Biology subjects

Etienne, L.

Publications and source records attributed to Etienne, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A widespread NADase domain links bacterial immunity with human TEP1

Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune systems therefore have the potential to illuminate fundamental biological mechanisms throughout the tree of life. Here, we report that DUF4062 domains - which we rename NIR (NADase in bacterial immunity and vault ribonucleoproteins) - function in bacterial immunity against phages. We first identified NIR as an effector of Avs defense proteins, where it depletes cellular NAD+ to block viral infection. We then show that NIR domains are recurrently found as effectors in diverse defense systems. We use this association to uncover Vulcan and Vesta, two defense systems which trigger NAD+ depletion upon sensing distinct viral signals. Remarkably, NIR domains are widespread in eukaryotes where they are embedded in multiple NLR-like proteins. In particular, we identified a NIR domain with conserved NADase activity in the human TEP1 protein, a component of the telomerase complex and vault ribonucleoproteins. Together, these findings reveal an enzymatic activity shared between bacterial immunity and enigmatic eukaryotic machineries.

microbiology↗

bioRxiv2025

Extensive adaptive changes in bat interferon pathway reveal specific molecular functions at the forefront of host - virus coevolution

The interferon (IFN) response is a fundamental component of the mammalian innate immune system, orchestrating a broad antiviral state through a network of interferon-stimulated genes (ISGs). In bats, which are natural reservoirs for diverse viruses, several ISGs exhibit lineage-specific evolutionary adaptations, reflecting unique immune strategies. While previous research has typically focused on individual ISGs or broad-scale genomic analyses, here, we conducted an evolutionary analysis of type I IFN-upregulated genes across diverse bat species to elucidate the forces shaping the full repertoire of their ISG responses. Our results reveal that key components of bats antiviral signaling, including viral dsRNA sensors, PARP-mediated ADP-ribosylation enzymes, and cytokine/chemokine signaling molecules, have been recurrent targets of strong positive selection. Notably, immune sensors such as TLR3, RIG-I, and MDA5 show adaptive changes in their RNA-binding domains, suggesting modified viral recognition. Members of the PARP family exhibit repeated selection in both macro and catalytic domains, consistent with intense host-virus conflict and immune modulation. Strikingly, chemokine genes--especially CXCL10 and CXCL16--and their receptors display some of the strongest and most concerted selection signatures, particularly in ligand-binding loops, consistent with arms-race coevolution potentially driven by viral mimicry. Several positively selected genes have pleiotropic functions in tissue repair, inflammation, and tumor control, suggesting that some of these adaptations may influence several physiological pathways. Altogether, our findings uncover a bat-specific antiviral architecture shaped by concerted adaptive evolution, highlighting a balance between viral control and immune tolerance, likely underlying bats exceptional resilience to disease. Author summaryBats exhibit a remarkable capacity to host a wide range of viral families, including viruses highly pathogenic to humans, while rarely displaying overt clinical symptoms. This resilience suggests unique immune adaptations to control infections while avoiding harmful inflammation. To investigate the genetic basis of this trait, we conducted a comparative evolutionary analysis of genes involved in the type I interferon (IFN) pathway, a core component of the mammalian antiviral response, across multiple bat species and other mammals. Our results reveal strong signatures of positive selection on key antiviral effectors in bats, including sensors of viral nucleic acids, ADP-ribosylating PARP enzymes, and components of chemokine signaling pathways. Notably, several chemokines and their receptors display accelerated evolution, pointing to a critical role in modulating immune responses. We further identify viral chemokine-binding proteins (vCKBPs) from poxviruses as one likely driver of natural selection, suggesting ongoing evolutionary arms races between host immune signaling and viral immune evasion. Overall, these findings fit with a model in which bats have evolved a balance with potent antiviral activity and controlled immune activation. Elucidating these mechanisms offers promising insights for developing novel approaches to managing inflammation and viral infections in humans.

