Magister Scientiae - MSc / Nevirapine (NVP) is a cheap anti-retroviral drug used in poor countries worldwide, administered to pregnant women at the onset of labour to inhibit HIV enzyme reverse transcriptase. Viruses which may get transmitted to newborns are deficient in this enzyme, and HIV-1 infection cannot be established, thereby preventing mother to child transmission (MTCT). In some cases, babies get infected and positive selection for viruses resistant to nevirapine may be inferred. Positive selection can be inferred from sequence data, when the rate of nonsynonymous substitutions is significantly greater than the rate of synonymous substitutions. Unfortunately, it is found that available positive selection methods should not be used to analyse before- and after- NVP treatment sequence pairs associated with MTCT. Methods which use phylogenetic trees to infer positive selection trace synonymous and nonsynonymous substitutions further back in time than the short time duration during which selection for NVP occurred. The other group of methods for inferring positive selection, the pairwise methods, do not have appreciable power, because they average susbtituion rates over all codons in a sequence pair and not just at single codons. We introduce a simple counting method which we call the Pairwise Homologous Codons (PHoCs) method with which we have inferred positive selection resulting from NVP treatment in longitudinal HIV-1 reverse transcriptase sequences. The PHoCs method estimates rates of substitutions between before- and after- NVP treatment codons, using a simple pairwise method. / South Africa

Retrons are genetic elements encoding reverse transcriptase (RT) usually located on the chromosome of a wide variety of mostly Gram-negative bacteria. Here we describe a new retron, designated Ne144, found in the chromosome of the myxobacterium Nannocystis exedens. This element codes for a 515-amino-acid RT that is most closely related to those found in other myxobacterial retrons. The RT is responsible for the production of a small satellite DNA called msDNA. This msDNA is composed of a 144 base, single-stranded DNA that is linked to a 72 base single-stranded RNA. The RNA strand is joined to the 5′ end of the DNA chain via a 2′-5′ linkage that occurs from the 2′ position of an internal guanosine residue in the RNA. In addition to the retron element, the chromosome of N. exedens also contains several partial copies of the msDNA sequence as revealed by DNA hybridization experiments using msDNA as a probe. One of these partial copies was characterized from a chromosome restriction fragment and found to contain a sequence that matches the last 82 bases of the DNA strand and five bases of the RNA strand in msDNA-Ne144. This partial copy of msDNA is very likely a retrotransposed sequence that was generated by reverse transcription using an RNA (the primer-template RNA for msDNA) as a template and the 3′ end of a nick in the chromosome as a primer, followed by incorporation into an open reading frame. The presence of this truncated copy of msDNA is strong evidence of retrotransposition in N. exedens causing an alteration in the bacterial genome.

Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus that forms persistent latently infected reservoirs that are the remaining major hurdle for current HIV-1 treatments. APOBEC3 (A3) proteins are intrinsic retroviral restriction factors that introduce GA mutations during reverse transcription, while Reverse Transcriptase (RT) introduces on average 2-3 mutations every reverse transcription cycle due to a lack of proofreading ability. The goal of this research is to characterize the infectivity and activation of mutated HIV-1 viruses that display reduced transcription upon infection, viruses that we term latency prone viruses (LPVs). We hypothesize that GA transition mutations in the HIV-1 Long Terminal Repeat (LTR) region of the LPVs introduced through Reverse Transcriptase and low levels of A3 protein activity can create HIV-1 sequences that display a reversible, latency-like phenotype. Variable levels of transcription and promoter activation were seen among the LPVs when tested against four classes of Latency Reversing Agents (LRAs). Subsequently, three tested LPVs demonstrated an initial latency-like phenotype before rebounding in infectivity. This project demonstrates for the first time that HIV-1 latency is not simply a byproduct of the infection timing and cellular conditions, but that replication-competent HIV-1 latent viruses can also be created through sublethal mutagenesis of their viral promoter sequence introduced through A3 and RT exposure. The characterization of the complete mechanism of HIV-1 latency induction, maintenance, and reversal is critical in the development of sterilizing and functional cures for HIV-1 infection.

No description available.

