Optimizing HIV-1 protease production in Escherichia coli as fusion protein

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Piubelli Luciano

2011-06-01

Full Text Available Abstract Background Human immunodeficiency virus (HIV is the etiological agent in AIDS and related diseases. The aspartyl protease encoded by the 5' portion of the pol gene is responsible for proteolytic processing of the gag-pol polyprotein precursor to yield the mature capsid protein and the reverse transcriptase and integrase enzymes. The HIV protease (HIV-1Pr is considered an attractive target for designing inhibitors which could be used to tackle AIDS and therefore it is still the object of a number of investigations. Results A recombinant human immunodeficiency virus type 1 protease (HIV-1Pr was overexpressed in Escherichia coli cells as a fusion protein with bacterial periplasmic protein dithiol oxidase (DsbA or glutathione S-transferase (GST, also containing a six-histidine tag sequence. Protein expression was optimized by designing a suitable HIV-1Pr cDNA (for E. coli expression and to avoid autoproteolysis and by screening six different E. coli strains and five growth media. The best expression yields were achieved in E. coli BL21-Codon Plus(DE3-RIL host and in TB or M9 medium to which 1% (w/v glucose was added to minimize basal expression. Among the different parameters assayed, the presence of a buffer system (based on phosphate salts and a growth temperature of 37°C after adding IPTG played the main role in enhancing protease expression (up to 10 mg of chimeric DsbA:HIV-1Pr/L fermentation broth. GST:HIVPr was in part (50% produced as soluble protein while the overexpressed DsbA:HIV-1Pr chimeric protein largely accumulated in inclusion bodies as unprocessed fusion protein. A simple refolding procedure was developed on HiTrap Chelating column that yielded a refolded DsbA:HIV-1Pr with a > 80% recovery. Finally, enterokinase digestion of resolubilized DsbA:HIV-1Pr gave more than 2 mg of HIV-1Pr per liter of fermentation broth with a purity ≤ 80%, while PreScission protease cleavage of soluble GST:HIVPr yielded ~ 0.15 mg of pure HIV-1

Nucleolar protein trafficking in response to HIV-1 Tat: rewiring the nucleolus.

Science.gov (United States)

Jarboui, Mohamed Ali; Bidoia, Carlo; Woods, Elena; Roe, Barbara; Wynne, Kieran; Elia, Giuliano; Hall, William W; Gautier, Virginie W

2012-01-01

The trans-activator Tat protein is a viral regulatory protein essential for HIV-1 replication. Tat trafficks to the nucleoplasm and the nucleolus. The nucleolus, a highly dynamic and structured membrane-less sub-nuclear compartment, is the site of rRNA and ribosome biogenesis and is involved in numerous cellular functions including transcriptional regulation, cell cycle control and viral infection. Importantly, transient nucleolar trafficking of both Tat and HIV-1 viral transcripts are critical in HIV-1 replication, however, the role(s) of the nucleolus in HIV-1 replication remains unclear. To better understand how the interaction of Tat with the nucleolar machinery contributes to HIV-1 pathogenesis, we investigated the quantitative changes in the composition of the nucleolar proteome of Jurkat T-cells stably expressing HIV-1 Tat fused to a TAP tag. Using an organellar proteomic approach based on mass spectrometry, coupled with Stable Isotope Labelling in Cell culture (SILAC), we quantified 520 proteins, including 49 proteins showing significant changes in abundance in Jurkat T-cell nucleolus upon Tat expression. Numerous proteins exhibiting a fold change were well characterised Tat interactors and/or known to be critical for HIV-1 replication. This suggests that the spatial control and subcellular compartimentaliation of these cellular cofactors by Tat provide an additional layer of control for regulating cellular machinery involved in HIV-1 pathogenesis. Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. We present here the first differential profiling of the nucleolar proteome of T-cells expressing HIV-1 Tat. We discuss how these

Super-resolution imaging of ESCRT-proteins at HIV-1 assembly sites.

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Jens Prescher

2015-02-01

Full Text Available The cellular endosomal sorting complex required for transport (ESCRT machinery is involved in membrane budding processes, such as multivesicular biogenesis and cytokinesis. In HIV-infected cells, HIV-1 hijacks the ESCRT machinery to drive HIV release. Early in the HIV-1 assembly process, the ESCRT-I protein Tsg101 and the ESCRT-related protein ALIX are recruited to the assembly site. Further downstream, components such as the ESCRT-III proteins CHMP4 and CHMP2 form transient membrane associated lattices, which are involved in virus-host membrane fission. Although various geometries of ESCRT-III assemblies could be observed, the actual membrane constriction and fission mechanism is not fully understood. Fission might be driven from inside the HIV-1 budding neck by narrowing the membranes from the outside by larger lattices surrounding the neck, or from within the bud. Here, we use super-resolution fluorescence microscopy to elucidate the size and structure of the ESCRT components Tsg101, ALIX, CHMP4B and CHMP2A during HIV-1 budding below the diffraction limit. To avoid the deleterious effects of using fusion proteins attached to ESCRT components, we performed measurements on the endogenous protein or, in the case of CHMP4B, constructs modified with the small HA tag. Due to the transient nature of the ESCRT interactions, the fraction of HIV-1 assembly sites with colocalizing ESCRT complexes was low (1.5%-3.4%. All colocalizing ESCRT clusters exhibited closed, circular structures with an average size (full-width at half-maximum between 45 and 60 nm or a diameter (determined using a Ripley's L-function analysis of roughly 60 to 100 nm. The size distributions for colocalizing clusters were narrower than for non-colocalizing clusters, and significantly smaller than the HIV-1 bud. Hence, our results support a membrane scission process driven by ESCRT protein assemblies inside a confined structure, such as the bud neck, rather than by large lattices

Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins.

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Khan, Sheraz; Iqbal, Mazhar; Tariq, Muhammad; Baig, Shahid M; Abbas, Wasim

2018-01-01

HIV-1 latency allows the virus to persist until reactivation, in a transcriptionally silent form in its cellular reservoirs despite the presence of effective cART. Such viral persistence represents a major barrier to HIV eradication since treatment interruption leads to rebound plasma viremia. Polycomb group (PcG) proteins have recently got a considerable attention in regulating HIV-1 post-integration latency as they are involved in the repression of proviral gene expression through the methylation of histones. This epigenetic regulation plays an important role in the establishment and maintenance of HIV-1 latency. In fact, PcG proteins act in complexes and modulate the epigenetic signatures of integrated HIV-1 promoter. Key role played by PcG proteins in the molecular control of HIV-1 latency has led to hypothesize that PcG proteins may represent a valuable target for future HIV-1 therapy in purging HIV-1 reservoirs. In this regard, various small molecules have been synthesized or explored to specifically block the epigenetic activity of PcG. In this review, we will highlight the possible therapeutic approaches to achieve either a functional or sterilizing cure of HIV-1 infection with special focus on histone methylation by PcG proteins together with current and novel pharmacological approaches to reactivate HIV-1 from latency that could ultimately lead towards a better clearance of viral latent reservoirs.

Detection of HIV-1 and Human Proteins in Urinary Extracellular Vesicles from HIV+ Patients

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Samuel I. Anyanwu

2018-01-01

Full Text Available Background. Extracellular vesicles (EVs are membrane bound, secreted by cells, and detected in bodily fluids, including urine, and contain proteins, RNA, and DNA. Our goal was to identify HIV and human proteins (HPs in urinary EVs from HIV+ patients and compare them to HIV− samples. Methods. Urine samples were collected from HIV+ (n=35 and HIV− (n=12 individuals. EVs were isolated by ultrafiltration and characterized using transmission electron microscopy, tandem mass spectrometry (LC/MS/MS, and nanoparticle tracking analysis (NTA. Western blots confirmed the presence of HIV proteins. Gene ontology (GO analysis was performed using FunRich and HIV Human Interaction database (HHID. Results. EVs from urine were 30–400 nm in size. More EVs were in HIV+ patients, P<0.05, by NTA. HIV+ samples had 14,475 HPs using LC/MS/MS, while only 111 were in HIV−. HPs in the EVs were of exosomal origin. LC/MS/MS showed all HIV+ samples contained at least one HIV protein. GO analysis showed differences in proteins between HIV+ and HIV− samples and more than 50% of the published HPs in the HHID interacted with EV HIV proteins. Conclusion. Differences in the proteomic profile of EVs from HIV+ versus HIV− samples were found. HIV and HPs in EVs could be used to detect infection and/or diagnose HIV disease syndromes.

Quantitative analysis of differentially expressed saliva proteins in human immunodeficiency virus type 1 (HIV-1) infected individuals

International Nuclear Information System (INIS)

Zhang, Nawei; Zhang, Zhenyu; Feng, Shan; Wang, Qingtao; Malamud, Daniel; Deng, Haiteng

2013-01-01

Highlights: ► A high-throughput method for profiling and quantification of the differentially expressed proteins in saliva samples was developed. ► Identified that DMBT1, S100A7, S100A8, S100A9 and alpha defensin were up-regulated in saliva from HIV-1 seropositive patients. ► Established analytical strategies are translatable to the clinical setting. -- Abstract: In the present study, we have established a new methodology to analyze saliva proteins from HIV-1-seropositive patients before highly active antiretroviral therapy (HAART) and seronegative controls. A total of 593 and 601 proteins were identified in the pooled saliva samples from 5 HIV-1 subjects and 5 controls, respectively. Forty-one proteins were found to be differentially expressed. Bioinformatic analysis of differentially expressed salivary proteins showed an increase of antimicrobial proteins and decrease of protease inhibitors upon HIV-1 infection. To validate some of these differentially expressed proteins, a high-throughput quantitation method was established to determine concentrations of 10 salivary proteins in 40 individual saliva samples from 20 seropositive patients before HAART and 20 seronegative subjects. This method was based on limited protein separation within the zone of the stacking gel of the 1D SDS PAGE and using isotope-coded synthetic peptides as internal standards. The results demonstrated that a combination of protein profiling and targeted quantitation is an efficient method to identify and validate differentially expressed salivary proteins. Expression levels of members of the calcium-binding S100 protein family and deleted in malignant brain tumors 1 protein (DMBT1) were up-regulated while that of Mucin 5B was down-regulated in HIV-1 seropositive saliva samples, which may provide new perspectives for monitoring HIV-infection and understanding the mechanism of HIV-1 infectivity

Quantitative analysis of differentially expressed saliva proteins in human immunodeficiency virus type 1 (HIV-1) infected individuals

Energy Technology Data Exchange (ETDEWEB)

Zhang, Nawei; Zhang, Zhenyu [Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing (China); Feng, Shan [MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing (China); Wang, Qingtao [Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing (China); Malamud, Daniel [NYU College of Dentistry, 345 East 24th Street, New York, NY 10010 (United States); Deng, Haiteng, E-mail: dht@mail.tsinghua.edu.cn [MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing (China)

2013-04-24

Highlights: ► A high-throughput method for profiling and quantification of the differentially expressed proteins in saliva samples was developed. ► Identified that DMBT1, S100A7, S100A8, S100A9 and alpha defensin were up-regulated in saliva from HIV-1 seropositive patients. ► Established analytical strategies are translatable to the clinical setting. -- Abstract: In the present study, we have established a new methodology to analyze saliva proteins from HIV-1-seropositive patients before highly active antiretroviral therapy (HAART) and seronegative controls. A total of 593 and 601 proteins were identified in the pooled saliva samples from 5 HIV-1 subjects and 5 controls, respectively. Forty-one proteins were found to be differentially expressed. Bioinformatic analysis of differentially expressed salivary proteins showed an increase of antimicrobial proteins and decrease of protease inhibitors upon HIV-1 infection. To validate some of these differentially expressed proteins, a high-throughput quantitation method was established to determine concentrations of 10 salivary proteins in 40 individual saliva samples from 20 seropositive patients before HAART and 20 seronegative subjects. This method was based on limited protein separation within the zone of the stacking gel of the 1D SDS PAGE and using isotope-coded synthetic peptides as internal standards. The results demonstrated that a combination of protein profiling and targeted quantitation is an efficient method to identify and validate differentially expressed salivary proteins. Expression levels of members of the calcium-binding S100 protein family and deleted in malignant brain tumors 1 protein (DMBT1) were up-regulated while that of Mucin 5B was down-regulated in HIV-1 seropositive saliva samples, which may provide new perspectives for monitoring HIV-infection and understanding the mechanism of HIV-1 infectivity.

Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein

OpenAIRE

Wu, Tiyun; Heilman-Miller, Susan L.; Levin, Judith G.

2007-01-01

HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which is required for highly specific and efficient reverse transcription. Here, we demonstrate that local structure of acceptor RNA at a potential nucleation site, rather than overall thermodynamic stability, is a critical determinant for the minus-strand transfer step (annealing of acceptor RNA to (−) strong-stop DNA followed by reverse transcriptase (RT)-catalyzed DNA extension). In our system, destabilization of a stem-loop stru...

In vitro nuclear interactome of the HIV-1 Tat protein.

LENUS (Irish Health Repository)

Gautier, Virginie W

2009-01-01

BACKGROUND: One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86-101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry. RESULTS: Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied in silico analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture. CONCLUSION: We have completed the in vitro Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

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Boucher Charles AB

2010-07-01

Full Text Available Abstract Background The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics. Results Our analyses show that human proteins interacting with HIV form a densely connected and central sub-network within the total human protein interaction network. The evaluation of this sub-network for connectivity and centrality resulted in a set of proteins essential for the HIV life-cycle. Remarkably, we were able to associate proteins involved in RNA polymerase II transcription with hubs and proteasome formation with bottlenecks. Inferred network motifs show significant over-representation of positive and negative feedback patterns between virus and host. Strikingly, such patterns have never been reported in combined virus-host systems. Conclusions HIV infection results in a reprioritization of cellular processes reflected by an increase in the relative importance of transcriptional machinery and proteasome formation. We conclude that during the evolution of HIV, some patterns of interaction have been selected for resulting in a system where virus proteins preferably interact with central human proteins for direct control and with proteasomal proteins for indirect control over the cellular processes. Finally, the patterns described by network motifs illustrate how virus and host interact with one another.

Fibroblast growth factors 1 and 2 in cerebrospinal fluid are associated with HIV disease, methamphetamine use, and neurocognitive functioning

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Bharti AR

2016-04-01

Full Text Available Ajay R Bharti,1 Steven Paul Woods,2 Ronald J Ellis,3 Mariana Cherner,2 Debra Rosario,3 Michael Potter,3 Robert K Heaton,2 Ian P Everall,4 Eliezer Masliah,5 Igor Grant,2 Scott L Letendre1 On behalf of the Translational Methamphetamine AIDS Research Center Group 1Department of Medicine, 2Department of Psychiatry, 3Department of Neurosciences, University of California San Diego, San Diego, CA, USA; 4Department of Psychiatry, University of Melbourne, Victoria, Australia; 5Department of Pathology, University of Californa San Diego, San Diego, CA, USA Background: Human immunodeficiency virus (HIV and methamphetamine use commonly affect neurocognitive (NC functioning. We evaluated the relationships between NC functioning and two fibroblast growth factors (FGFs in volunteers who differed in HIV serostatus and methamphetamine dependence (MAD. Methods: A total of 100 volunteers were categorized into four groups based on HIV serostatus and MAD in the prior year. FGF-1 and FGF-2 were measured in cerebrospinal fluid by enzyme-linked immunosorbent assays along with two reference biomarkers (monocyte chemotactic protein [MCP]-1 and neopterin. Comprehensive NC testing was summarized by global and domain impairment ratings. Results: Sixty-three volunteers were HIV+ and 59 had a history of MAD. FGF-1, FGF-2, and both reference biomarkers differed by HIV and MAD status. For example, FGF-1 levels were lower in subjects who had either HIV or MAD than in HIV– and MAD– controls (P=0.003. Multivariable regression identified that global NC impairment was associated with an interaction between FGF-1 and FGF-2 (model R2=0.09, P=0.01: higher FGF-2 levels were only associated with neurocognitive impairment among subjects who had lower FGF-1 levels. Including other covariates in the model (including antidepressant use strengthened the model (model R2=0.18, P=0.004 but did not weaken the association with FGF-1 and FGF-2. Lower FGF-1 levels were associated with impairment

HIV-1 proteins dysregulate motivational processes and dopamine circuitry.

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Bertrand, Sarah J; Mactutus, Charles F; Harrod, Steven B; Moran, Landhing M; Booze, Rosemarie M

2018-05-18

Motivational alterations, such as apathy, in HIV-1+ individuals are associated with decreased performance on tasks involving frontal-subcortical circuitry. We used the HIV-1 transgenic (Tg) rat to assess effect of long-term HIV-1 protein exposure on motivated behavior using sucrose (1-30%, w/v) and cocaine (0.01-1.0 mg/kg/infusion) maintained responding with fixed-ratio (FR) and progressive-ratio (PR) schedules of reinforcement. For sucrose-reinforced responding, HIV-1 Tg rats displayed no change in EC 50 relative to controls, suggesting no change in sucrose reinforcement but had a downward shifted concentration-response curves, suggesting a decrease in response vigor. Cocaine-maintained responding was attenuated in HIV-1 Tg rats (FR1 0.33 mg/kg/infusion and PR 1.0 mg/kg/infusion). Dose-response tests (PR) revealed that HIV-1 Tg animals responded significantly less than F344 control rats and failed to earn significantly more infusions of cocaine as the unit dose increased. When choosing between cocaine and sucrose, control rats initially chose sucrose but with time shifted to a cocaine preference. In contrast, HIV-1 disrupted choice behaviors. DAT function was altered in the striatum of HIV-1 Tg rats; however, prior cocaine self-administration produced a unique effect on dopamine homeostasis in the HIV-1 Tg striatum. These findings of altered goal directed behaviors may determine neurobiological mechanisms of apathy in HIV-1+ patients.

Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

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Gomez Shawn M

2010-04-01

Full Text Available Abstract Background In the course of infection, viruses such as HIV-1 must enter a cell, travel to sites where they can hijack host machinery to transcribe their genes and translate their proteins, assemble, and then leave the cell again, all while evading the host immune system. Thus, successful infection depends on the pathogen's ability to manipulate the biological pathways and processes of the organism it infects. Interactions between HIV-encoded and human proteins provide one means by which HIV-1 can connect into cellular pathways to carry out these survival processes. Results We developed and applied a computational approach to predict interactions between HIV and human proteins based on structural similarity of 9 HIV-1 proteins to human proteins having known interactions. Using functional data from RNAi studies as a filter, we generated over 2000 interaction predictions between HIV proteins and 406 unique human proteins. Additional filtering based on Gene Ontology cellular component annotation reduced the number of predictions to 502 interactions involving 137 human proteins. We find numerous known interactions as well as novel interactions showing significant functional relevance based on supporting Gene Ontology and literature evidence. Conclusions Understanding the interplay between HIV-1 and its human host will help in understanding the viral lifecycle and the ways in which this virus is able to manipulate its host. The results shown here provide a potential set of interactions that are amenable to further experimental manipulation as well as potential targets for therapeutic intervention.

Human-Phosphate-Binding-Protein inhibits HIV-1 gene transcription and replication

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Candolfi Ermanno

2011-07-01

Full Text Available Abstract The Human Phosphate-Binding protein (HPBP is a serendipitously discovered lipoprotein that binds phosphate with high affinity. HPBP belongs to the DING protein family, involved in various biological processes like cell cycle regulation. We report that HPBP inhibits HIV-1 gene transcription and replication in T cell line, primary peripherical blood lymphocytes and primary macrophages. We show that HPBP is efficient in naïve and HIV-1 AZT-resistant strains. Our results revealed HPBP as a new and potent anti HIV molecule that inhibits transcription of the virus, which has not yet been targeted by HAART and therefore opens new strategies in the treatment of HIV infection.

Brain transcriptome-wide screen for HIV-1 Nef protein interaction partners reveals various membrane-associated proteins.

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Ellen C Kammula

Full Text Available HIV-1 Nef protein contributes essentially to the pathology of AIDS by a variety of protein-protein-interactions within the host cell. The versatile functionality of Nef is partially attributed to different conformational states and posttranslational modifications, such as myristoylation. Up to now, many interaction partners of Nef have been identified using classical yeast two-hybrid screens. Such screens rely on transcriptional activation of reporter genes in the nucleus to detect interactions. Thus, the identification of Nef interaction partners that are integral membrane proteins, membrane-associated proteins or other proteins that do not translocate into the nucleus is hampered. In the present study, a split-ubiquitin based yeast two-hybrid screen was used to identify novel membrane-localized interaction partners of Nef. More than 80% of the hereby identified interaction partners of Nef are transmembrane proteins. The identified hits are GPM6B, GPM6A, BAP31, TSPAN7, CYB5B, CD320/TCblR, VSIG4, PMEPA1, OCIAD1, ITGB1, CHN1, PH4, CLDN10, HSPA9, APR-3, PEBP1 and B3GNT, which are involved in diverse cellular processes like signaling, apoptosis, neurogenesis, cell adhesion and protein trafficking or quality control. For a subfraction of the hereby identified proteins we present data supporting their direct interaction with HIV-1 Nef. We discuss the results with respect to many phenotypes observed in HIV infected cells and patients. The identified Nef interaction partners may help to further elucidate the molecular basis of HIV-related diseases.

RRE-dependent HIV-1 Env RNA effects on Gag protein expression, assembly and release

International Nuclear Information System (INIS)

López, Claudia S.; Sloan, Rachel; Cylinder, Isabel; Kozak, Susan L.; Kabat, David; Barklis, Eric

2014-01-01

The HIV-1 Gag proteins are translated from the full-length HIV-1 viral RNA (vRNA), whereas the envelope (Env) protein is translated from incompletely spliced Env mRNAs. Nuclear export of vRNAs and Env mRNAs is mediated by the Rev accessory protein which binds to the rev-responsive element (RRE) present on these RNAs. Evidence has shown there is a direct or indirect interaction between the Gag protein, and the cytoplasmic tail (CT) of the Env protein. Our current work shows that env gene expression impacts HIV-1 Gag expression and function in two ways. At the protein level, full-length Env expression altered Gag protein expression, while Env CT-deletion proteins did not. At the RNA level, RRE-containing Env mRNA expression reduced Gag expression, processing, and virus particle release from cells. Our results support models in which Gag is influenced by the Env CT, and Env mRNAs compete with vRNAs for nuclear export. - Highlights: • At the protein level, full-length HIV-1 Env alters Gag protein expression. • HIV-1 Env RNA expression reduces Gag levels and virus release. • Env RNA effects on Gag are dependent on the RRE. • RRE-containing Env RNAs compete with vRNAs for nuclear export

Morphogenesis of the infectious HIV-1 virion

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Jun-Ichi eSakuragi

2011-12-01

Full Text Available The virion of HIV-1 is spherical and viral glycoprotein spikes (gp120, gp41 protrude from its envelope. The characteristic cone-shaped core exists within the virion, caging the ribonucleoprotein (RNP complex, which is comprised of viral RNA, nucleocapsid (NC and viral enzymes. The HIV-1 virion is budded and released from the infected cell as an immature donut-shaped particle. During or immediately after release, viral protease (PR is activated and subsequently processes the viral structural protein Gag. Through this maturation process, virions acquire infectivity, but its mechanism and transition of morphology largely remain unclear. Recent technological advances in experimental devices and techniques have made it possible to closely dissect the viral production site on the cell, the exterior – or even the interior – of an individual virion, and many new aspects on virion morphology and maturation. In this manuscript, I review the morphogenesis of HIV-1 virions. I focus on several studies, including some of our recent findings, which examined virion formation and/or maturation processes. The story of novel compound, which inhibits virion maturation, and the importance of maturation research are also discussed.

Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation

DEFF Research Database (Denmark)

Yusim, K.; Kesmir, Can; Gaschen, B.

2002-01-01

The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published, and compiled in the HIV Molecular Immunology Database. Maps of CTL epitopes on HIV-1 protein sequenc...

Boosting of HIV-1 neutralizing antibody responses by a distally related retroviral envelope protein.

Science.gov (United States)

Uchtenhagen, Hannes; Schiffner, Torben; Bowles, Emma; Heyndrickx, Leo; LaBranche, Celia; Applequist, Steven E; Jansson, Marianne; De Silva, Thushan; Back, Jaap Willem; Achour, Adnane; Scarlatti, Gabriella; Fomsgaard, Anders; Montefiori, David; Stewart-Jones, Guillaume; Spetz, Anna-Lena

2014-06-15

Our knowledge of the binding sites for neutralizing Abs (NAb) that recognize a broad range of HIV-1 strains (bNAb) has substantially increased in recent years. However, gaps remain in our understanding of how to focus B cell responses to vulnerable conserved sites within the HIV-1 envelope glycoprotein (Env). In this article, we report an immunization strategy composed of a trivalent HIV-1 (clade B envs) DNA prime, followed by a SIVmac239 gp140 Env protein boost that aimed to focus the immune response to structurally conserved parts of the HIV-1 and simian immunodeficiency virus (SIV) Envs. Heterologous NAb titers, primarily to tier 1 HIV-1 isolates, elicited during the trivalent HIV-1 env prime, were significantly increased by the SIVmac239 gp140 protein boost in rabbits. Epitope mapping of Ab-binding reactivity revealed preferential recognition of the C1, C2, V2, V3, and V5 regions. These results provide a proof of concept that a distally related retroviral SIV Env protein boost can increase pre-existing NAb responses against HIV-1. Copyright © 2014 by The American Association of Immunologists, Inc.

Solution Properties of Murine Leukemia Virus Gag Protein: Differences from HIV-1 Gag▿

Science.gov (United States)

Datta, Siddhartha A. K.; Zuo, Xiaobing; Clark, Patrick K.; Campbell, Stephen J.; Wang, Yun-Xing; Rein, Alan

2011-01-01

Immature retrovirus particles are assembled from the multidomain Gag protein. In these particles, the Gag proteins are arranged radially as elongated rods. We have previously characterized the properties of HIV-1 Gag in solution. In the absence of nucleic acid, HIV-1 Gag displays moderately weak interprotein interactions, existing in monomer-dimer equilibrium. Neutron scattering and hydrodynamic studies suggest that the protein is compact, and biochemical studies indicate that the two ends can approach close in three-dimensional space, implying the need for a significant conformational change during assembly. We now describe the properties of the Gag protein of Moloney murine leukemia virus (MLV), a gammaretrovirus. We found that this protein is very different from HIV-1 Gag: it has much weaker protein-protein interaction and is predominantly monomeric in solution. This has allowed us to study the protein by small-angle X-ray scattering and to build a low-resolution molecular envelope for the protein. We found that MLV Gag is extended in solution, with an axial ratio of ∼7, comparable to its dimensions in immature particles. Mutational analysis suggests that runs of prolines in its matrix and p12 domains and the highly charged stretch at the C terminus of its capsid domain all contribute to this extended conformation. These differences between MLV Gag and HIV-1 Gag and their implications for retroviral assembly are discussed. PMID:21917964

Possible roles of HIV-1 nucleocapsid protein in the specificity of proviral DNA synthesis and in its variability.

Science.gov (United States)

Lapadat-Tapolsky, M; Gabus, C; Rau, M; Darlix, J L

1997-05-02

Retroviral nucleocapsid (NC) protein is an integral part of the virion nucleocapsid where it coats the dimeric RNA genome. Due to its nucleic acid binding and annealing activities, NC protein directs the annealing of the tRNA primer to the primer binding site and greatly facilitates minus strand DNA elongation and transfer while protecting the nucleic acids against nuclease degradation. To understand the role of NCp7 in viral DNA synthesis, we examined the influence of NCp7 on self-primed versus primer-specific reverse transcription. The results show that HIV-1 NCp7 can extensively inhibit self-primed reverse transcription of viral and cellular RNAs while promoting primer-specific synthesis of proviral DNA. The role of NCp7 vis-a-vis the presence of mutations in the viral DNA during minus strand elongation was examined. NCp7 maximized the annealing between a cDNA(-) primer containing one to five consecutive errors and an RNA representing the 3' end of the genome. The ability of reverse transcriptase (RT) in the presence of NCp7 to subsequently extend the mutated primers depended upon the position of the mismatch within the primer:template complex. When the mutations were at the polymerisation site, primer extension by RT in the presence of NCp7 was very high, about 40% for one mismatch and 3% for five consecutive mismatches. Mutations within the DNA primer or at its 5' end had little effect on the extension of viral DNA by RT. Taken together these results indicate that NCp7 plays major roles in proviral DNA synthesis within the virion core due to its ability to promote prime-specific proviral DNA synthesis while concurrently inhibiting non-specific reverse transcription of viral and cellular RNAs. Moreover, the observation that NCp7 enhances the incorporation of mutations during minus strand DNA elongation favours the notion that NCp7 is a factor contributing to the high mutation rate of HIV-1.

Human Polycomb group EED protein negatively affects HIV-1 assembly and release

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Darlix Jean-Luc

2007-06-01

Full Text Available Abstract Background The human EED protein, a member of the superfamily of Polycomb group (PcG proteins with WD-40 repeats, has been found to interact with three HIV-1 components, namely the structural Gag matrix protein (MA, the integrase enzyme (IN and the Nef protein. The aim of the present study was to analyze the possible biological role of EED in HIV-1 replication, using the HIV-1-based vector HIV-Luc and EED protein expressed by DNA transfection of 293T cells. Results During the early phase of HIV-1 infection, a slight negative effect on virus infectivity occurred in EED-expressing cells, which appeared to be dependent on EED-MA interaction. At late times post infection, EED caused an important reduction of virus production, from 20- to 25-fold as determined by CAp24 immunoassay, to 10- to 80-fold based on genomic RNA levels, and this decrease was not due to a reduction of Gag protein synthesis. Coexpression of WTNef, or the non-N-myristoylated mutant NefG2A, restored virus yields to levels obtained in the absence of exogenous EED protein. This effect was not observed with mutant NefΔ57 mimicking the Nef core, or with the lipid raft-retargeted fusion protein LAT-Nef. LATAA-Nef, a mutant defective in the lipid raft addressing function, had the same anti-EED effect as WTNef. Cell fractionation and confocal imaging showed that, in the absence of Nef, EED mainly localized in membrane domains different from the lipid rafts. Upon co-expression with WTNef, NefG2A or LATAA-Nef, but not with NefΔ57 or LAT-Nef, EED was found to relocate into an insoluble fraction along with Nef protein. Electron microscopy of HIV-Luc producer cells overexpressing EED showed significant less virus budding at the cell surface compared to control cells, and ectopic assembly and clustering of nuclear pore complexes within the cytoplasm. Conclusion Our data suggested that EED exerted an antiviral activity at the late stage of HIV-1 replication, which included genomic

Mimicking protein-protein interactions through peptide-peptide interactions: HIV-1 gp120 and CXCR4

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Andrea eGross

2013-09-01

Full Text Available We have recently designed a soluble synthetic peptide that functionally mimics the HIV-1 coreceptor CXCR4, which is a chemokine receptor that belongs to the family of seven-transmembrane GPCRs. This CXCR4 mimetic peptide, termed CX4-M1, presents the three extracellular loops (ECLs of the receptor. In binding assays involving recombinant proteins, as well as in cellular infection assays, CX4-M1 was found to selectively recognize gp120 from HIV-1 strains that use CXCR4 for cell entry (X4 tropic HIV-1. Furthermore, anti-HIV-1 antibodies modulate this interaction in a molecular mechanism related to that of their impact on the gp120-CXCR4 interaction. We could now show that the selectivity of CX4-M1 pertains not only to gp120 from X4 tropic HIV-1, but also to synthetic peptides presenting the V3 loops of these gp120 proteins. The V3 loop is thought to be an essential part of the coreceptor binding site of gp120 that contacts the second ECL of the coreceptor. We were able to experimentally confirm this notion in binding assays using substitution analogs of CX4-M1 and the V3 loop peptides, respectively, as well as in cellular infection assays. These results indicate that interactions of the HIV-1 Env with coreceptors can be mimicked by synthetic peptides, which may be useful to explore these interactions at the molecular level in more detail.

Bovine leukemia virus nucleocapsid protein is an efficient nucleic acid chaperone

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Qualley, Dominic F.; Sokolove, Victoria L.; Ross, James L.

2015-01-01

Nucleocapsid proteins (NCs) direct the rearrangement of nucleic acids to form the most thermodynamically stable structure, and facilitate many steps throughout the life cycle of retroviruses. NCs bind strongly to nucleic acids (NAs) and promote NA aggregation by virtue of their cationic nature; they also destabilize the NA duplex via highly structured zinc-binding motifs. Thus, they are considered to be NA chaperones. While most retroviral NCs are structurally similar, differences are observed both within and between retroviral genera. In this work, we compare the NA binding and chaperone activity of bovine leukemia virus (BLV) NC to that of two other retroviral NCs: human immunodeficiency virus type 1 (HIV-1) NC, which is structurally similar to BLV NC but from a different retrovirus genus, and human T-cell leukemia virus type 1 (HTLV-1) NC, which possesses several key structural differences from BLV NC but is from the same genus. Our data show that BLV and HIV-1 NCs bind to NAs with stronger affinity in relation to HTLV-1 NC, and that they also accelerate the annealing of complementary stem-loop structures to a greater extent. Analysis of kinetic parameters derived from the annealing data suggests that while all three NCs stimulate annealing by a two-step mechanism as previously reported, the relative contributions of each step to the overall annealing equilibrium are conserved between BLV and HIV-1 NCs but are different for HTLV-1 NC. It is concluded that while BLV and HTLV-1 belong to the same genus of retroviruses, processes that rely on NC may not be directly comparable. - Highlights: • BLV NC binds strongly to DNA and RNA. • BLV NC promotes mini-TAR annealing as well as HIV-1 NC. • Annealing kinetics suggest a low degree of similarity between BLV NC and HTLV-1 NC

Bovine leukemia virus nucleocapsid protein is an efficient nucleic acid chaperone

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Qualley, Dominic F., E-mail: dqualley@berry.edu; Sokolove, Victoria L.; Ross, James L.

