Dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Medicine. Johannesburg, 2011 / The HIV-1 integrase (IN) enzyme is an integral part of the viral replication cycle and has no known human homologues, making it an ideal target for antiretroviral therapy. To date, only one inhibitor of IN strand transfer activity (Raltegravir, IsentressTM) is available for human use. However, the inevitable emergence of antiretroviral drug resistance requires ongoing research into new/novel therapies. There are currently no assays to screen for IN inhibitors against HIV-1 subtype C in South Africa (and worldwide), therefore, the overall objective of this study was to generate and characterize locally relevant, soluble, functional recombinant HIV-1 subtype C IN proteins for use in strand transfer assays. Recombinant integrase genes, including a soluble HIV-1 subtype C mutant (05ZAFV6 with C56S, C65S, W131D, F185D and C280S) and HIV-1 subtype C Y143C mutant (05ZAFV6 soluble with Y143C) were designed, generated and cloned in frame into pET15b. Optimal bacterial expression conditions for the expression of these constructs as well as an HIV-1 subtype C wild type (05ZAFV6), subtype B wild type (NL4-3), and subtype B soluble (NL4-3 with F185K and C280S; as controls) IN, in E.coli BL21 cells were determined. All five recombinant IN were successfully purified using nickel affinity chromatography, and subsequently used to establish a strand transfer assay to assess their activity and their response to two well-known integrase inhibitors, L-Chicoric acid and Raltegravir. All five recombinant IN proteins were found to be biologically active, with INY143C (116.67%) showing equivalent activity to INBwt (117.37%), while INCsol (52.96%) was the lowest. The IC50 values of L-Chicoric acid were higher than the expected values for all five recombinant IN, with the subtype B and C IN solubility mutations contributing to an increased resistance to inhibition by L-Chicoric acid. The dose responses to Raltegravir for INCwt and INBsol were as expected, with IC50’s in line with published data, and the INY143C mutant (known mutation conferring resistance to Raltegravir) was resistant to inhibition of strand transfer activity at all Raltegravir concentrations tested except the highest (50 μM). Finally, methods to complex the INY143C mutant to thiolated-DNA were evaluated, however definitive data could not be obtained. Future work should focus on optimization of the purification and characterization of the IN-DNA complexes. Overall, this study has led to the establishment of functional strand transfer assays based on HIV-1 subtype C recombinant IN proteins, and established a framework for screening of novel HIV-1 subtype C IN inhibitors.

HIV-1 integrase (IN) enzyme employs several viral and cellular proteins for nuclear translocation and crucial integration of viral cDNA. Successful identification of new viral/cellular interactions may shed light for better understanding of HIV-1 replication. 293T cells were transiently transfected with pYEF-1-TAP-IN and cell lysate were subjected to Tandem Affinity Purification system to pull down putative IN-interacting cellular partners. A number of distinct bands from the Coomassie-stained gel were excised followed by in-gel digestion and mass spectrometry. Putative cellular partners of HIV-1 IN were heat shock protein 60 (HSP60), β-tubulin, γ-actin, ATP synthase alpha subunit and histone H1.2 were identified by mass spectrometry. Additionally, SF3A3 (splicing factor 3A3), another previously reported factor, was successfully co-immunoprecipitated with IN. The C-terminal portion of IN was found to be the region of interaction with SF3A3. Overall, this study has provided better understanding of IN dynamics enriching existing knowledge of HIV-1 IN biology.

HIV-1 integrase (IN) enzyme employs several viral and cellular proteins for nuclear translocation and crucial integration of viral cDNA. Successful identification of new viral/cellular interactions may shed light for better understanding of HIV-1 replication. 293T cells were transiently transfected with pYEF-1-TAP-IN and cell lysate were subjected to Tandem Affinity Purification system to pull down putative IN-interacting cellular partners. A number of distinct bands from the Coomassie-stained gel were excised followed by in-gel digestion and mass spectrometry. Putative cellular partners of HIV-1 IN were heat shock protein 60 (HSP60), β-tubulin, γ-actin, ATP synthase alpha subunit and histone H1.2 were identified by mass spectrometry. Additionally, SF3A3 (splicing factor 3A3), another previously reported factor, was successfully co-immunoprecipitated with IN. The C-terminal portion of IN was found to be the region of interaction with SF3A3. Overall, this study has provided better understanding of IN dynamics enriching existing knowledge of HIV-1 IN biology.

