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Ramos S, Hartenian E, Santos JC, Walch P, Broz P. NINJ1 induces plasma membrane rupture and release of damage-associated molecular pattern molecules during ferroptosis. EMBO J 2024; 43:1164-1186. [PMID: 38396301 PMCID: PMC10987646 DOI: 10.1038/s44318-024-00055-y] [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: 07/18/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Ferroptosis is a regulated form of necrotic cell death caused by iron-dependent accumulation of oxidized phospholipids in cellular membranes, culminating in plasma membrane rupture (PMR) and cell lysis. PMR is also a hallmark of other types of programmed necrosis, such as pyroptosis and necroptosis, where it is initiated by dedicated pore-forming cell death-executing factors. However, whether ferroptosis-associated PMR is also actively executed by proteins or driven by osmotic pressure remains unknown. Here, we investigate a potential ferroptosis role of ninjurin-1 (NINJ1), a recently identified executor of pyroptosis-associated PMR. We report that NINJ1 oligomerizes during ferroptosis, and that Ninj1-deficiency protects macrophages and fibroblasts from ferroptosis-associated PMR. Mechanistically, we find that NINJ1 is dispensable for the initial steps of ferroptosis, such as lipid peroxidation, channel-mediated calcium influx, and cell swelling. In contrast, NINJ1 is required for early loss of plasma membrane integrity, which precedes complete PMR. Furthermore, NINJ1 mediates the release of cytosolic proteins and danger-associated molecular pattern (DAMP) molecules from ferroptotic cells, suggesting that targeting NINJ1 could be a therapeutic option to reduce ferroptosis-associated inflammation.
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Affiliation(s)
- Saray Ramos
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Ella Hartenian
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - José Carlos Santos
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Philipp Walch
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Petr Broz
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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2
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Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature 2023; 618:1065-1071. [PMID: 37198476 PMCID: PMC10307626 DOI: 10.1038/s41586-023-05991-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/21/2023] [Indexed: 05/19/2023]
Abstract
Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1-7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.
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Affiliation(s)
- Morris Degen
- Biozentrum, University of Basel, Basel, Switzerland
| | - José Carlos Santos
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Kristyna Pluhackova
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075, University of Stuttgart, Stuttgart, Germany.
| | | | - Saray Ramos
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | | | - Ella Hartenian
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Undina Guillerm
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Bastian Kohl
- Biozentrum, University of Basel, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Timm Maier
- Biozentrum, University of Basel, Basel, Switzerland
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland
| | - Christian Sieben
- Nanoscale Infection Biology Group, Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Petr Broz
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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3
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Hartenian E, Mendez AS, Didychuk AL, Khosla S, Glaunsinger B. DNA processing by the Kaposi's sarcoma-associated herpesvirus alkaline exonuclease SOX contributes to viral gene expression and infectious virion production. Nucleic Acids Res 2022; 51:182-197. [PMID: 36537232 PMCID: PMC9841436 DOI: 10.1093/nar/gkac1190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Alkaline exonucleases (AE) are present in several large DNA viruses including bacteriophage λ and herpesviruses, where they play roles in viral DNA processing during genome replication. Given the genetic conservation of AEs across viruses infecting different kingdoms of life, these enzymes likely assume central roles in the lifecycles of viruses where they have yet to be well characterized. Here, we applied a structure-guided functional analysis of the bifunctional AE in the oncogenic human gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV), called SOX. In addition to identifying a preferred DNA substrate preference for SOX, we define key residues important for DNA binding and DNA processing, and how SOX activity on DNA partially overlaps with its functionally separable cleavage of mRNA. By engineering these SOX mutants into KSHV, we reveal roles for its DNase activity in viral gene expression and infectious virion production. Our results provide mechanistic insight into gammaherpesviral AE activity as well as areas of functional conservation between this mammalian virus AE and its distant relative in phage λ.
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Affiliation(s)
| | - Aaron S Mendez
- Correspondence may also be addressed to Aaron S. Mendez.
| | - Allison L Didychuk
- Department of Plant and Microbial Biology, University of California Berkeley, CA 94720, USA,Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shivani Khosla
- Department of Molecular and Cell Biology, University of California Berkeley, CA 94720, USA
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4
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Mendez AS, Ly M, González-Sánchez AM, Hartenian E, Ingolia NT, Cate JH, Glaunsinger BA. The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression. Cell Rep 2021; 37:109841. [PMID: 34624207 PMCID: PMC8481097 DOI: 10.1016/j.celrep.2021.109841] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 06/02/2021] [Revised: 08/16/2021] [Accepted: 09/24/2021] [Indexed: 01/23/2023] Open
Abstract
Nonstructural protein 1 (nsp1) is a coronavirus (CoV) virulence factor that restricts cellular gene expression by inhibiting translation through blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We perform a detailed structure-guided mutational analysis of severe acute respiratory syndrome (SARS)-CoV-2 nsp1, revealing insights into how it coordinates these activities against host but not viral mRNA. We find that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, both enhancing its restriction of host gene expression and enabling mRNA containing the SARS-CoV-2 leader sequence to escape translational repression. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in SARS-CoV-2 nsp1 could attenuate the virus.
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Affiliation(s)
- Aaron S Mendez
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angélica M González-Sánchez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, USA
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Jamie H Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Britt A Glaunsinger
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA.
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5
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Duncan-Lewis C, Hartenian E, King V, Glaunsinger BA. Cytoplasmic mRNA decay represses RNA polymerase II transcription during early apoptosis. eLife 2021; 10:e58342. [PMID: 34085923 PMCID: PMC8192121 DOI: 10.7554/elife.58342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/28/2020] [Accepted: 06/03/2021] [Indexed: 12/22/2022] Open
Abstract
RNA abundance is generally sensitive to perturbations in decay and synthesis rates, but crosstalk between RNA polymerase II transcription and cytoplasmic mRNA degradation often leads to compensatory changes in gene expression. Here, we reveal that widespread mRNA decay during early apoptosis represses RNAPII transcription, indicative of positive (rather than compensatory) feedback. This repression requires active cytoplasmic mRNA degradation, which leads to impaired recruitment of components of the transcription preinitiation complex to promoter DNA. Importin α/β-mediated nuclear import is critical for this feedback signaling, suggesting that proteins translocating between the cytoplasm and nucleus connect mRNA decay to transcription. We also show that an analogous pathway activated by viral nucleases similarly depends on nuclear protein import. Collectively, these data demonstrate that accelerated mRNA decay leads to the repression of mRNA transcription, thereby amplifying the shutdown of gene expression. This highlights a conserved gene regulatory mechanism by which cells respond to threats.
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Affiliation(s)
- Christopher Duncan-Lewis
- Department of Molecular and Cell Biology; University of California, BerkeleyBerkeleyUnited States
| | - Ella Hartenian
- Department of Molecular and Cell Biology; University of California, BerkeleyBerkeleyUnited States
| | - Valeria King
- Department of Molecular and Cell Biology; University of California, BerkeleyBerkeleyUnited States
| | - Britt A Glaunsinger
- Department of Molecular and Cell Biology; University of California, BerkeleyBerkeleyUnited States
- Department of Plant and Microbial Biology; University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, BerkeleyBerkeleyUnited States
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6
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Abstract
Few human pathogens have been the focus of as much concentrated worldwide attention as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID-19. Its emergence into the human population and ensuing pandemic came on the heels of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), two other highly pathogenic coronavirus spillovers, which collectively have reshaped our view of a virus family previously associated primarily with the common cold. It has placed intense pressure on the collective scientific community to develop therapeutics and vaccines, whose engineering relies on a detailed understanding of coronavirus biology. Here, we present the molecular virology of coronavirus infection, including its entry into cells, its remarkably sophisticated gene expression and replication mechanisms, its extensive remodeling of the intracellular environment, and its multifaceted immune evasion strategies. We highlight aspects of the viral life cycle that may be amenable to antiviral targeting as well as key features of its biology that await discovery.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Divya Nandakumar
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Azra Lari
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica M Tucker
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Britt A Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA.