2015-03-13

Nucleocapsid proteins (NCs) direct the rearrangement of nucleic acids to form the most thermodynamically stable structure, and facilitate many steps throughout the life cycle of retroviruses. NCs bind strongly to nucleic acids (NAs) and promote NA aggregation by virtue of their cationic nature; they also destabilize the NA duplex via highly structured zinc-binding motifs. Thus, they are considered to be NA chaperones. While most retroviral NCs are structurally similar, differences are observed both within and between retroviral genera. In this work, we compare the NA binding and chaperone activity of bovine leukemia virus (BLV) NC to that of two other retroviral NCs: human immunodeficiency virus type 1 (HIV-1) NC, which is structurally similar to BLV NC but from a different retrovirus genus, and human T-cell leukemia virus type 1 (HTLV-1) NC, which possesses several key structural differences from BLV NC but is from the same genus. Our data show that BLV and HIV-1 NCs bind to NAs with stronger affinity in relation to HTLV-1 NC, and that they also accelerate the annealing of complementary stem-loop structures to a greater extent. Analysis of kinetic parameters derived from the annealing data suggests that while all three NCs stimulate annealing by a two-step mechanism as previously reported, the relative contributions of each step to the overall annealing equilibrium are conserved between BLV and HIV-1 NCs but are different for HTLV-1 NC. It is concluded that while BLV and HTLV-1 belong to the same genus of retroviruses, processes that rely on NC may not be directly comparable. - Highlights: • BLV NC binds strongly to DNA and RNA. • BLV NC promotes mini-TAR annealing as well as HIV-1 NC. • Annealing kinetics suggest a low degree of similarity between BLV NC and HTLV-1 NC.

Proteomic Profiling of a Primary CD4+ T Cell Model of HIV-1 Latency Identifies Proteins Whose Differential Expression Correlates with Reactivation of Latent HIV-1.

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Saha, Jamaluddin Md; Liu, Hongbing; Hu, Pei-Wen; Nikolai, Bryan C; Wu, Hulin; Miao, Hongyu; Rice, Andrew P

2018-01-01

The latent HIV-1 reservoir of memory CD4 + T cells that persists during combination antiviral therapy prevents a cure of infection. Insight into mechanisms of latency and viral reactivation are essential for the rational design of strategies to reduce the latent reservoir. In this study, we quantified the levels of >2,600 proteins in the CCL19 primary CD4 + T cell model of HIV-1 latency. We profiled proteins under conditions that promote latent infection and after cells were treated with phorbol 12-myristate 13-acetate (PMA) + ionomycin, which is known to efficiently induce reactivation of latent HIV-1. In an analysis of cells from two healthy blood donors, we identified 61 proteins that were upregulated ≥2-fold, and 36 proteins that were downregulated ≥2-fold under conditions in which latent viruses were reactivated. These differentially expressed proteins are, therefore, candidates for cellular factors that regulate latency or viral reactivation. Two unexpected findings were obtained from the proteomic data: (1) the interactions among the majority of upregulated proteins are largely undetermined in published protein-protein interaction networks and (2) downregulated proteins are strongly associated with Gene Ontology terms related to mitochondrial protein synthesis. This proteomic data set provides a useful resource for future mechanistic studies of HIV-1 latency.

Rational design of highly potent HIV-1 fusion inhibitory proteins: Implication for developing antiviral therapeutics

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Ni Ling; Gao, George F.; Tien Po

2005-01-01

Recombinant protein containing one heptad-repeat 1 (HR1) segment and one HR2 segment of the HIV-1 gp41 (HR1-HR2) has been shown to fold into thermally stable six-helix bundle, representing the fusogenic core of gp41. In this study, we have used the fusogenic core as a scaffold to design HIV-1 fusion inhibitory proteins by linking another HR1 to the C terminus of HR1-HR2 (HR121) or additional HR2 to the N terminus of HR1-HR2 (HR212). Both recombinant proteins could be abundantly and solubly expressed and easily purified, exhibiting high stability and potent inhibitory activity on HIV-1 fusion with IC 50 values of 16.2 ± 2.8 and 2.8 ± 0.63 nM, respectively. These suggest that these rationally designed proteins can be further developed as novel anti-HIV-1 therapeutics

HIV-1 Tat protein induces glial cell autophagy through enhancement of BAG3 protein levels.

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Bruno, Anna Paola; De Simone, Francesca Isabella; Iorio, Vittoria; De Marco, Margot; Khalili, Kamel; Sariyer, Ilker Kudret; Capunzo, Mario; Nori, Stefania Lucia; Rosati, Alessandra

2014-01-01

BAG3 protein has been described as an anti-apoptotic and pro-autophagic factor in several neoplastic and normal cells. We previously demonstrated that BAG3 expression is elevated upon HIV-1 infection of glial and T lymphocyte cells. Among HIV-1 proteins, Tat is highly involved in regulating host cell response to viral infection. Therefore, we investigated the possible role of Tat protein in modulating BAG3 protein levels and the autophagic process itself. In this report, we show that transfection with Tat raises BAG3 levels in glioblastoma cells. Moreover, BAG3 silencing results in highly reducing Tat- induced levels of LC3-II and increasing the appearance of sub G0/G1 apoptotic cells, in keeping with the reported role of BAG3 in modulating the autophagy/apoptosis balance. These results demonstrate for the first time that Tat protein is able to stimulate autophagy through increasing BAG3 levels in human glial cells.

Selection of unadapted, pathogenic SHIVs encoding newly transmitted HIV-1 envelope proteins.

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Del Prete, Gregory Q; Ailers, Braiden; Moldt, Brian; Keele, Brandon F; Estes, Jacob D; Rodriguez, Anthony; Sampias, Marissa; Oswald, Kelli; Fast, Randy; Trubey, Charles M; Chertova, Elena; Smedley, Jeremy; LaBranche, Celia C; Montefiori, David C; Burton, Dennis R; Shaw, George M; Markowitz, Marty; Piatak, Michael; KewalRamani, Vineet N; Bieniasz, Paul D; Lifson, Jeffrey D; Hatziioannou, Theodora

2014-09-10

Infection of macaques with chimeric viruses based on SIVMAC but expressing the HIV-1 envelope (Env) glycoproteins (SHIVs) remains the most powerful model for evaluating prevention and therapeutic strategies against AIDS. Unfortunately, only a few SHIVs are currently available. Furthermore, their generation has required extensive adaptation of the HIV-1 Env sequences in macaques so they may not accurately represent HIV-1 Env proteins circulating in humans, potentially limiting their translational utility. We developed a strategy for generating large numbers of SHIV constructs expressing Env proteins from newly transmitted HIV-1 strains. By inoculating macaques with cocktails of multiple SHIV variants, we selected SHIVs that can replicate and cause AIDS-like disease in immunologically intact rhesus macaques without requiring animal-to-animal passage. One of these SHIVs could be transmitted mucosally. We demonstrate the utility of the SHIVs generated by this method for evaluating neutralizing antibody administration as a protection against mucosal SHIV challenge. Copyright © 2014 Elsevier Inc. All rights reserved.

The Natural Killer Cell Cytotoxic Function Is Modulated by HIV-1 Accessory Proteins

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Edward Barker

2011-07-01

Full Text Available Natural killer (NK cells’ major role in the control of viruses is to eliminate established infected cells. The capacity of NK cells to kill virus-infected cells is dependent on the interactions between ligands on the infected cell and receptors on the NK cell surface. Because of the importance of ligand-receptor interactions in modulating the NK cell cytotoxic response, HIV has developed strategies to regulate various NK cell ligands making the infected cell surprisingly refractory to NK cell lysis. This is perplexing because the HIV-1 accessory protein Vpr induces expression of ligands for the NK cell activating receptor, NKG2D. In addition, the accessory protein Nef removes the inhibitory ligands HLA-A and -B. The reason for the ineffective killing by NK cells despite the strong potential to eliminate infected cells is due to HIV-1 Vpu’s ability to down modulate the co-activation ligand, NTB-A, from the cell surface. Down modulation of NTB-A prevents efficient NK cell degranulation. This review will focus on the mechanisms through which the HIV-1 accessory proteins modulate their respective ligands, and its implication for NK cell killing of HIV-infected cells.

A vaccine formulation combining rhoptry proteins NcROP40 and NcROP2 improves pup survival in a pregnant mouse model of neosporosis.

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Pastor-Fernández, Iván; Arranz-Solís, David; Regidor-Cerrillo, Javier; Álvarez-García, Gema; Hemphill, Andrew; García-Culebras, Alicia; Cuevas-Martín, Carmen; Ortega-Mora, Luis M

2015-01-30

Currently there are no effective vaccines for the control of bovine neosporosis. During the last years several subunit vaccines based on immunodominant antigens and other proteins involved in adhesion, invasion and intracellular proliferation of Neospora caninum have been evaluated as targets for vaccine development in experimental mouse infection models. Among them, the rhoptry antigen NcROP2 and the immunodominant NcGRA7 protein have been assessed with varying results. Recent studies have shown that another rhoptry component, NcROP40, and NcNTPase, a putative dense granule antigen, exhibit higher expression levels in tachyzoites of virulent N. caninum isolates, suggesting that these could be potential vaccine candidates to limit the effects of infection. In the present work, the safety and efficacy of these recombinant antigens formulated in Quil-A adjuvant as monovalent vaccines or pair-wise combinations (rNcROP40+rNcROP2 and rNcGRA7+rNcNTPase) were evaluated in a pregnant mouse model of neosporosis. All the vaccine formulations elicited a specific immune response against their respective native proteins after immunization. Mice vaccinated with rNcROP40 and rNcROP2 alone or in combination produced the highest levels of IFN-γ and exhibited low parasite burdens and low IgG antibody levels after the challenge. In addition, most of the vaccine formulations were able to increase the median survival time in the offspring. However, pup survival only ensued in the groups vaccinated with rNcROP40+rNcROP2 (16.2%) and rNcROP2 (6.3%). Interestingly, vertical transmission was not observed in those survivor pups immunized with rNcROP40+rNcROP2, as shown by PCR analyses. These results show a partial protection against N. caninum infection after vaccination with rNcROP40+rNcROP2, suggesting a synergistic effect of the two recombinant rhoptry antigens. Copyright © 2014 Elsevier B.V. All rights reserved.

Retrovirus-specific differences in matrix and nucleocapsid protein-nucleic acid interactions: implications for genomic RNA packaging.

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Sun, Meng; Grigsby, Iwen F; Gorelick, Robert J; Mansky, Louis M; Musier-Forsyth, Karin

2014-01-01

Retroviral RNA encapsidation involves a recognition event between genomic RNA (gRNA) and one or more domains in Gag. In HIV-1, the nucleocapsid (NC) domain is involved in gRNA packaging and displays robust nucleic acid (NA) binding and chaperone functions. In comparison, NC of human T-cell leukemia virus type 1 (HTLV-1), a deltaretrovirus, displays weaker NA binding and chaperone activity. Mutation of conserved charged residues in the deltaretrovirus bovine leukemia virus (BLV) matrix (MA) and NC domains affects virus replication and gRNA packaging efficiency. Based on these observations, we hypothesized that the MA domain may generally contribute to NA binding and genome encapsidation in deltaretroviruses. Here, we examined the interaction between HTLV-2 and HIV-1 MA proteins and various NAs in vitro. HTLV-2 MA displays higher NA binding affinity and better chaperone activity than HIV-1 MA. HTLV-2 MA also binds NAs with higher affinity than HTLV-2 NC and displays more robust chaperone function. Mutation of two basic residues in HTLV-2 MA α-helix II, previously implicated in BLV gRNA packaging, reduces NA binding affinity. HTLV-2 MA binds with high affinity and specificity to RNA derived from the putative packaging signal of HTLV-2 relative to nonspecific NA. Furthermore, an HIV-1 MA triple mutant designed to mimic the basic character of HTLV-2 MA α-helix II dramatically improves binding affinity and chaperone activity of HIV-1 MA in vitro and restores RNA packaging to a ΔNC HIV-1 variant in cell-based assays. Taken together, these results are consistent with a role for deltaretrovirus MA proteins in viral RNA packaging.

Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system.

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Cândida F Pereira

Full Text Available Due to its small size and versatility, the biarsenical-tetracysteine system is an attractive way to label viral proteins for live cell imaging. This study describes the genetic labeling of the human immunodeficiency virus type 1 (HIV-1 structural proteins (matrix, capsid and nucleocapsid, enzymes (protease, reverse transcriptase, RNAse H and integrase and envelope glycoprotein 120 with a tetracysteine tag in the context of a full-length virus. We measure the impact of these modifications on the natural virus infection and, most importantly, present the first infectious HIV-1 construct containing a fluorescently-labeled nucleocapsid protein. Furthermore, due to the high background levels normally associated with the labeling of tetracysteine-tagged proteins we have also optimized a metabolic labeling system that produces infectious virus containing the natural envelope glycoproteins and specifically labeled tetracysteine-tagged proteins that can easily be detected after virus infection of T-lymphocytes. This approach can be adapted to other viral systems for the visualization of the interplay between virus and host cell during infection.

Role of protein disulfide isomerase and other thiol-reactive proteins in HIV-1 envelope protein-mediated fusion

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Ou Wu; Silver, Jonathan

2006-01-01

Cell-surface protein disulfide isomerase (PDI) has been proposed to promote disulfide bond rearrangements in HIV-1 envelope protein (Env) that accompany Env-mediated fusion. We evaluated the role of PDI in ways that have not been previously tested by downregulating PDI with siRNA and by overexpressing wild-type or variant forms of PDI in transiently and stably transfected cells. These manipulations, as well as treatment with anti-PDI antibodies, had only small effects on infection or cell fusion mediated by NL4-3 or AD8 strains of HIV-1. However, the cell-surface thiol-reactive reagent 5, 5'-dithiobis(2-nitrobenzoic acid) (DTNB) had a much stronger inhibitory effect in our system, suggesting that cell-surface thiol-containing molecules other than PDI, acting alone or in concert, have a greater effect than PDI on HIV-1 Env-mediated fusion. We evaluated one such candidate, thioredoxin, a PDI family member reported to reduce a labile disulfide bond in CD4. We found that the ability of thioredoxin to reduce the disulfide bond in CD4 is enhanced in the presence of HIV-1 Env gp120 and that thioredoxin also reduces disulfide bonds in gp120 directly in the absence of CD4. We discuss the implications of these observations for identification of molecules involved in disulfide rearrangements in Env during fusion

Virus-producing cells determine the host protein profiles of HIV-1 virion cores

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2012-01-01

Background Upon HIV entry into target cells, viral cores are released and rearranged into reverse transcription complexes (RTCs), which support reverse transcription and also protect and transport viral cDNA to the site of integration. RTCs are composed of viral and cellular proteins that originate from both target and producer cells, the latter entering the target cell within the viral core. However, the proteome of HIV-1 viral cores in the context of the type of producer cells has not yet been characterized. Results We examined the proteomic profiles of the cores purified from HIV-1 NL4-3 virions assembled in Sup-T1 cells (T lymphocytes), PMA and vitamin D3 activated THP1 (model of macrophages, mMΦ), and non-activated THP1 cells (model of monocytes, mMN) and assessed potential involvement of identified proteins in the early stages of infection using gene ontology information and data from genome-wide screens on proteins important for HIV-1 replication. We identified 202 cellular proteins incorporated in the viral cores (T cells: 125, mMΦ: 110, mMN: 90) with the overlap between these sets limited to 42 proteins. The groups of RNA binding (29), DNA binding (17), cytoskeleton (15), cytoskeleton regulation (21), chaperone (18), vesicular trafficking-associated (12) and ubiquitin-proteasome pathway-associated proteins (9) were most numerous. Cores of the virions from SupT1 cells contained twice as many RNA binding proteins as cores of THP1-derived virus, whereas cores of virions from mMΦ and mMN were enriched in components of cytoskeleton and vesicular transport machinery, most probably due to differences in virion assembly pathways between these cells. Spectra of chaperones, cytoskeletal proteins and ubiquitin-proteasome pathway components were similar between viral cores from different cell types, whereas DNA-binding and especially RNA-binding proteins were highly diverse. Western blot analysis showed that within the group of overlapping proteins, the level of

Molecular cloning and characterization of NcROP2Fam-1, a member of the ROP2 family of rhoptry proteins in Neospora caninum that is targeted by antibodies neutralizing host cell invasion in vitro.

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Alaeddine, Ferial; Hemphill, Andrew; Debache, Karim; Guionaud, Christophe

2013-07-01

Recent publications demonstrated that a fragment of a Neospora caninum ROP2 family member antigen represents a promising vaccine candidate. We here report on the cloning of the cDNA encoding this protein, N. caninum ROP2 family member 1 (NcROP2Fam-1), its molecular characterization and localization. The protein possesses the hallmarks of ROP2 family members and is apparently devoid of catalytic activity. NcROP2Fam-1 is synthesized as a pre-pro-protein that is matured to 2 proteins of 49 and 55 kDa that localize to rhoptry bulbs. Upon invasion the protein is associated with the nascent parasitophorous vacuole membrane (PVM), evacuoles surrounding the host cell nucleus and, in some instances, the surface of intracellular parasites. Staining was also observed within the cyst wall of 'cysts' produced in vitro. Interestingly, NcROP2Fam-1 was also detected on the surface of extracellular parasites entering the host cells and antibodies directed against NcROP2Fam-1-specific peptides partially neutralized invasion in vitro. We conclude that, in spite of the general belief that ROP2 family proteins are intracellular antigens, NcROP2Fam-1 can also be considered as an extracellular antigen, a property that should be taken into account in further experiments employing ROP2 family proteins as vaccines.

The connection domain in reverse transcriptase facilitates the in vivo annealing of tRNALys3 to HIV-1 genomic RNA

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Niu Meijuan

2004-10-01

Full Text Available Abstract The primer tRNA for reverse transcription in HIV-1, tRNALys3, is selectively packaged into the virus during its assembly, and annealed to the viral genomic RNA. The ribonucleoprotein complex that is involved in the packaging and annealing of tRNALys into HIV-1 consists of Gag, GagPol, tRNALys, lysyl-tRNA synthetase (LysRS, and viral genomic RNA. Gag targets tRNALys for viral packaging through Gag's interaction with LysRS, a tRNALys-binding protein, while reverse transcriptase (RT sequences within GagPol (the thumb domain bind to tRNALys. The further annealing of tRNALys3 to viral RNA requires nucleocapsid (NC sequences in Gag, but not the NC sequences GagPol. In this report, we further show that while the RT connection domain in GagPol is not required for tRNALys3 packaging into the virus, it is required for tRNALys3 annealing to the viral RNA genome.

Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer

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Godet, Julien; Kenfack, Cyril; Przybilla, Frédéric; Richert, Ludovic; Duportail, Guy; Mély, Yves

2013-01-01

The HIV-1 nucleocapsid protein (NCp7) is a nucleic acid chaperone required during reverse transcription. During the first strand transfer, NCp7 is thought to destabilize cTAR, the (−)DNA copy of the TAR RNA hairpin, and subsequently direct the TAR/cTAR annealing through the zipping of their destabilized stem ends. To further characterize the destabilizing activity of NCp7, we locally probe the structure and dynamics of cTAR by steady-state and time resolved fluorescence spectroscopy. NC(11–55), a truncated NCp7 version corresponding to its zinc-finger domain, was found to bind all over the sequence and to preferentially destabilize the penultimate double-stranded segment in the lower part of the cTAR stem. This destabilization is achieved through zinc-finger–dependent binding of NC to the G10 and G50 residues. Sequence comparison further revealed that C•A mismatches close to the two G residues were critical for fine tuning the stability of the lower part of the cTAR stem and conferring to G10 and G50 the appropriate mobility and accessibility for specific recognition by NC. Our data also highlight the necessary plasticity of NCp7 to adapt to the sequence and structure variability of cTAR to chaperone its annealing with TAR through a specific pathway. PMID:23511968

The Effects of the Recombinant CCR5 T4 Lysozyme Fusion Protein on HIV-1 Infection.

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Qingwen Jin

Full Text Available Insertion of T4 lysozyme (T4L into the GPCR successfully enhanced GPCR protein stability and solubilization. However, the biological functions of the recombinant GPCR protein have not been analyzed.We engineered the CCR5-T4L mutant and expressed and purified the soluble recombinant protein using an E.coli expression system. The antiviral effects of this recombinant protein in THP-1 cell lines, primary human macrophages, and PBMCs from different donors were investigated. We also explored the possible mechanisms underlying the observed antiviral effects.Our data showed the biphasic inhibitory and promotion effects of different concentrations of soluble recombinant CCR5-T4L protein on R5 tropic human immunodeficiency virus-1 (HIV-1 infection in THP-1 cell lines, human macrophages, and PBMCs from clinical isolates. We demonstrated that soluble recombinant CCR5-T4L acts as a HIV-1 co-receptor, interacts with wild type CCR5, down-regulates the surface CCR5 expression in human macrophages, and interacts with CCL5 to inhibit macrophage migration. Using binding assays, we further determined that recombinant CCR5-T4L and [125I]-CCL5 compete for the same binding site on wild type CCR5.Our results suggest that recombinant CCR5-T4L protein marginally promotes HIV-1 infection at low concentrations and markedly inhibits infection at higher concentrations. This recombinant protein may be helpful in the future development of anti-HIV-1 therapeutic agents.

HIV protein sequence hotspots for crosstalk with host hub proteins.

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Mahdi Sarmady

Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

Interferon-inducible protein 10 (IP-10) is associated with viremia of early HIV-1 infection in Korean patients.

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Lee, SoYong; Chung, Yoon-Seok; Yoon, Cheol-Hee; Shin, YoungHyun; Kim, SeungHyun; Choi, Byeong-Sun; Kim, Sung Soon

2015-05-01

Cytokines/chemokines play key roles in modulating disease progression in human immunodeficiency virus (HIV) infection. Although it is known that early HIV-1 infection is associated with increased production of proinflammatory cytokines, the relationship between cytokine levels and HIV-1 pathogenesis is not clear. The concentrations of 18 cytokines/chemokines in 30 HIV-1 negative and 208 HIV-1 positive plasma samples from Korean patients were measured by the Luminex system. Early HIV-1 infection was classified according to the Fiebig stage (FS) based on the characteristics of the patients infected with HIV-1. Concentrations of interleukin-12 (IL-12), interferon-inducible protein-10 (IP-10), macrophage inflammatory protein-1α (MIP-1α) and regulated upon activation, normal T cells expressed and secreted (RANTES) were increased significantly during the early stage of HIV-1 infection (FS II-IV) compared with the HIV-1-negative group. Of these cytokines, an elevated level of IP-10 was the only factor to be correlated positively with a higher viral load during the early stages of HIV-1 infection (FS II-IV) in Koreans (R = 0.52, P IP-10 may be an indicator for HIV-1 viremia and associated closely with viral replication in patients with early HIV-1 infection. © 2015 Wiley Periodicals, Inc.

PrPC has nucleic acid chaperoning properties similar to the nucleocapsid protein of HIV-1.