evolutionary biology↗

bioRxiv2025

Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s

Human SAMD9 and SAMD9L are duplicated genes that encode innate immune proteins restricting poxviruses and lentiviruses, such as HIV, and implicated in life-threatening genetic diseases and cancer. Here, we combined structural similarity searches, phylogenetics and population genomics with experimental assays of SAMD9/9L functions to resolve the evolutionary and functional dynamics of these immune proteins, spanning from prokaryotes to primates. We discovered structural analogs of SAMD9/9L in the anti-bacteriophage defense system Avs, resulting from convergent evolution. Further, the predicted nuclease active site was conserved in bacterial analogs and was essential for cell death functions, suggesting a fundamental role in defense across different life kingdoms. Despite this ancestral immunity, we identified genomic signatures of evolutionary arms-races in mammals, with remarkable gene copy number variations targeted by natural selection. We further unveiled that the absence of SAMD9 in bonobos corresponds to a recent gene loss still segregating in the population. Finally, we found that chimp and bonobo SAMD9Ls have enhanced anti-HIV-1 functions, and that bonobo-specific SAMD9L polymorphisms confer increased anti-HIV-1 activity to human SAMD9L without compromising its effect on cell translation. These SAMD9/9L adaptations likely resulted from strong viral selective pressures, including by primate lentiviruses, and could contribute to lentiviral resistance in bonobos. Altogether, this study elucidates the interplay between ancient immune convergence across kingdoms and species-specific adaptations within the Avs9 and SAMD9/9L antiviral shared immunity. Significance statementThe SAMD9 gene family encodes antiviral factors of poxviruses and lentiviruses/HIV and is implicated in genetic diseases. Here, we found strong structural similarity with proteins from the Avs anti-bacteriophage system and uncovered ancient functional convergence in immune strategies between prokaryotes and metazoans. Within mammals, and more importantly in primates, we describe a highly dynamic evolutionary history of the SAMD9 gene family that underwent adaptive episodic gene losses. Unlike humans and chimps, some bonobos lack the SAMD9 gene entirely. Bonobos and chimps also possess unique variants of SAMD9L enhancing anti-HIV-1 activity without compromising cell functions, suggesting super-restrictors. This could also participate in shaping SIVcpz evolution and contribute to the absence of lentivirus-infected bonobos. Overall, the seeming dichotomy between the ancient evolutionary convergence in different kingdoms and recent functional adaptation within primates highlights the arms-races between key immune defense systems and viruses. This study paves the way for evolutionary medicine, where evolutionary-based discoveries may have application to human health, providing a deeper understanding of how the immune system adapts to fight viral infections over billion years of evolution.

evolutionary biology↗

bioRxiv2025

Genomic and functional adaptations in guanylate-binding protein 5 (GBP5) highlight specificities of bat antiviral innate immunity

Bats are asymptomatic reservoirs of several zoonotic viruses. This may result from long-term coevolution between viruses and bats, that have led to host adaptations contributing to an effective balance between strong antiviral responses with innate immune tolerance. To better understand these virus-host interactions, we combined comparative transcriptomics, phylogenomics and functional assays to characterize the evolution of bat innate immune antiviral factors. First, we stimulated the type I interferon immune pathway in Myotis yumanensis primary cells and identified guanylate-binding protein 5 (GBP5) as the most differentially expressed interferon-stimulated gene (ISG). Phylogenomic analyses showed that bat GBP5 has been under strong episodic positive selection, with numerous rapidly evolving sites and species-specific gene duplications, suggesting past evolutionary arms races. Functional tests on GBP5 orthologs from ten bat species covering the >60 million years of Chiroptera evolution revealed species- and virus-specific restrictions against RNA viruses (retrovirus HIV, and rhabdoviruses European bat lyssavirus and VSV), which are typical signatures of adaptations to past viral epidemics. Interestingly, we also observed a lineage-specific loss of the GBP5 prenylation motif in the common ancestor of Pipistrellus and Eptesicus bats, associated with different GBP5 subcellular localization and loss of antiviral functions. Resurrection of the ancestral prenylation motif in Eptesicus fuscus GBP5 rescued its subcellular localization, but not the complete antiviral activities, suggesting that additional determinants are necessary for the antiviral restriction. Altogether, our results highlight adaptations that contribute to bat specific immunity and provide insights into the functional evolution of antiviral effector GBP5. Key FindingsO_LIGBP5 is the most differentially expressed gene upon type I interferon stimulation of Myotis yumanensis primary cells. C_LIO_LIBat GBP5 has evolved under strong episodic genomic and genetic diversification, including early stop codon leading to protein truncation and loss of prenylation motif. C_LIO_LIGBP5 diversification in bats impacts their subcellular localization and antiviral functions. C_LIO_LIBat GBP5s exhibit species- and virus-specificity in their ability to inhibit infectivity of viral particles, bearing glycoproteins from retroviral HIV, vesicular stomatitis virus and European bat lyssavirus-1. C_LIO_LIResurrection of the ancestral prenylation motif in a bat GBP5 rescues its subcellular localization but not its full antiviral activity C_LI