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7
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Hartenian E, Gilbertson S, Federspiel JD, Cristea IM, Glaunsinger BA. RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters. PLoS Pathog 2020; 16:e1008269. [PMID: 32032393 PMCID: PMC7032723 DOI: 10.1371/journal.ppat.1008269] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 04/03/2019] [Revised: 02/20/2020] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68-induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. This reduced Pol II occupancy is accompanied by down-regulation of multiple Pol II subunits and TFIIB in the nucleus of infected cells, as revealed by mass spectrometry-based global measurements of protein abundance. Viral genes, despite the fact that they require Pol II for transcription, escape transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We propose a model in which the ability to escape from transcriptional repression is linked to the localization of viral DNA within replication compartments, providing a means for these viruses to counteract decay-induced transcript loss. While transcription and messenger RNA (mRNA) decay are often considered to be the unlinked beginning and end of gene expression, recent data indicate that alterations to either stage can impact the other. Here we study this connection in the context of lytic gammaherpesvirus infection, which accelerates mRNA degradation through the expression of the viral endonuclease muSOX. We show that RNA polymerase II promoter occupancy is broadly reduced across mammalian promoters in response to infection-induced mRNA decay, and that this phenotype correlates with a reduction in the abundance of several proteins involved in transcription. Notably, gammaherpesviral promoters are resistant to the ensuing transcriptional repression. We show that viral transcriptional escape is conferred by localization of the viral DNA within the protective environment of replication compartments, which are sites of viral genome replication and transcription during infection. Collectively, these findings clarify how mRNA degradation by gammaherpesviruses reshapes the cellular environment and selectively dampens host gene transcription.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
| | - Sarah Gilbertson
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
| | - Joel D. Federspiel
- Department of Molecular Biology, Princeton University, Princeton, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, United States of America
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California Berkeley, CA, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, CA, United States of America
- * E-mail:
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8
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Hartenian E, Glaunsinger BA. Feedback to the central dogma: cytoplasmic mRNA decay and transcription are interdependent processes. Crit Rev Biochem Mol Biol 2019; 54:385-398. [PMID: 31656086 PMCID: PMC6871655 DOI: 10.1080/10409238.2019.1679083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/22/2019] [Revised: 09/13/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Transcription and RNA decay are key determinants of gene expression; these processes are typically considered as the uncoupled beginning and end of the messenger RNA (mRNA) lifecycle. Here we describe the growing number of studies demonstrating interplay between these spatially disparate processes in eukaryotes. Specifically, cells can maintain mRNA levels by buffering against changes in mRNA stability or transcription, and can also respond to virally induced accelerated decay by reducing RNA polymerase II gene expression. In addition to these global responses, there is also evidence that mRNAs containing a premature stop codon can cause transcriptional upregulation of homologous genes in a targeted fashion. In each of these systems, RNA binding proteins (RBPs), particularly those involved in mRNA degradation, are critical for cytoplasmic to nuclear communication. Although their specific mechanistic contributions are yet to be fully elucidated, differential trafficking of RBPs between subcellular compartments are likely to play a central role in regulating this gene expression feedback pathway.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, Berkeley, CA 94720
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9
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Gilbertson S, Federspiel JD, Hartenian E, Cristea IM, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. eLife 2018; 7:37663. [PMID: 30281021 PMCID: PMC6203436 DOI: 10.7554/elife.37663] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [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: 04/18/2018] [Accepted: 09/28/2018] [Indexed: 12/21/2022] Open
Abstract
Alterations in global mRNA decay broadly impact multiple stages of gene expression, although signals that connect these processes are incompletely defined. Here, we used tandem mass tag labeling coupled with mass spectrometry to reveal that changing the mRNA decay landscape, as frequently occurs during viral infection, results in subcellular redistribution of RNA binding proteins (RBPs) in human cells. Accelerating Xrn1-dependent mRNA decay through expression of a gammaherpesviral endonuclease drove nuclear translocation of many RBPs, including poly(A) tail-associated proteins. Conversely, cells lacking Xrn1 exhibited changes in the localization or abundance of numerous factors linked to mRNA turnover. Using these data, we uncovered a new role for relocalized cytoplasmic poly(A) binding protein in repressing recruitment of TATA binding protein and RNA polymerase II to promoters. Collectively, our results show that changes in cytoplasmic mRNA decay can directly impact protein localization, providing a mechanism to connect seemingly distal stages of gene expression. The nucleus of a cell harbors DNA, which contains all information needed to build an organism. The instructions are stored as a genetic code that serves as a blueprint for making proteins – molecules that are important for almost every process in the body – and to assemble cells. But first, the code on the DNA needs to be translated with the help of a ‘middle man’, known as messenger RNA. These molecules carry information to other parts of the cell, wherever it is needed. Messenger RNA is produced in the nucleus of a cell, and then exported into the material within a cell, called the cytoplasm, as a template to produce proteins. Once this process has finished, the template is destroyed. The rate at which the messenger RNA is made affects the flow of genetic information. However, recent evidence suggests that the speed at which messenger RNA is destroyed in the cytoplasm can influence how much of it is made in the nucleus, i.e., if high levels of RNA are destroyed, the production is stopped. For example, it has been shown that certain viruses possess proteins that speed up the destruction of messenger RNA to gain control over the host cell. Here, Gilbertson et al. wanted to find out more about how the breakdown of RNA can signal the nucleus to stop producing these molecules. Messenger RNAs are coated with proteins, which are released when the RNA is destroyed. To test if some of those proteins travel back to the nucleus to influence the production of messenger RNA, proteins in human cells grown in the laboratory were labeled with specific trackers. RNA destruction was induced, in a way that is similar to what happens during a virus attack. The experiments revealed that many RNA-binding proteins indeed return to the nucleus when RNA is destroyed. One of these proteins, named cytoplasmic poly(A)-binding protein, played a key role in transmitting the signal between the cytoplasm and the nucleus to control the production messenger RNA. The amount of messenger RNA can change in many ways throughout the life of a cell. For example, viral infections can lower it and limit the growth and health of cells. A drop in these molecules could act as an early warning of ill health in cells and trigger responses in the nucleus. This new link between messenger RNA destruction and production may help to shed new light on how cells use different signals to control the production of their own genes while restricting pathogens from taking over. A next step will be to determine how these signals communicate with the RNA production machinery in the nucleus and how certain viruses can subvert this process to activate their own genes.
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Affiliation(s)
- Sarah Gilbertson
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Britt Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Department of Plant & Microbial Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, United States
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10
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Tenthorey JL, Haloupek N, López-Blanco JR, Grob P, Adamson E, Hartenian E, Lind NA, Bourgeois NM, Chacón P, Nogales E, Vance RE. The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion. Science 2018; 358:888-893. [PMID: 29146805 PMCID: PMC5842810 DOI: 10.1126/science.aao1140] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022]
Abstract
Robust innate immune detection of rapidly evolving pathogens is critical for host defense. Nucleotide-binding domain leucine-rich repeat (NLR) proteins function as cytosolic innate immune sensors in plants and animals. However, the structural basis for ligand-induced NLR activation has so far remained unknown. NAIP5 (NLR family, apoptosis inhibitory protein 5) binds the bacterial protein flagellin and assembles with NLRC4 to form a multiprotein complex called an inflammasome. Here we report the cryo-electron microscopy structure of the assembled ~1.4-megadalton flagellin-NAIP5-NLRC4 inflammasome, revealing how a ligand activates an NLR. Six distinct NAIP5 domains contact multiple conserved regions of flagellin, prying NAIP5 into an open and active conformation. We show that innate immune recognition of multiple ligand surfaces is a generalizable strategy that limits pathogen evolution and immune escape.