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Derrington, Edmund; Gabus, Caroline; Leblanc, Pascal; Chnaidermann, Jonas; Grave, Linda; Dormont, Dominique; Swietnicki, Wieslaw; Morillas, Manuel; Marck, Daniel; Nandi, Pradip; Darlix, Jean-Luc

2002-01-01

The function of the cellular prion protein (PrPC) remains obscure. Studies suggest that PrPC functions in several processes including signal transduction and Cu2+ metabolism. PrPC has also been established to bind nucleic acids. Therefore we investigated the properties of PrPC as a putative nucleic acid chaperone. Surprisingly, PrPC possesses all the nucleic acid chaperoning properties previously specific to retroviral nucleocapsid proteins. PrPC appears to be a molecular mimic of NCP7, the nucleocapsid protein of HIV-1. Thus PrPC, like NCP7, chaperones the annealing of tRNA(Lys) to the HIV-1 primer binding site, the initial step of retrovirus replication. PrPC also chaperones the two DNA strand transfers required for production of a complete proviral DNA with LTRs. Concerning the functions of NCP7 during budding, PrPC also mimices NCP7 by dimerizing the HIV-1 genomic RNA. These data are unprecedented because, although many cellular proteins have been identified as nucleic acid chaperones, none have the properties of retroviral nucleocapsid proteins.

On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?▿

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Datta, Siddhartha A. K.; Temeselew, Lakew G.; Crist, Rachael M.; Soheilian, Ferri; Kamata, Anne; Mirro, Jane; Harvin, Demetria; Nagashima, Kunio; Cachau, Raul E.; Rein, Alan

2011-01-01

Expression of a retroviral protein, Gag, in mammalian cells is sufficient for assembly of immature virus-like particles (VLPs). VLP assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We have investigated the role of SP1, a spacer between CA and NC in HIV-1 Gag, in VLP assembly. Mutational analysis showed that even subtle changes in the first 4 residues of SP1 destroy the ability of Gag to assemble correctly, frequently leading to formation of tubes or other misassembled structures rather than proper VLPs. We also studied the conformation of the CA-SP1 junction region in solution, using both molecular dynamics simulations and circular dichroism. Consonant with nuclear magnetic resonance (NMR) studies from other laboratories, we found that SP1 is nearly unstructured in aqueous solution but undergoes a concerted change to an α-helical conformation when the polarity of the environment is reduced by addition of dimethyl sulfoxide (DMSO), trifluoroethanol, or ethanol. Remarkably, such a coil-to-helix transition is also recapitulated in an aqueous medium at high peptide concentrations. The exquisite sensitivity of SP1 to mutational changes and its ability to undergo a concentration-dependent structural transition raise the possibility that SP1 could act as a molecular switch to prime HIV-1 Gag for VLP assembly. We suggest that changes in the local environment of SP1 when Gag oligomerizes on nucleic acid might trigger this switch. PMID:21325421

Proteomic analysis of PBMCs: characterization of potential HIV-associated proteins

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Yin Lin

2010-03-01

Full Text Available Abstract Background The human immunodeficiency virus type 1 (HIV-1 pandemic has continued unabated for nearly 30 years. To better understand the influence of virus on host cells, we performed the differential proteome research of peripheral blood mononuclear cells (PBMCs from HIV-positive patients and healthy controls. Results 26 protein spots with more than 1.5-fold difference were detected in two dimensional electrophoresis (2DE gels. 12 unique up-regulated and one down-regulated proteins were identified in HIV-positive patients compared with healthy donors. The mRNA expression of 10 genes was analyzed by real time RT-PCR. It shows that the mRNA expression of talin-1, vinculin and coronin-1C were up-regulated in HIV positive patients and consistent with protein expression. Western blotting analysis confirmed the induction of fragments of vinculin, talin-1 and filamin-A in pooled and most part of individual HIV-positive clinical samples. Bioinformatic analysis showed that a wide host protein network was disrupted in HIV-positive patients. Conclusions Together, this work provided useful information to facilitate further investigation of the underlying mechanism of HIV and host cell protein interactions, and discovered novel potential biomarkers such as fragment of vinculin, filamin-A and talin-1 for anti-HIV research.

The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.

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Meyer, Austin G; Wilke, Claus O

2015-10-06

Protein structure acts as a general constraint on the evolution of viral proteins. One widely recognized structural constraint explaining evolutionary variation among sites is the relative solvent accessibility (RSA) of residues in the folded protein. In influenza virus, the distance from functional sites has been found to explain an additional portion of the evolutionary variation in the external antigenic proteins. However, to what extent RSA and distance from a reference site in the protein can be used more generally to explain protein adaptation in other viruses and in the different proteins of any given virus remains an open question. To address this question, we have carried out an analysis of the distribution and structural predictors of site-wise dN/dS in HIV-1. Our results indicate that the distribution of dN/dS in HIV follows a smooth gamma distribution, with no special enrichment or depletion of sites with dN/dS at or above one. The variation in dN/dS can be partially explained by RSA and distance from a reference site in the protein, but these structural constraints do not act uniformly among the different HIV-1 proteins. Structural constraints are highly predictive in just one of the three enzymes and one of three structural proteins in HIV-1. For these two proteins, the protease enzyme and the gp120 structural protein, structure explains between 30 and 40% of the variation in dN/dS. Finally, for the gp120 protein of the receptor-binding complex, we also find that glycosylation sites explain just 2% of the variation in dN/dS and do not explain gp120 evolution independently of either RSA or distance from the apical surface. © 2015 The Author(s).

Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

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Perry Evans

Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information.

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Yi, Hai-Cheng; You, Zhu-Hong; Huang, De-Shuang; Li, Xiao; Jiang, Tong-Hai; Li, Li-Ping

2018-06-01

The interactions between non-coding RNAs (ncRNAs) and proteins play an important role in many biological processes, and their biological functions are primarily achieved by binding with a variety of proteins. High-throughput biological techniques are used to identify protein molecules bound with specific ncRNA, but they are usually expensive and time consuming. Deep learning provides a powerful solution to computationally predict RNA-protein interactions. In this work, we propose the RPI-SAN model by using the deep-learning stacked auto-encoder network to mine the hidden high-level features from RNA and protein sequences and feed them into a random forest (RF) model to predict ncRNA binding proteins. Stacked assembling is further used to improve the accuracy of the proposed method. Four benchmark datasets, including RPI2241, RPI488, RPI1807, and NPInter v2.0, were employed for the unbiased evaluation of five established prediction tools: RPI-Pred, IPMiner, RPISeq-RF, lncPro, and RPI-SAN. The experimental results show that our RPI-SAN model achieves much better performance than other methods, with accuracies of 90.77%, 89.7%, 96.1%, and 99.33%, respectively. It is anticipated that RPI-SAN can be used as an effective computational tool for future biomedical researches and can accurately predict the potential ncRNA-protein interacted pairs, which provides reliable guidance for biological research. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

The mitochondrial translocator protein, TSPO, inhibits HIV-1 envelope glycoprotein biosynthesis via the endoplasmic reticulum-associated protein degradation pathway.

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Zhou, Tao; Dang, Ying; Zheng, Yong-Hui

2014-03-01

The HIV-1 Env glycoprotein is folded in the endoplasmic reticulum (ER), which is necessary for viral entry and replication. Currently, it is still unclear how this process is regulated. The glycoprotein folding in the ER is controlled by the ER-associated protein degradation (ERAD) pathway, which specifically targets misfolded proteins for degradation. Previously, we reported that HIV-1 replication is restricted in the human CD4(+) T cell line CEM.NKR (NKR). To understand this mechanism, we first analyzed cellular protein expression in NKR cells and discovered that levels of the mitochondrial translocator protein TSPO were upregulated by ∼64-fold. Notably, when NKR cells were treated with TSPO antagonist PK-11195, Ro5-4864, or diazepam, HIV restriction was completely disrupted, and TSPO knockdown by short hairpin RNAs (shRNAs) achieved a similar effect. We next analyzed viral protein expression, and, interestingly, we discovered that Env expression was specifically inhibited. Both TSPO knockdown and treatment with TSPO antagonist could restore Env expression in NKR cells. We further discovered that Env proteins were rapidly degraded and that kifunensine, an ERAD pathway inhibitor, could restore Env expression and viral replication, indicating that Env proteins were misfolded and degraded through the ERAD pathway in NKR cells. We also knocked out the TSPO gene in 293T cells using CRISPR/Cas9 (clustered, regularly interspaced, short palindromic repeat [CRISPR]/CRISPR-associated-9) technology and found that TSPO could similarly inhibit Env expression in these cells. Taken together, these results demonstrate that TSPO inhibits Env protein expression through the ERAD pathway and suggest that mitochondria play an important role in regulating the Env folding process. The HIV-1 Env glycoprotein is absolutely required for viral infection, and an understanding of its expression pathway in infected cells will identify new targets for antiretroviral therapies. Env proteins

Effects of Inner Nuclear Membrane Proteins SUN1/UNC-84A and SUN2/UNC-84B on the Early Steps of HIV-1 Infection.

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Schaller, Torsten; Bulli, Lorenzo; Pollpeter, Darja; Betancor, Gilberto; Kutzner, Juliane; Apolonia, Luis; Herold, Nikolas; Burk, Robin; Malim, Michael H

2017-10-01

Human immunodeficiency virus type 1 (HIV-1) infection of dividing and nondividing cells involves regulatory interactions with the nuclear pore complex (NPC), followed by translocation to the nucleus and preferential integration into genomic areas in proximity to the inner nuclear membrane (INM). To identify host proteins that may contribute to these processes, we performed an overexpression screen of known membrane-associated NE proteins. We found that the integral transmembrane proteins SUN1/UNC84A and SUN2/UNC84B are potent or modest inhibitors of HIV-1 infection, respectively, and that suppression corresponds to defects in the accumulation of viral cDNA in the nucleus. While laboratory strains (HIV-1 NL4.3 and HIV-1 IIIB ) are sensitive to SUN1-mediated inhibition, the transmitted founder viruses RHPA and ZM247 are largely resistant. Using chimeric viruses, we identified the HIV-1 capsid (CA) protein as a major determinant of sensitivity to SUN1, and in vitro -assembled capsid-nucleocapsid (CANC) nanotubes captured SUN1 and SUN2 from cell lysates. Finally, we generated SUN1 -/- and SUN2 -/- cells by using CRISPR/Cas9 and found that the loss of SUN1 had no effect on HIV-1 infectivity, whereas the loss of SUN2 had a modest suppressive effect. Taken together, these observations suggest that SUN1 and SUN2 may function redundantly to modulate postentry, nuclear-associated steps of HIV-1 infection. IMPORTANCE HIV-1 causes more than 1 million deaths per year. The life cycle of HIV-1 has been studied extensively, yet important steps that occur between viral capsid release into the cytoplasm and the expression of viral genes remain elusive. We propose here that the INM components SUN1 and SUN2, two members of the linker of nucleoskeleton and cytoskeleton (LINC) complex, may interact with incoming HIV-1 replication complexes and affect key steps of infection. While overexpression of these proteins reduces HIV-1 infection, disruption of the individual SUN2 and SUN1 genes

Use of Nonantiretroviral Medications That May Impact Neurocognition: Patterns and Predictors in a Large, Long-Term HIV Cohort Study.

