Ali Saïb

Paris Diderot University, Lutetia Parisorum, Île-de-France, France

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Publications (76)419.41 Total impact

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    ABSTRACT: Genomic integration, an obligate step in the HIV-1 replication cycle, is blocked by the integrase inhibitor raltegravir. A consequence is an excess of unintegrated viral DNA genomes, which undergo intramolecular ligation and accumulate as 2-LTR circles. These circularized genomes are also reliably observed in vivo in the absence of antiviral therapy and they persist in non-dividing cells. However, they have long been considered as dead-end products that are not precursors to integration and further viral propagation. Here, we show that raltegravir action is reversible and that unintegrated viral DNA is integrated in the host cell genome after raltegravir removal leading to HIV-1 replication. Using quantitative PCR approach, we analyzed the consequences of reversing prolonged raltegravir-induced integration blocks. We observed, after RAL removal, a decrease of 2-LTR circles and a transient increase of linear DNA that is subsequently integrated in the host cell genome and fuel new cycles of viral replication. Our data highly suggest that 2-LTR circles can be used as a reserve supply of genomes for proviral integration highlighting their potential role in the overall HIV-1 replication cycle.
    Full-text · Article · Dec 2015 · Retrovirology
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    ABSTRACT: Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs. JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared to existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files. JASSA is freely accessible at {{http://www.jassa.fr/}}. Website is implemented in PHP and MySQL, with all major browsers supported. guillaume.beauclair@inserm.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. © The Author (2015). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
    No preview · Article · Jul 2015 · Bioinformatics
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    ABSTRACT: Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. Copyright © 2015, American Association for the Advancement of Science.
    Full-text · Article · May 2015 · Science
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    ABSTRACT: LEDGF/p75 (LEDGF) is the main cellular cofactor of HIV-1 integrase (IN). It acts as a tethering factor for IN, and targets the integration of HIV in actively transcribed gene regions of chromatin. A recently developed class of IN allosteric inhibitors can inhibit the LEDGF-IN interaction. We describe a new series of IN-LEDGF allosteric inhibitors, the most active of which is Mut101. We determined the crystal structure of Mut101 in complex with IN and showed that the compound binds to the LEDGF-binding pocket, promoting conformational changes of IN which explain at the atomic level the allosteric effect of the IN/LEDGF interaction inhibitor on IN functions. In vitro, Mut101 inhibited both IN-LEDGF interaction and IN strand transfer activity while enhancing IN-IN interaction. Time of addition experiments indicated that Mut101 behaved as an integration inhibitor. Mut101 was fully active on HIV-1 mutants resistant to INSTIs and other classes of anti-HIV drugs, indicative that this compound has a new mode of action. However, we found that Mut101 also displayed a more potent antiretroviral activity at a post-integration step. Infectivity of viral particles produced in presence of Mut101 was severely decreased. This latter effect also required the binding of the compound to the LEDGF-binding pocket. Mut101 has dual anti-HIV-1 activity, at integration and post-integration steps of the viral replication cycle, by binding to a unique target on IN (the LEDGF-binding pocket). The post-integration block of HIV-1 replication in virus-producer cells is the mechanism by which Mut101 is most active as an antiretroviral. To explain this difference between Mut101 antiretroviral activity at integration and post-integration stages, we propose the following model: LEDGF is a nuclear, chromatin-bound protein that is absent in the cytoplasm. Therefore, LEDGF can outcompete compound binding to IN in the nucleus of target cells lowering its antiretroviral activity at integration, but not in the cytoplasm where post- integration production of infectious viral particles takes place.
    Full-text · Article · Nov 2013 · Retrovirology
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    Full-text · Article · Sep 2013 · Retrovirology
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    ABSTRACT: Nef is a human immunodeficiency virus type 1 (HIV-1) auxiliary protein that plays an important role in virus replication and the onset of acquired immunodeficiency. Although known functions of Nef might explain its contribution to HIV-1-associated pathogenesis, how Nef increases virus infectivity is still an open question. In vitro, Nef-deleted viruses have a defect that prevents efficient completion of early steps of replication. We have previously shown that this restriction is not due to the absence of Nef in viral particles. Rather, a loss of function in virus-producing cells accounts for the lower infectivity of nef-deleted viruses compared to wild-type (WT) viruses. Here we used DiGE and iTRAQ to identify differences between the proteomes of WT and nef-deleted viruses. We observe that glucosidase II is enriched in WT virions, whereas Ezrin, ALG-2, CD81, and EHD4 are enriched in nef-deleted virions. Functional analysis shows that glucosidase II, ALG-2, and CD81 have no or only Nef-independent effect on infectivity. In contrast, Ezrin and EHD4 are involved in the ability of Nef to increase virus infectivity (referred to thereafter as Nef potency). Indeed, simultaneous Ezrin and EHD4 depletion in SupT1 and 293T virus-producing cells result in an ∼30 and ∼70% decrease of Nef potency, respectively. Finally, while Ezrin behaves as an inhibitory factor counteracted by Nef, EHD4 should be considered as a cofactors required by Nef to increase virus infectivity.
    Full-text · Article · Jan 2013 · Journal of Virology
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    ABSTRACT: Simian foamy viruses (SFV) are widespread retroviruses among non-human primates (NHP). SFV actively replicates in their oral cavity and can be transmitted to humans after NHP bites, giving rise to a persistent infection even decades after primary infection. Very few data are available on the genetic structure of such SFV found in humans.In the framework of ongoing studies searching for SFV-infected humans in South Cameroon rainforest villages, we studied 38 SFV-infected hunters whose time of infection were presumably determined. By long-term co-cultures of PBMCs with BHK-21 cells, we isolated 5 new SFV strains, providing complete genomes of SFVcpz Pan troglodytes troglodytes (BAD327, AG15), SFVcni Cercopithecus nictitans (AG16) and SFVggo Gorilla gorilla (BAK74 and BAD468). These zoonotic strains share a very high similarity with their NHP counterparts with a high conservation of the genetic elements important for viral replication. Interestingly, FV DNA sequences obtained before cultivation revealed in both U3 and tas some deletion variants that may correlate with in vivo chronicity in humans. Genomic changes in bet (premature stop codon) and gag were also observed. To know if such changes were specific to zoonotic strains, we studied local SFV-infected chimpanzees and found the same genomic changes.Our study reveals that natural polymorphism of SFV strains does exist, at both inter-subspecies level (gag, bet) and intra-subspecies level (U3, tas) but seems not to reflect a viral adaptation specific to zoonotic SFV strains.
    Full-text · Article · Sep 2012 · Journal of Virology