immunology↗

bioRxiv2025

Microtubule remodeling by the innate immune factor Trim69 compromises dynein-dependent migration of HIV virion cores towards the nucleus

Like many viruses, HIV relies on the microtubule (MT) cytoskeleton for successful infection. MT-associated proteins (MAPs) regulate MT functions and thus bear the potential to modulate viral infection. However, while several MAPs are known to exert pro-viral effects on HIV, little is known about antiviral ones. We previously described the Tripartite motif protein 69 (Trim69) as an innate immune factor that remodels MTs, leading to inhibition of a broad spectrum of viruses, including HIV. Through in silico modeling, TIRF microscopy and cell-based assays, we determine that Trim69 binding to MTs is determined by a basic surface in its SPRY domain that interacts with the C-terminal tails of tubulins. This surface is conserved among mammalian Trim69s and is critical for its functions. We demonstrate that by binding and remodeling MTs, Trim69 inhibits the docking and the migration of virion cores on MTs by promoting the stalling of the dynein/dynactin motor complexes. Altogether, these findings shed light on a novel mechanism of viral defense that involves an innate immune regulation of the MT cytoskeleton.

cell biology↗

bioRxiv2024

Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats

Summary ParagraphThe genus Myotis is one of the largest clades of bats, and exhibits some of the most extreme variation in lifespans among mammals alongside unique adaptations to viral tolerance and immune defense1-3. To study the evolution of these phenotypes we generated cell lines and near-complete genome assemblies for eight closely related Myotis species. Using genome-wide screens of positive selection, analyses of structural variation, and functional experiments in primary cells, we identify patterns of adaptation contributing to longevity, cancer resistance, and viral interactions. We demonstrate distinct modes of adaptation to DNA and RNA viruses compared to all other mammals, with bats exhibiting genome-wide overrepresentation of positive selection for DNA virus-interacting proteins and elevated rates of copy number variation for RNA virus-interacting proteins. Characterization of Myotis-specific duplications of the key immune factor protein kinase R (PKR) reveals multiple ancient segregating trans-species copy number polymorphisms. We show that the recurrent evolution of longevity seen in Myotis is associated with positive selection in cancer pathways, and demonstrate a unique response to DNA damage in primary cells of the long-lived M. lucifugus. Together, our results suggest that bats remarkable longevity and immunity are linked through pleiotropic adaptations to viruses and aging-related disease.

genomics↗

bioRxiv2024

HIV Vpr activates a nucleolar-specific ATR pathway to degrade the nucleolar stress sensor CCDC137