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Radtke, Kendra K; Bacchetti, Peter; Anastos, Kathryn; Merenstein, Daniel; Crystal, Howard; Karim, Roksana; Weber, Kathleen M; Edmonds, Andrew; Sheth, Anandi N; Fischl, Margaret A; Vance, David; Greenblatt, Ruth M; Rubin, Leah H

2018-06-01

Neurocognitive impairment is a frequent and often disabling comorbidity of HIV infection. In addition to antiretroviral therapies, individuals with HIV infection may commonly use nonantiretroviral medications that are known to cause neurocognitive adverse effects (NC-AE). The contribution of NC-AE to neurocognitive impairment is rarely considered in the context of HIV and could explain part of the variability in neurocognitive performance among individuals with HIV. Women's Interagency HIV Study, a prospective, multisite, observational study of US women with and without HIV. After a literature review, 79 medications (excluding statins) with NC-AE were identified and reported by Women's Interagency HIV Study participants. We examined factors associated with self-reported use of these medications over a 10-year period. Generalized estimating equations for binary outcomes were used to assess sociodemographic, behavioral, and clinical characteristics associated with NC-AE medication use. Three thousand three hundred women (71% with HIV) and data from ∼42,000 visits were studied. HIV infection was associated with NC-AE medication use (odds ratio = 1.52; 95% confidence interval: 1.35 to 1.71). After adjustment for HIV infection status, other predictors of NC-AE medication use included having health insurance, elevated depressive symptoms, prior clinical AIDS, noninjection recreational drug use, and an annual household income of <$12,000 (Ps < 0.004). NC-AE medication use was less likely among women who drank 1-7 or 8-12 alcoholic drinks/week (vs. abstaining) (P < 0.04). HIV infection was associated with NC-AE medication use, which may influence determinations of HIV-associated neurocognitive impairment. Providers should consider the impact of NC-AE medications when evaluating patients with HIV and concurrent neurocognitive symptoms.

Temporal expression of HIV-1 envelope proteins in baculovirus-infected insect cells: Implications for glycosylation and CD4 binding

International Nuclear Information System (INIS)

Murphy, C.I.; Lennick, M.; Lehar, S.M.; Beltz, G.A.; Young, E.

1990-01-01

Three different human immunodeficiency virus type I (HIV-1) envelope derived recombinant proteins and the full length human CD4 polypeptide were expressed in Spodoptera frugiperda (Sf9) cells. DNA constructs encoding CD4, gp120, gp160, and gp160 delta were cloned into the baculovirus expression vector pVL941 or a derivative and used to generate recombinant viruses in a cotransfection with DNA from Autographa californica nuclear polyhedrosis virus (AcMNPV). Western blotting of cell extracts of the recombinant HIV-1 proteins showed that for each construct two major bands specifically reacted with anti-HIV-1 envelope antiserum. These bands corresponded to glycosylated and nonglycosylated versions of the HIV proteins as determined by 3H-mannose labeling and tunicamycin treatment of infected cells. A time course of HIV envelope expression revealed that at early times post-infection (24 hours) the proteins were fully glycosylated and soluble in nonionic detergents. However, at later times postinfection (48 hours), expression levels of recombinant protein reached a maximum but most of the increase was due to a rise in the level of the nonglycosylated species, which was largely insoluble in nonionic detergents. Thus, it appears that Sf9 cells cannot process large amounts of glycosylated recombinant proteins efficiently. As a measure of biological activity, the CD4 binding ability of both glycosylated and nonglycosylated recombinant HIV envelope proteins was tested in a coimmunoprecipitation assay. The results showed that CD4 and the glycosylated versions of recombinant gp120 or gp160 delta specifically associated with one another in this analysis. Nonglycosylated gp120 or gp160 delta proteins from tunicamycin-treated cultures did immunoprecipitate with anti-HIV-1 antiserum but did not interact with CD4

Isotype Diversification of IgG Antibodies to HIV Gag Proteins as a Therapeutic Vaccination Strategy for HIV Infection.

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French, Martyn A; Abudulai, Laila N; Fernandez, Sonia

2013-08-09

The development of vaccines to treat and prevent human immunodeficiency virus (HIV) infection has been hampered by an incomplete understanding of "protective" immune responses against HIV. Natural control of HIV-1 infection is associated with T-cell responses against HIV-1 Gag proteins, particularly CD8⁺ T-cell responses restricted by "protective" HLA-B alleles, but other immune responses also contribute to immune control. These immune responses appear to include IgG antibodies to HIV-1 Gag proteins, interferon-a-dependant natural killer (NK) cell responses and plasmacytoid dendritic cell (pDC) responses. Here, it is proposed that isotype diversification of IgG antibodies against HIV-1 Gag proteins, to include IgG2, as well as IgG3 and IgG1 antibodies, will broaden the function of the antibody response and facilitate accessory cell responses against HIV-1 by NK cells and pDCs. We suggest that this should be investigated as a vaccination strategy for HIV-1 infection.

Isotype Diversification of IgG Antibodies to HIV Gag Proteins as a Therapeutic Vaccination Strategy for HIV Infection

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Sonia Fernandez

2013-08-01

Full Text Available The development of vaccines to treat and prevent human immunodeficiency virus (HIV infection has been hampered by an incomplete understanding of “protective” immune responses against HIV. Natural control of HIV-1 infection is associated with T-cell responses against HIV-1 Gag proteins, particularly CD8+ T-cell responses restricted by “protective” HLA-B alleles, but other immune responses also contribute to immune control. These immune responses appear to include IgG antibodies to HIV-1 Gag proteins, interferon-a-dependant natural killer (NK cell responses and plasmacytoid dendritic cell (pDC responses. Here, it is proposed that isotype diversification of IgG antibodies against HIV-1 Gag proteins, to include IgG2, as well as IgG3 and IgG1 antibodies, will broaden the function of the antibody response and facilitate accessory cell responses against HIV-1 by NK cells and pDCs. We suggest that this should be investigated as a vaccination strategy for HIV-1 infection.

Cloning, Expression and Purification of the Recombinant HIV-1 Tat-Nef Fusion Protein in Prokaryotic Expression System

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Somayeh Kadkhodayan; Shiva Irani; Seyed Mehdi Sadat; Fatemeh Fotouhi; Azam Bolhassani

2016-01-01

Abstract Background: Nef is one of the HIV-1 critical proteins, because it is essential for viral replication and AIDS disease progression and induction of immune response against it can partially inhibit viral infection. Moreover, a domain of the HIV-1 Trans-Activator of Transcription (Tat, 48-60 aa) could act as a cell penetrating peptide (CPP). In current study, cloning and expression of Tat-Nef fusion protein was performed in E. coli for the first time. The protein expression was confi...

Antigenic properties of a transport-competent influenza HA/HIV Env chimeric protein

International Nuclear Information System (INIS)

Ye Ling; Sun Yuliang; Lin Jianguo; Bu Zhigao; Wu Qingyang; Jiang, Shibo; Steinhauer, David A.; Compans, Richard W.; Yang Chinglai

2006-01-01

The transmembrane subunit (gp41) of the HIV Env glycoprotein contains conserved neutralizing epitopes which are not well-exposed in wild-type HIV Env proteins. To enhance the exposure of these epitopes, a chimeric protein, HA/gp41, in which the gp41 of HIV-1 89.6 envelope protein was fused to the C-terminus of the HA1 subunit of the influenza HA protein, was constructed. Characterization of protein expression showed that the HA/gp41 chimeric proteins were expressed on cell surfaces and formed trimeric oligomers, as found in the HIV Env as well as influenza HA proteins. In addition, the HA/gp41 chimeric protein expressed on the cell surface can also be cleaved into 2 subunits by trypsin treatment, similar to the influenza HA. Moreover, the HA/gp41 chimeric protein was found to maintain a pre-fusion conformation. Interestingly, the HA/gp41 chimeric proteins on cell surfaces exhibited increased reactivity to monoclonal antibodies against the HIV Env gp41 subunit compared with the HIV-1 envelope protein, including the two broadly neutralizing monoclonal antibodies 2F5 and 4E10. Immunization of mice with a DNA vaccine expressing the HA/gp41 chimeric protein induced antibodies against the HIV gp41 protein and these antibodies exhibit neutralizing activity against infection by an HIV SF162 pseudovirus. These results demonstrate that the construction of such chimeric proteins can provide enhanced exposure of conserved epitopes in the HIV Env gp41 and may represent a novel vaccine design strategy for inducing broadly neutralizing antibodies against HIV

Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics

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Debnath, Utsab; Verma, Saroj; Jain, Surabhi; Katti, Setu B.; Prabhakar, Yenamandra S.

2013-07-01

CoMFA and CoMSIA based 3D-QSAR of HIV-1 RT wild and mutant (K103, Y181C, and Y188L) inhibitory activities of 4-benzyl/benzoyl pyridin-2-ones followed by protein informatics of corresponding non-nucleoside inhibitors' binding pockets from pdbs 2BAN, 3MED, 1JKH, and 2YNF were analysed to discover consensus features of the compounds for broad-spectrum activity. The CoMFA/CoMSIA models indicated that compounds with groups which lend steric-cum-electropositive fields in the vicinity of C5, hydrophobic field in the vicinity of C3 of pyridone region and steric field in aryl region produce broad-spectrum anti-HIV-1 RT activity. Also, a linker rendering electronegative field between pyridone and aryl moieties is common requirement for the activities. The protein informatics showed considerable alteration in residues 181 and 188 characteristics on mutation. Also, mutants' isoelectric points shifted in acidic direction. The study offered fresh avenues for broad-spectrum anti-HIV-1 agents through designing new molecules seeded with groups satisfying common molecular fields and concerns of mutating residues.

Improved innate and adaptive immunostimulation by genetically modified HIV-1 protein expressing NYVAC vectors.

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Esther D Quakkelaar

Full Text Available Attenuated poxviruses are safe and capable of expressing foreign antigens. Poxviruses are applied in veterinary vaccination and explored as candidate vaccines for humans. However, poxviruses express multiple genes encoding proteins that interfere with components of the innate and adaptive immune response. This manuscript describes two strategies aimed to improve the immunogenicity of the highly attenuated, host-range restricted poxvirus NYVAC: deletion of the viral gene encoding type-I interferon-binding protein and development of attenuated replication-competent NYVAC. We evaluated these newly generated NYVAC mutants, encoding HIV-1 env, gag, pol and nef, for their ability to stimulate HIV-specific CD8 T-cell responses in vitro from blood mononuclear cells of HIV-infected subjects. The new vectors were evaluated and compared to the parental NYVAC vector in dendritic cells (DCs, RNA expression arrays, HIV gag expression and cross-presentation assays in vitro. Deletion of type-I interferon-binding protein enhanced expression of interferon and interferon-induced genes in DCs, and increased maturation of infected DCs. Restoration of replication competence induced activation of pathways involving antigen processing and presentation. Also, replication-competent NYVAC showed increased Gag expression in infected cells, permitting enhanced cross-presentation to HIV-specific CD8 T cells and proliferation of HIV-specific memory CD8 T-cells in vitro. The recombinant NYVAC combining both modifications induced interferon-induced genes and genes involved in antigen processing and presentation, as well as increased Gag expression. This combined replication-competent NYVAC is a promising candidate for the next generation of HIV vaccines.

HIV-1 accessory proteins VPR and Vif modulate antiviral response by targeting IRF-3 for degradation

International Nuclear Information System (INIS)

Okumura, Atsushi; Alce, Tim; Lubyova, Barbora; Ezelle, Heather; Strebel, Klaus; Pitha, Paula M.

2008-01-01

The activation of IRF-3 during the early stages of viral infection is critical for the initiation of the antiviral response; however the activation of IRF-3 in HIV-1 infected cells has not yet been characterized. We demonstrate that the early steps of HIV-1 infection do not lead to the activation and nuclear translocation of IRF-3; instead, the relative levels of IRF-3 protein are decreased due to the ubiquitin-associated proteosome degradation. Addressing the molecular mechanism of this effect we show that the degradation is independent of HIV-1 replication and that virion-associated accessory proteins Vif and Vpr can independently degrade IRF-3. The null mutation of these two genes reduced the capacity of the HIV-1 virus to down modulate IRF-3 levels. The degradation was associated with Vif- and Vpr-mediated ubiquitination of IRF-3 and was independent of the activation of IRF-3. N-terminal lysine residues were shown to play a critical role in the Vif- and Vpr-mediated degradation of IRF-3. These data implicate Vif and Vpr in the disruption of the initial antiviral response and point to the need of HIV-1 to circumvent the antiviral response during the very early phase of replication

Novel host restriction factors implicated in HIV-1 replication.