  • No preview · Article · Sep 2012 · Virologie
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    ABSTRACT: L’intégration du génome viral dans le génome de la cellule hôte est une étape indispensable à la réplication des rétroéléments, vecteurs adaptés à la thérapie génique mais aussi agents mutagènes potentiels. Récemment, de nombreuses études ont montré que les sites d’intégration ne sont pas distribués aléatoirement sur le génome mais, au contraire, préférentiellement localisés dans certaines régions, démontrant que la spécificité d’intégration est un mécanisme hautement régulé. Plusieurs protéines virales et facteurs cellulaires jouent un rôle fondamental dans l’étape d’intégration, certains d’entre eux participant également à la spécificité d’intégration. Cette revue décrit les avancées récentes sur l’intégration des rétroéléments, se focalisant sur les mécanismes impliqués dans la sélectivité et la spécificité d’intégration, ainsi que dans l’étape d’ancrage chromatinien précédant l’insertion du provirus.
    No preview · Article · Mar 2012
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    ABSTRACT: Integration into the genome of the host cell is an obligatory step in the replication of retroelements. This feature accounts for the fact that these elements are both potential mutagens as well as vectors suitable for long-term gene therapy. Recently, many studies have reported that proviral insertion is not random but, rather, targets specific regions in the genome. Additionally, it has become clear that this process is highly regulated at the molecular level. Both viral proteins and cellular factors participate in the integration step, explaining why different retroelements have distinct integration profiles. This review describes recent advances about the integration of retroelements, focusing particularly on the mechanisms involved in the selectivity and specificity of integration and the chromatin-anchoring step, which precedes the insertion of the provirus.
    No preview · Article · Mar 2012 · Virologie
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    ABSTRACT: Small regions called protein transduction domains (PTDs), identified in cellular and viral proteins, have been reported to efficiently cross biological membranes. Here we show that the structural Gag protein of the prototypic foamy virus (PFV) is apparently able to move from cell to cell and to transport the green fluorescent protein (GFP) from few transfected cells to the nuclei of the entire monolayer. Deletion studies showed that this property lies within the second glycine/arginine (GRII) box in the C-terminus of the protein. We also found that uptake and nuclear accumulation of Gag GRII expressed as GFP-fusion protein in recipient cells was observed only following methanol fixation, but never in living cells or when cells were fixed with glutaraldehyde or treated with trichloroacetic acid prior to methanol fixation. Absence of intercellular spreading in vivo was further confirmed using a sensitive luciferase activity assay based on transactivation of the PFV long terminal repeats. Thus, we conclude that intercellular spreading of PFV Gag represents an artificial diffusion event occurring during cell fixation, followed by nuclear retention mediated by the chromatin-binding sequence within the Gag GRII box. In light of these results, we advise caution before defining a peptide as PTD on the basis of intercellular spreading observed by fluorescence microscopy.
    Full-text · Article · Feb 2012 · PLoS ONE
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    ABSTRACT: In order to characterize simian foamy retroviruses (SFVs) in wild-born nonhuman primates (NHPs) in Gabon and to investigate cross-species transmission to humans, we obtained 497 NHP samples, composed of 286 blood and 211 tissue (bush meat) samples. Anti-SFV antibodies were found in 31 of 286 plasma samples (10.5%). The integrase gene sequence was found in 38/497 samples, including both blood and tissue samples, with novel SFVs in several Cercopithecus species. Of the 78 humans, mostly hunters, who had been bitten or scratched by NHPs, 19 were SFV seropositive, with 15 cases confirmed by PCR. All but one were infected with ape SFV. We thus found novel SFV strains in NHPs in Gabon and high cross-species transmission of SFVs from gorilla bites.
    Full-text · Article · Nov 2011 · Journal of Virology
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    Full-text · Article · Oct 2011 · Retrovirology