The lentiviral accessory protein Vpr engages an extensive network of cellular pathways to drive diverse host consequences. Of its many phenotypes, CRL4A-E3 ubiquitin ligase complex co-option, DNA damage response (DDR) engagement, and G2/M arrest are conserved and thus proposed to be functionally important. How Vpr effects these functions and whether they explain how Vpr dysregulates additional cellular pathways remain unclear. Here we leverage the ability of Vpr to deplete the nucleolar protein CCDC137 to understand how Vpr-induced DDR activation impacts nucleolar processes. We characterize CCDC137 as an indirect Vpr target whose degradation does not correlate with Vpr-induced G2/M arrest. Yet, degradation is conserved among Vpr from the pandemic HIV-1 and related SIVcpz/SIVgor, and it is triggered by genomic insults that activate a nucleolar ATR pathway in a manner similar to camptothecin. We determine that Vpr causes ATR-dependent features of nucleolar stress that correlate with CCDC137 degradation, including redistribution of nucleolar proteins, altered nucleolar morphology, and repressed ribosome biogenesis. Together, this data distinguishes CCDC137 as a non-canonical Vpr target that may serve as a sensor of nucleolar disruption, and in doing so, identifies a novel role for Vpr in nucleolar stress. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/612530v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@d43859org.highwire.dtl.DTLVardef@bf95f4org.highwire.dtl.DTLVardef@dec82org.highwire.dtl.DTLVardef@22802c_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Exploring the role of cultivar, year and plot age in the incidence of grapevine trunk diseases: insights from 20 years of regional surveys in France

Grapevine trunk diseases cause yield losses and vine mortality in vineyards worldwide. However, there have been few quantitative studies evaluating grapevine dieback on a large spatial and temporal scale. Here, we consolidated and standardized databases from the 13 main wine regions of France, compiling records of leaf symptoms associated with esca and Eutypa dieback from 2082 plots and 36 cultivars over a 20-year period. This large dataset was used (a) for quantitative analysis of the prevalence (number of plots with at least one symptomatic plant) and incidence (percentage of symptomatic plants) of esca and Eutypa dieback; and (b) to decipher the effects of cultivar, year and plot age on both the prevalence and incidence of esca leaf symptoms by temporal Bayesian modelling. Esca was present on a mean of 74 {+/-} 2% plots annually, with an incidence of 3.1 {+/-} 0.1%. Eutypa dieback occurred in 41 {+/-} 3% of the plots, with an incidence of 1.4 {+/-} 0.1%. Our modelling approach revealed that the cultivar had a significant impact on the prevalence of esca, but not on its incidence when prevalence is greater than zero. Esca prevalence remained stable, whereas esca incidence was higher than the mean value in six of the years after 2012. We also found a significant non-linear effect of plot age, with 10- to 30-year-old plots significantly more susceptible, depending on the cultivar. This study clearly illustrates the importance of considering extensive and continuous monitoring to improve our understanding of the impact and evolution of crop diseases.

plant biology↗

bioRxiv2024

Deciphering lentiviral Vpr/x determinants required for HUSH and SAMHD1 antagonism highlights the molecular plasticity of these evolutionary conflicts

SAMHD1 and the HUSH complex constitute two blocks during primate lentivirus infection, the first by limiting reverse transcription and the second by inhibiting proviral expression. Vpr and Vpx of specific lentiviral lineages have evolved to antagonize these antiviral proteins. While the antagonism of SAMHD1 has been well characterized, the evolutionary and molecular determinants of the antagonism against HUSH are unknown. We used chimeric Vpr proteins between SIVagm.Ver and SIVagm.Gri lentiviruses infecting two African green monkey species, to investigate viral determinants involved in HUSH and SAMHD1 antagonisms. We found that different interfaces of closely related Vpr proteins are engaged to degrade different SAMHD1 haplotypes. In addition, we identified distinct viral determinants in SIVagm.Ver Vpr for SAMHD1 and HUSH degradation. The substitution of one residue in SIVagm.Gri Vpr is sufficient to gain the capacity to degrade SAMHD1, while the substitution of -helix-3 confers HUSH antagonism. We also found that Vpx proteins of HIV-2 from people living with HIV have different abilities to degrade HUSH. These phenotypes rely on small changes in either the N or C terminal part of Vpx, depending on the context. On the host side, we found that HIV-2 and SIVsmm Vpx degrading HUSH from human and vervet monkey cells cannot not degrade HUSH in owl monkey cells, suggesting some host species-specificity. Altogether, we highlight the molecular plasticity and constraints of viral proteins to adapt to host restrictions. HUSH, like SAMHD1, may have been engaged in ancient and more recent coevolution with lentiviruses and a player in viral fitness. IMPORTANCEAntiviral host proteins, the so-called restriction factors, block lentiviruses at different steps of their viral life cycle. In return, primate lentiviruses may counteract these immune proteins to efficiently spread in vivo. HIV-2 and some SIVs, but not HIV-1, inactivate SAMHD1 and HUSH, two host antiviral proteins, thanks to their Vpx or Vpr viral proteins. First, we uncovered here viral determinants involved in the function of closely related Vpr proteins from SIVs of African green monkeys and of HIV-2 Vpx alleles from people living with HIV-2. We show how these small viral proteins differently adapted to SAMHD1 polymorphism or to HUSH restriction and highlight their molecular plasticity. Finally, the capacity of divergent lentiviral proteins, including HIV-2 Vpx, to induce the degradation of HUSH depends of the cell/host species. Altogether, our results suggest that HUSH has been engaged in a molecular arms-race along evolution, and therefore is a key player in host-pathogens interaction.