This research focuses on non-Long Terminal Repeat (non-LTR) retrotransposons in the African malaria mosquito, Anopheles gambiae and other mosquito species. An unprecedented diversity of non-LTRs was discovered by genome analysis of the An. gambiae genome assembly. One hundred and four families were found by a reiterative and comprehensive search using the conserved reverse transcriptase domains of known non-LTRs from a number of organisms as the starting queries. These families range in copy number from a few to approximately 2000 and occupy at least 3% of the genome. An. gambiae non-LTRs represent 8 of the 15 previously defined clades, plus two novel clades, Loner and Outcast, raising the total number of known clades to 17. The first invertebrate L1 clade representatives were also found. All clades except one have families with sequence characteristics suggesting recent activity. Juan, a non-LTR of the Jockey clade originally discovered in the mosquito Culex pipiens quinquefasciatus (Mouches et al. 1991), has been implicated in horizontal transfer in three non-sibling species of the Aedes genus (Mouches, Bensaadi, and Salvado 1992). PCR was used to obtain sequences from 18 mosquito species of six genera. Phylogenetic analysis demonstrates predominant vertical inheritance of Juan elements among these species. There is strong evidence from sequence analysis supporting the recent activity of Juan in several divergent species. We hypothesize that the sustained activity (versus quick inactivation) of non-LTRs in mosquitoes may contribute to the diversity we observe in the An. gambiae genome today. Promoter and transcriptional analyses were performed for several families previously identified as potentially active elements based on sequence analysis. RT-PCR results indicate that transcripts are present in An. gambiae cell lines that contain sequences corresponding to 13 of 15 tested non-LTR families. The 5' UTRs of An. gambiae non-LTRs from the I, Jockey, and L1 clades support basal transcription in divergent mosquito cell lines from 3 species. The Jen-1 5'UTR did not support transcription in Ae. aegypti and had low activity in Ae. albopictus. In summary, this research shows that Non-LTRs have been highly successful genomic elements that have flourished in many divergent mosquito species. / Ph. D.

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No description available.

Les traitements actuels dirigés contre le VIH ne sont que partiellement efficaces en raison de l'apparition de mutations qui confèrent au virus une grande capacité de résistance aux antirétroviraux existants. Un moyen d'améliorer la lutte contre le virus consiste par conséquent à trouver de nouvelles stratégies d'inhibition. Le complexe de reverse transcription est une des principales cibles pour le développement de traitement anti-SIDA, il catalyse une étape obligatoire du cycle de réplication du virus. Cependant, l'ensemble des inhibiteurs de la transcriptase inverse sont limités par l'apparition rapide de souches résistances. Dans ce contexte, mes travaux de thèse ont permis de développer des inhibiteurs ciblant spécifiquement la reverse transcriptase (RT) du VIH-1, basée sur des fragments d'anticorps dérivés des anticorps chaînes lourdes de dromadaire appelés VHHs ou encore Nanobodies. Associé à une stratégie de vectorisation non invasive basée sur l'utilisation de peptides vecteurs pénétrants, les Nanobodies ont été délivré efficacement dans les cellules et par conséquent ils présentent tous une forte activité antivirale de l'ordre du nanomolaire. L'étude du mécanisme d'action du Nanobody leader NbRT20 montre qu'il agit en tant qu'inhibiteur conformationnel. Il interagit avec la forme intermédiaire inactive de la RT et empêche la mobilité du sous-domaine thumb requis pour le positionnement correct de la matrice/amorce sur la RT et inhibant l'incorporation des nucléotides dans la chaîne d'ADN naissante déstabilisant l'enzyme dans une conformation inactive, non processive. Pris ensemble, ces résultats montrent que la plate-forme Nanobody peut être très efficace pour générer des intracorps extrêmement puissants et sélectifs pour neutraliser la RT et la réplication virale.Mots clés : HIV-1, RT, Nanobodies, peptide vecteur pénétrant / The rapid emergence of drug-resistant viruses against all approved HIV clinical drugs together with inaccessible latent virus reservoirs and side effects of currently used compounds have limited the potency of existing anti-HIV-1 therapeutics. Therefore, there is a critical need for new safer drugs, active against resistant viral strains. Reverse transcriptase (RT) plays an essential role in the replication of human immunodeficiency virus type 1 (HIV-1) and remains a primary target of anti-HIV-1 drugs. To develop specific HIV inhibitors, we have elaborated a new strategy based on short antibody fragments derived from the unique Heavy-chain antibodies present in Camelidae called Nanobodies that targets RT-activation. The immunization of dromedaries with RT has lead to the isolation of a panel of Nanobodies that tightly bind the two subunits of RT and inhibit its DNA-dependent DNA polymerase activity at nanomolar range. From that screen we have elaborated an intrabody (cell penetrating anti-RT Nanobody) NbRT20 that constitutes a potential interesting anti-HIV compound.We demonstrated that NbRT20 inhibits RT polymerase activity and exhibiting a potent antiviral activity with a subnanomolar IC50. NbRT20 binds the thumb subdomain and restricts its flexibility and mobility resulting in an inactive/non processive dimeric conformation of the enzyme. From a mechanistic point of view, we have showed that NbRT20 is a conformational inhibitor. it prevents proper binding of primer/template and of dNTP and destabilizes the enzyme in an inactive/non processive dimeric conformation.Taken together, these results demonstrated that, the Nanobody platform may be highly effective at generating extremely potent and selective intrabody to neutralize RT and HIV proliferation.Key words: HIV-1, RT, Nanobodies, cell penetrating peptide

No description available.