Os manguezais são ecossistemas costeiros de transição formados entre o ambiente marinho e terrestre de zonas tropicais e intertropicais, e estão sujeitos ao regime de marés. Devido a tais condições, os microrganismos que vivem nos sedimentos sofrem constante pressão adaptativa. Nesse contexto, os Elementos Genéticos Móveis (EGMs) (fagos, plasmídeos e transposons) são fatores genéticos diretamente relacionados com a transferência horizontal de genes e podem facilitar processos de adaptação. Neste trabalho foram estudados os EGMs dos sedimentos de três áreas de manguezais do estado de São Paulo, duas localizadas no município de Bertioga e uma na reserva ambiental da Ilha do Cardoso, em Cananeia. Foram avaliadas a frequência e expressão dos diferentes tipos de EGMs no microbioma dos manguezais a partir de metagenomas e metatranscriptomas dos sedimentos, além da utilização de uma biblioteca de fosmídeos, montada a partir de DNA do sedimento de uma das áreas de Bertioga. As sequências de DNA e mRNA foram obtidas de três pontos amostrados por área, sequenciadas em equipamento Illumina HiSeq2000 e anotadas automaticamente na plataforma do MG-RAST. Para a biblioteca de fosmídeo, foi sequenciado um pool de todos os clones em equipamento Illumina HiSeq 2000. Contigs dessas sequências foram montados e fagos e profagos foram preditos e anotados automaticamente pelo pipeline VirSorter. As sequências preditas como fagos ou profagos foram anotadas manualmente. A partir da análise das sequências de metagenômica foi possível verificar que a participação dos EGMs no metabolismo total do microbioma dos manguezais corresponde de 6 a 15 % dos genes preditos, sendo que fagos e profagos correspondem a 90% dos genes associados aos EGMs. A partir dos contigs montados para as sequências da biblioteca, foram preditos e anotados automaticamente 27 fagos, dos quais nove fagos foram anotados manualmente em etapa posterior. Foram encontrados genes que codificam proteínas típicas de fagos, como capsídeo, transposase e integrase, além de genes acessórios potencialmente importantes, como relacionados ao sistema de transporte ABC e sistema de transporte tipo II. A partir da anotação manual, genes conservados de fagos foram utilizados como base para predição da linhagem viral. Foram identificados 6 tipos de vírus pertencentes à ordem Caudovirales, que infectam Proteobacteria e Firmicutes. Esse trabalho sustenta a hipótese de que os fagos infectam os grupos bacterianos mais abundantes nos manguezais e podem carregar genes importantes consigo, desempenhando papel chave na evolução das bactérias nesse ambiente. / Mangroves are coastal transitional ecossystems between marine and terrestral environments of tropical and intertropical zones and are subject to tidal regime. Due those condictions, microorganisms that lives in the sediments suffer constant adaptative pressure. In this context, Mobile Genetic Elements (MGEs) (phages, plasmids and transposons) are genetic fators directly related with horizontal gene transfer and can facilitate adaptation processes. In this work MGEs were studied in the sediments of three mangrove areas in São Paulo state, two located in Bertioga county and one in environmental reserve of Ilha do Cardoso, in Cananeia. Frequency and expression were avaliated for diferente EGMs types in mangrove microbiome from the sediments metagenomes and metatranscriptomes, besides utilization os a fosmid library assembled from a Bertioga area sediment DNA. The sequences of DNA and mRNA were obtained from three sampled points, sequenced in Illumina HiSeq2000 equipment and automatically anotaded in MG-RAST plataform. A pool of all clone were sequenced for fosmid library in Illumina HiSeq2000 equipment. Contigs were assembled and phages and prophages were automatically predicted in VirSorter pipeline. The phages or prophages predicted sequences were manually anotaded. From the analisys os metagenomic sequences was possible to verify that the MGEs participation in total microbiome metabolism stands for 6 to 15% of predicted genes, wich 90% corresponds to phage associated genes. From contigs assembled of library sequences, 27 phages were predicted and annotaded, wich nine code for phage typical proteins, as capsid, transposase and integrase, besides accessory genes potencially important, as ABC transporter and type II transport related. Phage conserved genes were used as base for viral lineage prediction. 6 viral types belonging do Caudovirales order were identified, which infects Proteobacteria and Firmicutes. This work supports the hypothesis that phages infect the most abundant bacterial groups in mangroves and can carry important genes playing a key role in bacterial evolution in this environment.