microbiology↗

bioRxiv2023

MORC2 restriction factor silences HIV proviral expression

The HUSH complex (composed of TASOR, MPP8 and periphilin) represses HIV-1 expression by inducing both propagation of repressive epigenetic marks and degradation of the nascent transcript. Vpx from HIV-2, and Vpr proteins from some simian lentiviruses (SIVs), antagonize HUSH, thereby increasing proviral expression. The chromatin-remodeler MORC2 protein plays a critical role in the epigenetic silencing of host genes by HUSH. Here, we deciphered the role of MORC2 in HIV-1 silencing. We show that MORC2, in contrast to HUSH components, presents strong signatures of positive selection during primate evolution. However, while HUSH is degraded upon HIV-2 infection in a Vpx-dependent manner, MORC2 levels are rather increased, due to the loss of the HUSH-mediated repression. Our results suggest that lentiviral proteins from the Vpr/Vpx family have not driven primate MORC2 evolution. Our findings indicate that MORC2 negatively regulates HIV-1 provirus expression. Mechanistically, we show that MORC2 is recruited to the integrated HIV-1 provirus locus and is required for TASOR-mediated post-transcriptional HIV-1 silencing suggesting that MORC2 sets the stage for the HUSH-mediated HIV-1 nascent RNA degradation. We demonstrate that reducing MORC2 levels diminishes provirus silencing in both monoclonal and polyclonal cellular models of HIV-1 latency. These results suggest that MORC2 has evolved adaptations during primate diversification, possibly in response to challenges posed by DNA pathogens or retroelement integration into the host genome.

microbiology↗

bioRxiv2023

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease

The SARS-CoV-2 main protease (Mpro, or Nsp5) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. TRMT1 proteolysis results in elimination of TRMT1 tRNA methyltransferase activity and reduced tRNA binding affinity. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. Furthermore, we determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage show that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage, the functional roles of the TRMT1 zinc finger domain in tRNA binding and modification, and the regulation of TRMT1 activity by SARS-CoV-2 Mpro. These studies could inform future therapeutic design targeting Mpro and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis. Significance StatementViral proteases can strategically target human proteins to manipulate host biochemistry during infection. Here, we show that the SARS-CoV-2 main protease (Mpro) can specifically recognize and cleave the human tRNA methyltransferase enzyme TRMT1, and that cleavage of TRMT1 cripples its ability to install a key modification on human tRNAs that is critical for protein translation. Our structural and functional analysis of the Mpro-TRMT1 interaction shows how the flexible Mpro active site engages a conserved sequence in TRMT1 in an uncommon binding mode to catalyze its cleavage and inactivation. These studies provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

biochemistry↗

bioRxiv2023

The inflammatory and tumor suppressor SAMD9L acts through a Schlafen-like box to restrict HIV and inhibit cell translation in SAAD/ATXPC