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    ABSTRACT: HIV-1 integrase (IN) orchestrates the integration of the reverse transcribed viral cDNA into the host cell genome and participates also in other steps of HIV-1 replication. Cellular and viral factors assist IN in performing its multiple functions, and post-translational modifications contribute to modulate its activities. Here, we show that HIV-1 IN is modified by SUMO proteins and that phylogenetically conserved SUMOylation consensus motifs represent major SUMO acceptor sites. Viruses harboring SUMOylation site IN mutants displayed a replication defect that was mapped during the early stages of infection, before integration but after reverse transcription. Because SUMOylation-defective IN mutants retained WT catalytic activity, we hypothesize that SUMOylation might regulate the affinity of IN for co-factors, contributing to efficient HIV-1 replication.
    Preview · Article · Mar 2011 · Journal of Biological Chemistry
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    ABSTRACT: The Gag polyproteins play distinct roles during the replication cycle of retroviruses, hijacking many cellular machineries to fulfill them. In the case of the prototype foamy virus (PFV), Gag structural proteins undergo transient nuclear trafficking after their synthesis, returning back to the cytoplasm for capsid assembly and virus egress. The functional role of this nuclear stage as well as the molecular mechanism(s) responsible for Gag nuclear export are not understood. We have identified a leptomycin B (LMB)-sensitive nuclear export sequence (NES) within the N-terminus of PFV Gag that is absolutely required for the completion of late stages of virus replication. Point mutations of conserved residues within this motif lead to nuclear redistribution of Gag, preventing subsequent virus egress. We have shown that a NES-defective PFV Gag acts as a dominant negative mutant by sequestrating its wild-type counterpart in the nucleus. Trans-complementation experiments with the heterologous NES of HIV-1 Rev allow the cytoplasmic redistribution of FV Gag, but fail to restore infectivity. PFV Gag-Gag interactions are finely tuned in the cytoplasm to regulate their functions, capsid assembly, and virus release. In the nucleus, we have shown Gag-Gag interactions which could be involved in the nuclear export of Gag and viral RNA. We propose that nuclear export of unspliced and partially spliced PFV RNAs relies on two complementary mechanisms, which take place successively during the replication cycle.
    Preview · Article · Jan 2011 · Retrovirology
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    ABSTRACT: Each of the pathogenic human retroviruses (HIV-1/2 and HTLV-1) has a nonhuman primate counterpart, and the presence of these retroviruses in humans results from interspecies transmission. The passage of another simian retrovirus, simian foamy virus (SFV), from apes or monkeys to humans has been reported. Mandrillus sphinx, a monkey species living in central Africa, is naturally infected with SFV. We evaluated the natural history of the virus in a free-ranging colony of mandrills and investigated possible transmission of mandrill SFV to humans. We studied 84 semi-free-ranging captive mandrills at the Primate Centre of the Centre International de Recherches Médicales de Franceville (Gabon) and 15 wild mandrills caught in various areas of the country. The presence of SFV was also evaluated in 20 people who worked closely with mandrills and other nonhuman primates. SFV infection was determined by specific serological (Western blot) and molecular (nested PCR of the integrase region in the polymerase gene) assays. Seropositivity for SFV was found in 70/84 (83%) captive and 9/15 (60%) wild-caught mandrills and in 2/20 (10%) humans. The 425-bp SFV integrase fragment was detected in peripheral blood DNA from 53 captive and 8 wild-caught mandrills and in two personnel. Sequence and phylogenetic studies demonstrated the presence of two distinct strains of mandrill SFV, one clade including SFVs from mandrills living in the northern part of Gabon and the second consisting of SFV from animals living in the south. One man who had been bitten 10 years earlier by a mandrill and another bitten 22 years earlier by a macaque were found to be SFV infected, both at the Primate Centre. The second man had a sequence close to SFVmac sequences. Comparative sequence analysis of the virus from the first man and from the mandrill showed nearly identical sequences, indicating genetic stability of SFV over time. Our results show a high prevalence of SFV infection in a semi-free-ranging colony of mandrills, with the presence of two different strains. We also showed transmission of SFV from a mandrill and a macaque to humans.
    Full-text · Article · Dec 2010 · Retrovirology