Os manguezais são ecossistemas costeiros de transição formados entre o ambiente marinho e terrestre de zonas tropicais e intertropicais, e estão sujeitos ao regime de marés. Devido a tais condições, os microrganismos que vivem nos sedimentos sofrem constante pressão adaptativa. Nesse contexto, os Elementos Genéticos Móveis (EGMs) (fagos, plasmídeos e transposons) são fatores genéticos diretamente relacionados com a transferência horizontal de genes e podem facilitar processos de adaptação. Neste trabalho foram estudados os EGMs dos sedimentos de três áreas de manguezais do estado de São Paulo, duas localizadas no município de Bertioga e uma na reserva ambiental da Ilha do Cardoso, em Cananeia. Foram avaliadas a frequência e expressão dos diferentes tipos de EGMs no microbioma dos manguezais a partir de metagenomas e metatranscriptomas dos sedimentos, além da utilização de uma biblioteca de fosmídeos, montada a partir de DNA do sedimento de uma das áreas de Bertioga. As sequências de DNA e mRNA foram obtidas de três pontos amostrados por área, sequenciadas em equipamento Illumina HiSeq2000 e anotadas automaticamente na plataforma do MG-RAST. Para a biblioteca de fosmídeo, foi sequenciado um pool de todos os clones em equipamento Illumina HiSeq 2000. Contigs dessas sequências foram montados e fagos e profagos foram preditos e anotados automaticamente pelo pipeline VirSorter. As sequências preditas como fagos ou profagos foram anotadas manualmente. A partir da análise das sequências de metagenômica foi possível verificar que a participação dos EGMs no metabolismo total do microbioma dos manguezais corresponde de 6 a 15 % dos genes preditos, sendo que fagos e profagos correspondem a 90% dos genes associados aos EGMs. A partir dos contigs montados para as sequências da biblioteca, foram preditos e anotados automaticamente 27 fagos, dos quais nove fagos foram anotados manualmente em etapa posterior. Foram encontrados genes que codificam proteínas típicas de fagos, como capsídeo, transposase e integrase, além de genes acessórios potencialmente importantes, como relacionados ao sistema de transporte ABC e sistema de transporte tipo II. A partir da anotação manual, genes conservados de fagos foram utilizados como base para predição da linhagem viral. Foram identificados 6 tipos de vírus pertencentes à ordem Caudovirales, que infectam Proteobacteria e Firmicutes. Esse trabalho sustenta a hipótese de que os fagos infectam os grupos bacterianos mais abundantes nos manguezais e podem carregar genes importantes consigo, desempenhando papel chave na evolução das bactérias nesse ambiente. / Mangroves are coastal transitional ecossystems between marine and terrestral environments of tropical and intertropical zones and are subject to tidal regime. Due those condictions, microorganisms that lives in the sediments suffer constant adaptative pressure. In this context, Mobile Genetic Elements (MGEs) (phages, plasmids and transposons) are genetic fators directly related with horizontal gene transfer and can facilitate adaptation processes. In this work MGEs were studied in the sediments of three mangrove areas in São Paulo state, two located in Bertioga county and one in environmental reserve of Ilha do Cardoso, in Cananeia. Frequency and expression were avaliated for diferente EGMs types in mangrove microbiome from the sediments metagenomes and metatranscriptomes, besides utilization os a fosmid library assembled from a Bertioga area sediment DNA. The sequences of DNA and mRNA were obtained from three sampled points, sequenced in Illumina HiSeq2000 equipment and automatically anotaded in MG-RAST plataform. A pool of all clone were sequenced for fosmid library in Illumina HiSeq2000 equipment. Contigs were assembled and phages and prophages were automatically predicted in VirSorter pipeline. The phages or prophages predicted sequences were manually anotaded. From the analisys os metagenomic sequences was possible to verify that the MGEs participation in total microbiome metabolism stands for 6 to 15% of predicted genes, wich 90% corresponds to phage associated genes. From contigs assembled of library sequences, 27 phages were predicted and annotaded, wich nine code for phage typical proteins, as capsid, transposase and integrase, besides accessory genes potencially important, as ABC transporter and type II transport related. Phage conserved genes were used as base for viral lineage prediction. 6 viral types belonging do Caudovirales order were identified, which infects Proteobacteria and Firmicutes. This work supports the hypothesis that phages infect the most abundant bacterial groups in mangroves and can carry important genes playing a key role in bacterial evolution in this environment.