Sterile alpha motif domain-containing proteins 9 and 9L (SAMD9/9L) are associated with life-threatening genetic diseases and are restriction factors of poxviruses. Yet, their cellular function and the extent of their antiviral role are poorly known. Here, we found that interferon-stimulated SAMD9L, and not SAMD9, restricts HIV-1 replication at the translation step, with a strong inhibition of Transmitted/Founder HIV-1 patient strains. More broadly, SAMD9L restricts primate lentiviruses, but not another retrovirus (MLV) or two ssRNA viruses (MOPV, VSV). Using structural modeling and mutagenesis of SAMD9L, we identified a Schlafen(SLFN)-like active site necessary for HIV-1 restriction. By testing a germline gain-of-function variant from patients with SAMD9L-associated autoinflammatory disease (SAAD) and ataxia-pancytopenia (ATXPC), we determined that SAMD9L cellular and pathogenic functions also depend on the SLFN-like active site. Finally, we propose a model in which SAMD9L translational repression could be dependent on codon-usage, linking its cellular function and the virus-specific innate immunity. The identification of another Achilles heel of HIV, as well as the inflammatory SAMD9L effector and auto-regulatory determinants, provide novel avenues against infectious and genetic diseases. Significance statementThis study identifies SAMD9L as a potent HIV-1 antiviral factor from the interferon immunity and deciphers the host determinants underlying SAMD9L translational repression. The characterization of SAMD9L activity and determinants is also of medical importance for patients with rare genetic diseases bearing deleterious mutations in SAMD9L or with specific cancers. We demonstrate that a pathogenic SAMD9L patients variant is inactivated by the mutation of an identified active site in a SLFN-like box, resulting in an abolished translational shutdown. Furthermore, we describe SAMD9L, but not SAMD9, as an antiviral factor of HIV and lentiviruses, through a translational repression mediated by the SLFN-like box and potentially dependent on codon usage. These findings may have implications to better fight against HIV/AIDS as well as SAAD/ATXPC. Key findings- SAMD9L, but not SAMD9, restricts HIV-1, including Transmitted/Founder patient strains. - SAMD9L broadly restricts primate lentiviruses, but not the retrovirus MLV, nor two ssRNA viruses, the Rhabdovirus VSV and the Arenavirus MOPV. - SAMD9L inhibits viral and cellular translation through an essential E198/D243 active site in a SLFN-like box. - The SAMD9L-associated autoinflammatory disease (SAAD) F886Lfs*11 variant has enhanced HIV translational repression, unveiling an autoregulatory domain of the anti-lentiviral function.

immunology↗

bioRxiv2022

Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions

Several bat species act as asymptomatic reservoirs for many viruses that are instead highly pathogenic in other mammals. Here, we have characterized the functional diversification of the Protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats, in contrast to all studied mammals that possess a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. More importantly, we determined that duplicated PKRs of the Myotis species have undergone functional diversification allowing them to collectively escape from and enhance control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat specific immunity.

evolutionary biology↗

bioRxiv2022

Trim69 is a microtubule regulator that acts as a pantropic viral inhibitor

To identify novel cellular modulators of HIV-1 infection in IFN-stimulated myeloid cells, we have carried out a screen that combines functional and evolutionary analyses in THP-1-PMA cells that led us to the Tripartite Motif Protein 69 (Trim69), a poorly studied member of the Trim family of innate immunity regulators. Trim69 inhibits HIV-1, primate lentiviruses and the negative and positive-strand RNA viruses VSV and SARS-CoV2, overall indicating it is a broad-spectrum antiviral factor. Trim69 binds directly to microtubules and its antiviral activity is intimately linked to its ability to promote the accumulation of stable MTs, a specialized subset of microtubules. By analyzing the behavior of primary blood cells, we provide evidence that a program of MT stabilization is commonly observed in response to IFN-I in cells of the myeloid lineage and Trim69 is the key factor behind this program. Overall, our study identifies Trim69 as the first antiviral innate defense factor that regulates the properties of microtubules to limit viral spread, highlighting the possibility that the cytoskeleton may be a novel unappreciated fighting ground in the host-pathogen interactions that underlie viral infections.