Le virus de l'immunodéficience humain de type 1 VIH-1 est un rétrovirus responsable d'une pandémie touchant actuellement 34 millions de personnes dont près de 25 millons en sont morts. En dépit des grands progrès réalisés dans le développement de nouveaux médicaments visant à bloquer la réplication de ce virus, l'émergence rapide de souches virales mutantes résistantes imposent l'urgence et la nécessité de développer de nouvelles stratégies thérapeutiques pour combattre ce virus. La Reverse Transcriptase (RT) duVIH-1 joue un rôle majeur dans le cycle viral puisqu'elle est responsable de convertir l'ARN génomique simple brin en ADN double afin d'intégrer l'ADN génomique de la cellule hôte. La forme biologique de la RT est un hétérodimère formé de la sous unité p66 et la sous unité p51. Les sous unités sont constituées des sous domaines fingers, palm, « connection », thumb et RNase H, ce dernier étant absent sur la sous unité p51. L'activation de la RT est un processus en deux étapes : la première étape consiste en l'association rapide des deux sous unités, suivie d'une deuxième étape plus lente, correspondant à des changements conformationnels fins à l'interface entre p66/p51.Dans l'objectif d'inhiber la fonction de la RT, nous avons proposé une nouvelle stratégie fondée sur l'utilisation des peptides interfacials courts dérivant de séquences hautement conserver de la RT, capables de cibler efficacement les interactions protéine/protéine et de bloquer la dimérisation et l'activation par maturation de la RT. La dimérisation des deux sous unités implique leur interaction part les domaines de connexion. Dans la première partie de ce travail de thèse, nous avons criblé et isolé des peptides capables d'interférer avec cette interaction impliquant un « cluster » de résidus aromatiques. Nous avons identifié un peptide court PID4, et démontré que ce peptide induit un changement de conformation de la RT, entrainant la dissociation du complexe. La maturation implique l'interaction de résidus localisés au niveau de « hot spot » dans le domaine RNase H de p66 et thumb de p51. Dans la deuxième partie de cette thèse, nous avons sélectionné un peptide court, P27, issus du domaine thumb pouvant inhiber l'étape de la « maturation » (P27). Ces deux classes de peptides bloquent la réplication virale et sont efficaces sur plusieurs souches virales et sur des mutants résistants aux NNRTIS et NRTIS.Les résultats obtenus sur nos deux classes d'inhibiteurs peptidiques, démontrent bien que la dimérisation et la maturation de la RT constituent des cibles de choix pour bloquer l'activité polymérase de la RT et ainsi stopper la prolifération virale par un nouvel concept moins exposer à l'émergence des mutation de résistance. / The human immunodeficiency virus type 1 (HIV-1) is a retrovirus responsible of a disease currently affecting 34 million people and caused the death of 25 million people from its discovery in the 1980s. Despite the great progresses made in the development of new drugs to block the replication of the virus, the rapid emergence of resistant mutant strains requires the development of new therapeutic strategies to combat this agent.The Reverse transcriptase (RT) plays an essential role in the replication of human immunodeficiency virus type 1 (HIV-1) and remains a primary target of anti-HIV-1 drugs. The biologically active form of HIV-1 RT is a heterodimer of two subunits, p51 and p66, each consisting of distinct sub-domains: the fingers, the palm, the connection and the thumb are present in both of them. p66 contain also an RNAse H sub-domains. The formation of RT is a two-step mechanism, involving first the rapid association of the two subunits (Dimerization), followed by conformational changes (Maturation) yielding the biologically active form of the enzyme.In order to inhibit the function of RT, we have proposed and elaborated a new strategy based on short interfacial peptides that target protein-protein interfaces involved in RT- dimerization and activation. The dimerization of two subunits involves interaction between their connection domains. In the first part of this thesis, we screened and isolated peptides capable of interfering with the interaction, involving a "cluster" of aromatic residues. We identified a short peptide PID4, and demonstrated that induces a conformational change in the RT, resulting in dissociation of the heterodimer complex. Maturation involves the interaction of residues located at "hot spot" in the RNase H domain of p66 and the thumb domain of p51. The second part of this thesis is based on a screening of peptides, derived from the thumb domain of the enzyme. We have identified a short peptide (P27) which inhibits the maturation step and abolish replication of HIV-1 LAI. These two classes of peptides block viral replication and are effective in several viral strains and mutants resistant to NNRTIs and NRTIs.Taken together, the results of our two classes of peptides inhibitors, demonstrate that the dimerization and maturation of RT constitutes an attractive target for AIDS chemotherapeutics and for the design of more specific new antiviral drugs that can bypass resistance limitation.