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    ABSTRACT: Figure S. Phylogenetic tree of all clones from H1CIRMF and Mnd2ACDP. SFV clones of 425 bp of integrase fragments obtained from H1CIRMF (in red) were aligned with those from Mnd2ACDP (in blue). Phylogenetic analyses were done as described in the legend to Figure 2. Clones from H1CIRMF were identified as CIRMF (see Figure 6), a number, C (for clone) and another number (vg: CIRMF1C9). Clones from Mnd2ACDP are in two groups: on the day of injury: Mnd2A (the mandrill), followed by C (for clone, with a corresponding number) and ending with J0 (day of injury). The clones obtained 10 years after the injury have Y10 (10 years after) at the end. An outgroup is the sequence Mnd203SFV (reported by Calattini et al. [3] as originating from a drill, but clustering with Cercocebus species).
    Preview · Dataset · Dec 2010
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    ABSTRACT: The human T-lymphotropic virus type I oncoprotein Tax is critical for T-cell transformation, acting mainly through nuclear factor kappa B essential modulator (NEMO) binding and subsequent nuclear factor-κB activation. Tax localizes to Tax nuclear bodies and to the centrosome and is subjected to ubiquitylation and small ubiquitin-like modifier (SUMO)ylation, which are both necessary for complete transcriptional activation. Using the photoconvertible fluorophore Dendra-2 coupled with live video confocal microscopy, we show for the first time that the same Tax molecule shuttles among Tax nuclear bodies and between these nuclear bodies and the centrosome, depending on its posttranslational modifications. Ubiquitylation targets Tax to nuclear bodies to which NEMO is recruited and subsequently SUMOylated. We also demonstrate that Tax nuclear bodies contain the SUMOylation machinery including SUMO and the SUMO conjugating enzyme Ubc9, strongly suggesting that these nuclear bodies represent sites of active SUMOylation. Finally, both ubiquitylation and SUMOylation of Tax control NEMO targeting to the centrosome. Altogether, we are proposing a model where both ubiquitylation and SUMOylation of Tax control the shuttling of Tax and NEMO between the cytoplasmic and nuclear compartments.
    Full-text · Article · Oct 2010 · Blood
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    ABSTRACT: Post-translational modifications, such as SUMOylation, are examples of cellular machineries hijacked by viruses to efficiently replicate. SUMOylation, which consists in the conjugation of small ubiquitin-like modifier (SUMO) peptides to a substrate, is exploited or hampered by numerous viruses during infection. Several viral proteins are SUMOylated, causing modulation of sub-cellular localization, stability or modifications of protein activities. In this review, recently described viral examples have been chosen to highlight the different strategies used by viruses to hijack SUMOylation in order to promote replication. The link between pathologies due to viral infections and SUMOylation is discussed. Finally, the potential applications of SUMOylation inhibitors in the treatment of viral infections and associated cancer are evoked.
    No preview · Article · Sep 2010 · Virologie
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    ABSTRACT: Les modifications post-traductionnelles, telles que la SUMOylation, sont un exemple de machinerie cellulaire détournée par les virus. La SUMOylation, qui consiste en la liaison covalente d'un peptide SUMO (small ubiquitin-like modifier) à une protéine cible, a récemment été impliquée dans le cycle réplicatif de nombreux virus. Cette revue rappelle, par des exemples choisis à travers le monde viral et en insistant sur les dernières découvertes, les différentes façons dont la SUMOylation est détournée par les virus afin de créer un environnement favorable à la réplication. Le lien entre les pathologies impliquées par chaque virus et la SUMOylation est abordé. Enfin, les dernières avancées concernant l'utilisation des potentiels inhibiteurs de la SUMOylation dans le cadre de la lutte antivirale et anticancéreuse sont évoquées.
    No preview · Article · Sep 2010

Publication Stats

3k Citations
419.41 Total Impact Points

Institutions

  • 2008-2015
    • Paris Diderot University
      Lutetia Parisorum, Île-de-France, France
    • La Ligue contre le cancer
      Lutetia Parisorum, Île-de-France, France
  • 2006-2015
    • University of Paris-Est
      La Haye-Descartes, Centre, France
    • Institut Universitaire de France
      Lutetia Parisorum, Île-de-France, France
  • 2009-2013
    • Conservatoire National des Arts et Métiers
      Lutetia Parisorum, Île-de-France, France
  • 1998-2009
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France