bioRxiv Science⌕ Search

Biology subjects

Lieber, G.

Publications and source records attributed to Lieber, G..

3 recordsLinked to original sources

TRIM28 is a target for paramyxovirus V proteins

SUMO-modified Tripartite Motif Protein 28 (TRIM28; KAP1) plays a crucial role in repressing endogenous retroelement (ERE) transcription. We previously provided evidence that loss of SUMO-modified TRIM28 triggered by influenza A virus (IAV) infection promotes activation of host antiviral immunity via a mechanism involving derepression of EREs and production of immunostimulatory RNAs. While the IAV NS1 protein might limit consequences of such activation via its dsRNA-binding activity, we hypothesized that other human pathogenic viruses could have evolved more direct strategies to counteract this potential ERE-based defense system. Here, we reveal that V proteins from diverse paramyxoviruses, including Measles, Mumps, Parainfluenza, and Nipah/Hendra viruses, can all engage with TRIM28. Notably, the efficiency of engagement varies markedly between virus species, a phenotype that can be linked to specific residues within the C-terminal domain of V proteins. Further mapping showed that V proteins target both the TRIM28 Coiled-Coil domain and the TRIM28 PHD-Bromodomain, which contains the functionally-relevant TRIM28 SUMO-modification sites necessary for ERE repression. In this context, while paramyxovirus infection triggers canonical stress-associated phosphorylation of TRIM28, loss of SUMO-modified TRIM28 does not occur, and minimal induction of the TRIM28-dependent ERE RNA, HERVK14C, is observed. Furthermore, pre-infection with Parainfluenza virus type 2, which encodes a V protein that efficiently engages with TRIM28, limits subsequent IAV-triggered loss of SUMO-modified TRIM28 and upregulation of HERVK14C RNA. These findings dissect the interplay between paramyxoviruses and TRIM28, providing support for the concept of a TRIM28-regulated ERE-based antiviral defense system by uncovering a potential viral antagonistic measure. ImportanceHost recognition of viral nucleic acids is fundamental for stimulating antiviral immunity. To prevent aberrant immune activation, cells must precisely differentiate "non-self" from "self" nucleic acids. Endogenous retroelements (EREs), despite their self-origin, can produce immunostimulatory RNAs that blur this distinction, and may have been functionally co-opted to enhance antiviral immunity in response to some infections. Normally, ERE transcription is repressed by the host protein TRIM28, the function of which is dynamically modulated by SUMO-modification. Here, we demonstrate that paramyxoviruses engage TRIM28, maintaining it in its repressive, SUMO-modified form during infection. We propose that this virus-host interaction limits ERE activation and consequently suppresses ERE-driven immune signaling, revealing a previously unidentified mechanism of immune evasion by paramyxoviruses.

microbiology↗

Influenza A Virus NS1 Limits Recognition of Double-Stranded Transposable Elements by Cytosolic RNA Sensors

Influenza A virus (IAV) infection triggers de-repression of host transposable elements (TEs), which have the potential to form double-stranded (ds)RNAs and stimulate innate antiviral immunity. However, as wild-type IAV is generally a poor inducer of innate immunity, it remains unclear whether de-repressed TEs actually form dsRNAs recognizable by host cytosolic RNA sensors, or whether IAV might antagonize such sensing. Here, we performed strand-specific total RNA-Seq on nuclear and cytosolic fractions from cells infected with wild-type IAV or a recombinant IAV lacking NS1, a viral dsRNA-binding protein. Both infections led to global increases in host TE RNAs with bioinformatic and experimental evidence for double-strandedness. However, only NS1-deficient IAV infection led to significant amounts of TE-dsRNAs translocating to the cytosol, and co-precipitations identified that wild-type NS1 associates with TE-dsRNAs. Furthermore, a functional screen indicated that TE-dsRNAs can be engaged by various host cytosolic RNA sensors, including RIG-I, MDA5, ZBP1, and PKR. Our data reveal the double-stranded nature of infection-triggered host TEs and suggest an NS1-mediated sequestration mechanism to limit their cytosolic abundance and broad activation of diverse sensors.

immunology↗

In vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2

Remdesivir (RDV) is used widely for COVID-19 patients despite varying results in recent clinical trials. Here, we show how serially passaging SARS-CoV-2 in vitro in the presence of RDV selected for drug-resistant viral populations. We determined that the E802D mutation in the RNA-dependent RNA polymerase was sufficient to confer decreased RDV sensitivity without affecting viral fitness. Analysis of more than 200,000 sequences of globally circulating SARS-CoV-2 variants show no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we also observed changes in the Spike (i.e., H69 E484, N501, H655) corresponding to mutations identified in emerging SARS-CoV-2 variants indicating that they can arise in vitro in the absence of immune selection. This study illustrates SARS-CoV-2 genome plasticity and offers new perspectives on surveillance of viral variants. One Sentence SummarySARS-CoV-2 drug resistance & genome plasticity

microbiology↗