Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influ-enza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 50-m7G-cappedhost transcripts to prime viral mRNA synthesis (‘‘cap-snatching’’). We hypothesized that start codons withincap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We reportthe existence of this mechanism of gene origination, which we named ‘‘start-snatching.’’ Depending on thereading frame, start-snatching allows the translation of host and viral ‘‘untranslated regions’’ (UTRs) to createN-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show thatboth types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contributeto virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animaland plant viruses, a host-dependent mechanism allows the genesis of hybrid genes

The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.

The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis. Congenital mutations in RNA exosome genes are associated with neurodegenerative diseases. Little is known about the role of the RNA exosome in the cellular response to pathogens. Here, using NGS and human and mouse genetics, we show that influenza A virus (IAV) ribogenesis and growth are suppressed by impaired RNA exosome activity. Mechanistically, the nuclear RNA exosome coordinates the initial steps of viral transcription with RNAPII at host promoters. The viral polymerase complex co-opts the nuclear RNA exosome complex and cellular RNAs en route to 3 end degradation. Exosome deficiency uncouples chromatin targeting of the viral polymerase complex and the formation of cellular:viral RNA hybrids, which are essential RNA intermediates that license transcription of antisense genomic viral RNAs. Our results suggest that evolutionary arms races have shaped the cellular RNA quality control machinery

Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis

The human helicase senataxin (SETX) has been linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2). Here we identified a role for SETX in controlling the antiviral response. Cells that had undergone depletion of SETX and SETX-deficient cells derived from patients with AOA2 had higher expression of antiviral mediators in response to infection than did wild-type cells. Mechanistically, we propose a model whereby SETX attenuates the activity of RNA polymerase II (RNAPII) at genes stimulated after a virus is sensed and thus controls the magnitude of the host response to pathogens and the biogenesis of various RNA viruses (e.g., influenza A virus and West Nile virus). Our data indicate a potentially causal link among inborn errors in SETX, susceptibility to infection and the development of neurologic disorders

Influenza virus infection causes global RNAPII termination defects

Viral infection perturbs host cells and can be used to uncover regulatory mechanisms controlling cellular responses and susceptibility to infections. Using cell biological, biochemical, and genetic tools, we reveal that influenza A virus (IAV) infection induces global transcriptional defects at the 3' ends of active host genes and RNA polymerase II (RNAPII) run-through into extragenic regions. Deregulated RNAPII leads to expression of aberrant RNAs (3' extensions and host-gene fusions) that ultimately cause global transcriptional downregulation of physiological transcripts, an effect influencing antiviral response and virulence. This phenomenon occurs with multiple strains of IAV, is dependent on influenza NS1 protein, and can be modulated by SUMOylation of an intrinsically disordered region (IDR) of NS1 expressed by the 1918 pandemic IAV strain. Our data identify a strategy used by IAV to suppress host gene expression and indicate that polymorphisms in IDRs of viral proteins can affect the outcome of an infection

Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection (vol 44, pg 46, 2016)

Viruses are obligate parasites and thus require the machinery of the host cell to replicate. Inhibition of host factors co-opted during active infection is a strategy hosts use to suppress viral replication and a potential pan-antiviral therapy. To define the cellular proteins and processes required for a virus during infection is thus crucial to understanding the mechanisms of virally induced disease. In this report, we generated fully infectious tagged influenza viruses and used infection-based proteomics to identify pivotal arms of cellular signaling required for influenza virus growth and infectivity. Using mathematical modeling and genetic and pharmacologic approaches, we revealed that modulation of Sec61-mediated cotranslational translocation selectively impaired glycoprotein proteostasis of influenza as well as HIV and dengue viruses and led to inhibition of viral growth and infectivity. Thus, by studying virus-human protein-protein interactions in the context of active replication, we have identified targetable host factors for broad-spectrum antiviral therapies. Viruses are obligate parasites dependent on the host cell machinery. Using infection-based proteomics, biochemistry, and mathematical modeling, Marazzi and colleagues reveal that targeting host factors controlling essential cellular functions can provide broad-spectrum antiviral effects. Loss-of-function and chemical inhibition of one such factor, Sec61, inhibited influenza, HIV, and dengue virus replication.Fil: Heaton, Nicholas S.. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Moshkina, Natasha. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Fenouil, Romain. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Gardner, Thomas J.. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Aguirre, Sebastian. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Shah, Priya S.. University of California; Estados UnidosFil: Zhao, Nan. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Manganaro, Lara. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Hultquist, Judd F.. University of California; Estados UnidosFil: Noel, Justine. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Sachs, David H.. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Hamilton, Jennifer. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Leon, Paul E.. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Chawdury, Amit. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Tripathi, Shashank. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Melegari, Camilla. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Campisi, Laura. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Hai, Rong. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Metreveli, Giorgi. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Gamarnik, Andrea Vanesa. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: García Sastre, Adolfo. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Greenbaum, Benjamin. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Simon, Viviana. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Fernandez Sesma, Ana. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Krogan, Nevan J.. University of California; Estados UnidosFil: Mulder, Lubbertus C.F.. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: van Bakel, Harm. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Tortorella, Domenico. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Taunton, Jack. University of California; Estados UnidosFil: Palese, Peter. Icahn School Of Medicine At Mount Sinai; Estados UnidosFil: Marazzi, Ivan. Icahn School Of Medicine At Mount Sinai; Estados Unido

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes