of action (MOA), which involves halting retrograde vesicle transport to the endoplasmic reticulum (ER). CRISPRi genetic interaction analysis revealed Retro-2 activity resembles disruption of the transmembrane domain recognition complex (TRC) pathway, which mediates post-translational ER-targeting and insertion of tail-anchored (TA) proteins, including SNAREs required for retrograde transport. Cell-based and in vitro assays show that Retro-2 blocks delivery of newly-synthesized TA-proteins to the ER-targeting factor ASNA1 (TRC40). An ASNA1 point mutant identified using CRISPR-mediated mutagenesis abolishes both the cytoprotective effect of Retro-2 against ricin and its inhibitory effect on ASNA1-mediated ER-targeting. Together, our work explains how Retro-2 prevents retrograde trafficking of toxins by inhibiting TA-protein targeting, describes a general CRISPR strategy for predicting the MOA of small molecules, and paves the way for drugging the TRC pathway to treat broad classes of viruses known to be inhibited by Retro-2.
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Affiliation(s)
- David W Morgens
- Department of Genetics, Stanford University, Stanford, United States
| | - Charlene Chan
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Andrew J Kane
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Nicholas R Weir
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Amy Li
- Department of Genetics, Stanford University, Stanford, United States
| | | | - C Kimberly Tsui
- Department of Genetics, Stanford University, Stanford, United States
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, United States
| | - Adam Lavertu
- Biomedical Informatics Training Program, Stanford University, Stanford, United States
| | - Kyuho Han
- Department of Genetics, Stanford University, Stanford, United States
| | - Nicole Polyakov
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Jing Zhou
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Emma L Handy
- Department of Chemistry, Brown University, Providence, United States
| | - Philip Alabi
- Department of Chemistry, Brown University, Providence, United States
| | - Amanda Dombroski
- Department of Chemistry, Brown University, Providence, United States
| | - David Yao
- Department of Genetics, Stanford University, Stanford, United States
| | - Russ B Altman
- Department of Genetics, Stanford University, Stanford, United States.,Bioengineering, Stanford University, Stanford, United States
| | - Jason K Sello
- Department of Chemistry, Brown University, Providence, United States
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Northwest Labs, Harvard University, Cambridge, United States
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, United States.,Program in Cancer Biology, Stanford University, Stanford, United States.,Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, United States
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