microbiology↗

bioRxiv2022

Extensive uORF translation from HIV-1 transcripts conditions DDX3 dependency for expression of main ORFs and elicits specific T cell immune responses in infected individuals

Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus which relies on alternative splicing, translational and post-translational mechanisms to produce more than 15 functional proteins from its single [~]10kb transcriptional unit. Here, we have applied ribosome profiling and nascent protein labeling at different time points during infection of CD4+ T lymphocytes to characterize the translational landscape of cellular and viral transcripts during the course of infection. Our results indicate a strong impact of viral infection on host cellular transcript levels but a modest impact on global translation rates. Analysis of ribosome profiling reads from viral transcripts reveals extensive and productive non-AUG translation of small peptides from multiple upstream open reading-frames (uORFs) located in the 5 long terminal repeat. Remarkably, these uORFs derived peptides elicit specific T cell responses in HIV-infected individuals. uORFs are conserved among other retroviruses and, together with the TAR sequence, condition the dependency on DDX3 for efficient translation of the main viral open-reading frames.

microbiology↗

bioRxiv2022

Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19

The COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus that spilled from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional-genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus-host interfaces. Here, we performed high-throughput evolutionary analyses of 334 SARS- CoV-2 interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus-host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus-host arms-race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo important interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified functional adaptations involved in SARS- CoV-2 infection in bats and primates, critically enlightening modern genetic determinants of virus susceptibility and severity. Key findingsO_LIEvolutionary history of 334 SARS-CoV-2 interacting proteins (VIPs) in bats and primates identifying how the past has shaped modern viral reservoirs and humans - results publicly-available in an online resource. C_LIO_LIIdentification of 81 primate and 38 bat VIPs with signatures of adaptive evolution. The common ones among species delineate a core adaptive interactome, while the ones displaying distinct evolutionary trajectories enlighten host lineage-specific determinants. C_LIO_LIEvidence of primate specific adaptation of the entry factor TMPRSS2 pointing to its host- specific in vivo importance and predicting molecular interfaces. C_LIO_LIFYCO1 sites associated with severe COVID-19 in human (GWAS) display hallmarks of ancient adaptive evolution in primates, highlighting its importance in SARS-CoV-2 replication or pathogenesis and differences with the bat reservoir. C_LIO_LIIdentification of adaptive evolution in the bats multifunctional RIPK1 at residues that may differentially regulate inflammation. C_LI

evolutionary biology↗

bioRxiv2021

A conserved uORF impacts APOBEC3G translation and is essential for translational inhibition by the HIV-1 Vif protein

The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation and protein degradation) that together reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5 untranslated region (5UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky-scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation.

microbiology↗

bioRxiv2020

Rapid evolution of mammalian HERC6 and independent duplication of a chimeric HERC5/6 gene in rodents and bats suggest an overlooked role of HERCs in antiviral innate immunity

The antiviral innate immunity in mammals has evolved very rapidly in response to pathogen selective pressure. Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family including interferon-inducible antiviral effectors. Notably, HERC5 inhibits divergent viruses through the conjugation of ISG15 to diverse proteins-termed as ISGylation. Though HERC6 is the most closely-related protein of HERC5, it lacks the ISGylation function in humans. Interestingly, HERC6 is the main E3-ligase of ISG15 in mice, suggesting adaptive changes in HERC6 with implications in the innate immunity. Therefore, HERC5 and HERC6 have probably diversified through complex evolutionary history in mammals, and such characterization would require an extensive survey of mammalian evolution. Here, we performed mammalian-wide and lineage-specific phylogenetic and genomic analyses of HERC5 and HERC6. We used 83 orthologous sequences from bats, rodents, primates, artiodactyls and carnivores - the top five representative groups of mammalian evolution and the main hosts of viral diversity. We found that mammalian HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past genetic arms-races with viral pathogens. Importantly, we found accelerated evolution in the HERC6 spacer domain, suggesting that it might be a pathogen-mammal interface, targeting a viral protein and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat antiviral innate immunity. Altogether, we found major genetic innovations in mammalian HERC5 and HERC6. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.

evolutionary biology↗