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Affiliation(s)
- Jeannette L Tenthorey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicole Haloupek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - José Ramón López-Blanco
- Departamento de Química Física Biológica, Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Patricia Grob
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Elise Adamson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicholas A Lind
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Natasha M Bourgeois
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Pablo Chacón
- Departamento de Química Física Biológica, Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Russell E Vance
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Cancer Research Laboratory and Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, CA 94720, USA
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11
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Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG. Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol 2018; 36:179-189. [PMID: 29251726 PMCID: PMC5800952 DOI: 10.1038/nbt.4048] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [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: 03/13/2017] [Accepted: 11/04/2017] [Indexed: 12/21/2022]
Abstract
Combinatorial genetic screening using CRISPR-Cas9 is a useful approach to uncover redundant genes and to explore complex gene networks. However, current methods suffer from interference between the single-guide RNAs (sgRNAs) and from limited gene targeting activity. To increase the efficiency of combinatorial screening, we employ orthogonal Cas9 enzymes from Staphylococcus aureus and Streptococcus pyogenes. We used machine learning to establish S. aureus Cas9 sgRNA design rules and paired S. aureus Cas9 with S. pyogenes Cas9 to achieve dual targeting in a high fraction of cells. We also developed a lentiviral vector and cloning strategy to generate high-complexity pooled dual-knockout libraries to identify synthetic lethal and buffering gene pairs across multiple cell types, including MAPK pathway genes and apoptotic genes. Our orthologous approach also enabled a screen combining gene knockouts with transcriptional activation, which revealed genetic interactions with TP53. The "Big Papi" (paired aureus and pyogenes for interactions) approach described here will be widely applicable for the study of combinatorial phenotypes.
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Affiliation(s)
- Fadi J Najm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christine Strand
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Mudra Hegde
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kendall R Sanson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Emma W Vaimberg
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Ella Hartenian
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Nicolo Fusi
- Microsoft Research New England, Cambridge, Massachusetts, USA
| | | | - Scott T Younger
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Bradley E Bernstein
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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12
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Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers. Cell Syst 2016; 3:302-316.e4. [PMID: 27684187 PMCID: PMC5455996 DOI: 10.1016/j.cels.2016.09.001] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/11/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022]
Abstract
Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches. We interrogated 177 genes that we classified as essential for the proliferation of cancer cells exhibiting constitutive β-catenin activity and integrated data for each of the candidates, derived from orthogonal short hairpin RNA (shRNA) knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated gene editing knockout screens, to yield 69 validated genes. We then characterized the relationships between sets of these genes using complementary assays: medium-throughput stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry, yielding 3,639 protein-protein interactions, and a CRISPR-mediated pairwise double knockout screen, yielding 375 combinations exhibiting greater- or lesser-than-additive phenotypic effects indicating genetic interactions. These studies identify previously unreported regulators of β-catenin, define functional networks required for the survival of β-catenin-active cancers, and provide an experimental strategy that may be applied to define other signaling networks.
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Affiliation(s)
- Joseph Rosenbluh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Johnathan Mercer
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yashaswi Shrestha
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Rachel Oliver
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Pablo Tamayo
- Moores Cancer Center and School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Itay Tirosh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ella Hartenian
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Heiko Horn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lola Fagbami
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jacob Jaffe
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Kasper Lage
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA.
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13
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Hartenian E, Doench JG. Genetic screens and functional genomics using CRISPR/Cas9 technology. FEBS J 2015; 282:1383-93. [DOI: 10.1111/febs.13248] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/01/2015] [Accepted: 02/23/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cellular Biology; University of California Berkeley; Berkeley, CA USA
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14
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Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2014; 343:84-87. [PMID: 24336571 PMCID: PMC4089965 DOI: 10.1126/science.1247005] [Citation(s) in RCA: 3433] [Impact Index Per Article: 343.3] [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] [Indexed: 12/11/2022]
Abstract
The simplicity of programming the CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on a genome-wide scale. We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. First, we used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells. Next, in a melanoma model, we screened for genes whose loss is involved in resistance to vemurafenib, a therapeutic RAF inhibitor. Our highest-ranking candidates include previously validated genes NF1 and MED12, as well as novel hits NF2, CUL3, TADA2B, and TADA1. We observe a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation, demonstrating the promise of genome-scale screening with Cas9.
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Affiliation(s)
- Ophir Shalem
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neville E. Sanjana
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ella Hartenian
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
| | - Xi Shi
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David A. Scott
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tarjei Mikkelson
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin L. Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David E. Root
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author.
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