No description available.

HIV-1 integrase is an essential enzyme in the HIV replication cycle and is a validated target for antiretroviral drugs. Due to the inevitable emergence of drug resistance of HIV-1 strains to all currently approved FDA antiretroviral drugs, antivirals with new mechanisms of action are continuously investigated. As such, this study aimed to reposition existing drugs as HIV-1 integrase inhibitors by screening the NIH Clinical Collection compound library comprising 727 compounds. Recombinant integrase was expressed in bacterial cells, purified by nickel affinity chromatography, and used to set up a Scintillation Proximity Assay (SPA). The SPA was subsequently amended to an automated system to allow for rapid screening of compounds. The complete compound library was successfully screened using the newly established automated SPA. Overall, only two compounds were identified as HIV-1 IN inhibitors: cefixime trihydrate and a previously identified HIV integrase inhibitor, epigallocatechin gallate. These compounds exerted IC50 values < 10μM in the automated SPA. Cefixime trihydrate was not toxic to mammalian cells (CC50 > 200μM) while no appreciable antiretroviral activity was observed in in vitro phenotypic inhibition assays (23% inhibition of viral replication), thus concluding that this compound was non-selective. By contrast, epigallocatechin gallate was toxic to mammalian cells at the evaluated ranges (CC50 = 23 + 1μM) and therefore could not be validated as an integrase inhibitor in in vitro phenotypic inhibition assays. Overall, this study resulted in the establishment of an automated SPA, the successful screening of 727 compounds, and the availability of a platform to expedite the future screening of potential HIV-1 integrase inhibitors.

No description available.

In the HIV viral integration procedure, 3’-processing of the viral DNA by the integrase enzyme is an essential first step which is followed by the integration of viral DNA into the host genome. In 3’-processing, the integrase cleaves the backbone of the DNA substrate on the 3’ end of a conserved CA dinucleotide motif and inserts a helix between the two DNA strands, forcing them apart (Hare, S., 2012). Our study confirms that the presence of a G-amino group is crucial for 3’-processing. Substituting inosine for G in the CA step removes this amino group and results in loss of enzyme activity. Further work showed that the presence of a terminal duplex segment is not required for 3’-processing. Additional substrate modifications are studied in order to evaluate the actual importance of the CA step.

Advances in the antiretroviral therapy (ART) have dramatically reduced the death rate from human immunodeficiency virus type 1 (HIV-1) induced acquired immune deficiency syndrome (AIDS). However, it is still necessary to develop anti-HIV-1 new drugs. In this study, two projects were conducted and may contribute to the new drug development. The first project is focused on characterizing the anti-HIV activity of a kinase inhibitor Kenpaullone (Ken). We found a cyclin dependent kinase (CDK) and glycogen synthase kinase-3β (GSK-3β) inhibitor named Ken can significantly inhibit HIV-1 replication. Mechanistic analysis by RT-PCR revealed that Ken inhibited HIV-1 replication by disrupting transcription possibly through CDK-dependent pathways. The second project is focused on understanding the association between HIV-1 integrase (IN) and dynein components. Our investigation indicated that HIV-1 IN is associated with DIC1 and DYNLT1. Further investigation this IN/dynein component association may help to reveal new anti-HIV targets. / May 2016