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Ghimire, Dibya; Rai, Madhu; Gaur, Ritu

2018-04-01

Human immunodeficiency virus-1 (HIV-1) is known to interact with multiple host cellular proteins during its replication in the target cell. While many of these host cellular proteins facilitate viral replication, a number of them are reported to inhibit HIV-1 replication at various stages of its life cycle. These host cellular proteins, which are known as restriction factors, constitute an integral part of the host's first line of defence against the viral pathogen. Since the discovery of apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G) as an HIV-1 restriction factor, several human proteins have been identified that exhibit anti-HIV-1 restriction. While each restriction factor employs a distinct mechanism of inhibition, the HIV-1 virus has equally evolved complex counter strategies to neutralize their inhibitory effect. APOBEC3G, tetherin, sterile alpha motif and histidine-aspartate domain 1 (SAMHD1), and trim-5α are some of the best known HIV-1 restriction factors that have been studied in great detail. Recently, six novel restriction factors were discovered that exhibit significant antiviral activity: endoplasmic reticulum α1,2-mannosidase I (ERManI), translocator protein (TSPO), guanylate-binding protein 5 (GBP5), serine incorporator (SERINC3/5) and zinc-finger antiviral protein (ZAP). The focus of this review is to discuss the antiviral mechanism of action of these six restriction factors and provide insights into the probable counter-evasion strategies employed by the HIV-1 virus. The recent discovery of new restriction factors substantiates the complex host-pathogen interactions occurring during HIV-1 pathogenesis and makes it imperative that further investigations are conducted to elucidate the molecular basis of HIV-1 replication.

Regulatory CD4 T cells inhibit HIV-1 expression of other CD4 T cell subsets via interactions with cell surface regulatory proteins.

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Zhang, Mingce; Robinson, Tanya O; Duverger, Alexandra; Kutsch, Olaf; Heath, Sonya L; Cron, Randy Q

2018-03-01

During chronic HIV-1 infection, regulatory CD4 T cells (Tregs) frequently represent the largest subpopulation of CD4 T cell subsets, implying relative resistant to HIV-1. When HIV-1 infection of CD4 T cells was explored in vitro and ex vivo from patient samples, Tregs possessed lower levels of HIV-1 DNA and RNA in comparison with conventional effector and memory CD4 T cells. Moreover, Tregs suppressed HIV-1 expression in other CD4 T cells in an in vitro co-culture system. This suppression was mediated in part via multiple inhibitory surface proteins expressed on Tregs. Antibody blockade of CTLA-4, PD-1, and GARP on Tregs resulted in increased HIV-1 DNA integration and mRNA expression in neighboring CD4 T cells. Moreover, antibody blockade of Tregs inhibitory proteins resulted in increased HIV-1 LTR transcription in co-cultured CD4 T cells. Thus, Tregs inhibit HIV-1 infection of other CD4 T cell subsets via interactions with inhibitory cell surface proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Intracellular high mobility group B1 protein (HMGB1) represses HIV-1 LTR-directed transcription in a promoter- and cell-specific manner

International Nuclear Information System (INIS)

Naghavi, Mojgan H.; Nowak, Piotr; Andersson, Jan; Soennerborg, Anders; Yang Huan; Tracey, Kevin J.; Vahlne, Anders

2003-01-01

We investigated whether the high mobility group B 1 (HMGB1), an abundant nuclear protein in all mammalian cells, affects HIV-1 transcription. Intracellular expression of human HMGB1 repressed HIV-1 gene expression in epithelial cells. This inhibitory effect of HMGB1 was caused by repression of long terminal repeat (LTR)-mediated transcription. Other viral promoters/enhancers, including simian virus 40 or cytomegalovirus, were not inhibited by HMGB1. In addition, HMGB1 inhibition of HIV-1 subtype C expression was dependent on the number of NFκB sites in the LTR region. The inhibitory effect of HMGB1 on viral gene expression observed in HeLa cells was confirmed by an upregulation of viral replication in the presence of antisense HMGB1 in monocytic cells. In contrast to what was found in HeLa cells and monocytic cells, endogenous HMGB1 expression did not affect HIV-1 replication in unstimulated Jurkat cells. Thus, intracellular HMGB1 affects HIV-1 LTR-directed transcription in a promoter- and cell-specific manner

Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: implications for viral genomic RNA packaging.

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Webb, Joseph A; Jones, Christopher P; Parent, Leslie J; Rouzina, Ioulia; Musier-Forsyth, Karin

2013-08-01

Despite the vast excess of cellular RNAs, precisely two copies of viral genomic RNA (gRNA) are selectively packaged into new human immunodeficiency type 1 (HIV-1) particles via specific interactions between the HIV-1 Gag and the gRNA psi (ψ) packaging signal. Gag consists of the matrix (MA), capsid, nucleocapsid (NC), and p6 domains. Binding of the Gag NC domain to ψ is necessary for gRNA packaging, but the mechanism by which Gag selectively interacts with ψ is unclear. Here, we investigate the binding of NC and Gag variants to an RNA derived from ψ (Psi RNA), as well as to a non-ψ region (TARPolyA). Binding was measured as a function of salt to obtain the effective charge (Zeff) and nonelectrostatic (i.e., specific) component of binding, Kd(1M). Gag binds to Psi RNA with a dramatically reduced Kd(1M) and lower Zeff relative to TARPolyA. NC, GagΔMA, and a dimerization mutant of Gag bind TARPolyA with reduced Zeff relative to WT Gag. Mutations involving the NC zinc finger motifs of Gag or changes to the G-rich NC-binding regions of Psi RNA significantly reduce the nonelectrostatic component of binding, leading to an increase in Zeff. These results show that Gag interacts with gRNA using different binding modes; both the NC and MA domains are bound to RNA in the case of TARPolyA, whereas binding to Psi RNA involves only the NC domain. Taken together, these results suggest a novel mechanism for selective gRNA encapsidation.

Dissection of specific binding of HIV-1 Gag to the 'packaging signal' in viral RNA.

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Comas-Garcia, Mauricio; Datta, Siddhartha Ak; Baker, Laura; Varma, Rajat; Gudla, Prabhakar R; Rein, Alan

2017-07-20

Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis -acting RNA element called the 'packaging signal' (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength. These modifications all revealed high specificity for Ψ. This specificity is evidently obscured in physiological salt by non-specific, predominantly electrostatic interactions. This nonspecific activity was attenuated by mutations in the MA, CA, and NC domains, including CA mutations disrupting Gag-Gag interaction. We propose that gRNA is selectively packaged because binding to Ψ nucleates virion assembly with particular efficiency.

The HIV-1 Tat protein modulates CD4 expression in human T cells through the induction of miR-222.

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Orecchini, Elisa; Doria, Margherita; Michienzi, Alessandro; Giuliani, Erica; Vassena, Lia; Ciafrè, Silvia Anna; Farace, Maria Giulia; Galardi, Silvia

2014-01-01

Several cellular microRNAs show substantial changes in expression during HIV-1 infection and their active role in the viral life cycle is progressively emerging. In the present study, we found that HIV-1 infection of Jurkat T cells significantly induces the expression of miR-222. We show that this induction depends on HIV-1 Tat protein, which is able to increase the transcriptional activity of NFkB on miR-222 promoter. Moreover, we demonstrate that miR-222 directly targets CD4, a key receptor for HIV-1, thus reducing its expression. We propose that Tat, by inducing miR-222 expression, complements the CD4 downregulation activity exerted by other viral proteins (i.e., Nef, Vpu, and Env), and we suggest that this represents a novel mechanism through which HIV-1 efficiently represses CD4 expression in infected cells.

The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro

Directory of Open Access Journals (Sweden)

Gronenborn Angela M

2010-05-01

Full Text Available Abstract Background Lemay et al recently reported that the RNA binding protein HuR directly interacts with the ribonuclease H (RNase H domain of HIV-1 reverse transcriptase (RT and influences the efficiency of viral reverse transcription (Lemay et al., 2008, Retrovirology 5:47. HuR is a member of the embryonic lethal abnormal vision protein family and contains 3 RNA recognition motifs (RRMs that bind AU-rich elements (AREs. To define the structural determinants of the HuR-RT interaction and to elucidate the mechanism(s by which HuR influences HIV-1 reverse transcription activity in vitro, we cloned and purified full-length HuR as well as three additional protein constructs that contained the N-terminal and internal RRMs, the internal and C-terminal RRMs, or the C-terminal RRM only. Results All four HuR proteins were purified and characterized by biophysical methods. They are well structured and exist as monomers in solution. No direct protein-protein interaction between HuR and HIV-1 RT was detected using NMR titrations with 15N labeled HuR variants or the 15N labeled RNase H domain of HIV-1 RT. Furthermore, HuR did not significantly affect the kinetics of HIV-1 reverse transcription in vitro, even on RNA templates that contain AREs. Conclusions Our results suggest that HuR does not impact HIV-1 replication through a direct protein-protein interaction with the viral RT.

Incorporation of chimeric HIV-SIV-Env and modified HIV-Env proteins into HIV pseudovirions

International Nuclear Information System (INIS)

Devitt, Gerard; Emerson, Vanessa; Holtkotte, Denise; Pfeiffer, Tanya; Pisch, Thorsten; Bosch, Valerie

2007-01-01

Low level incorporation of the viral glycoprotein (Env) into human immunodeficiency virus (HIV) particles is a major drawback for vaccine strategies against HIV/AIDS in which HIV particles are used as immunogen. Within this study, we have examined two strategies aimed at achieving higher levels of Env incorporation into non-infectious pseudovirions (PVs). First, we have generated chimeric HIV/SIV Env proteins containing the truncated C-terminal tail region of simian immunodeficiency virus (SIV)mac239-Env767 stop , which mediates strongly increased incorporation of SIV-Env into SIV particles. In a second strategy, we have employed a truncated HIV-Env protein (Env-Tr752 N750K ) which we have previously demonstrated to be incorporated into HIV virions, generated in infected T-cells, to a higher level than that of Wt-HIV-Env. Although the chimeric HIV/SIV Env proteins were expressed at the cell surface and induced increased levels of cell-cell fusion in comparison to Wt-HIV-Env, they did not exhibit increased incorporation into either HIV-PVs or SIV-PVs. Only Env-Tr752 N750K exhibited significantly higher (threefold) levels of incorporation into HIV-PVs, an improvement, which, although not dramatic, is worthwhile for the large-scale preparation of non-infectious PVs for vaccine studies aimed at inducing Env humoral responses

A DEAD box protein facilitates HIV-1 replication as a cellular co-factor of Rev

International Nuclear Information System (INIS)

Fang Jianhua; Kubota, Satoshi; Yang Bin; Zhou Naiming; Zhang Hui; Godbout, Roseline; Pomerantz, Roger J.

2004-01-01

HIV-1 Rev escorts unspliced viral mRNAs out of the nucleus of infected cells, which allows formation of infectious HIV-1 virions. We have identified a putative DEAD box (Asp-Glu-Ala-Asp) RNA helicase, DDX1, as a cellular co-factor of Rev, through yeast and mammalian two-hybrid systems using the N-terminal motif of Rev as 'bait'. DDX1 is not a functional homolog of HIV-1 Rev, but down-regulation of DDX1 resulted in an alternative splicing pattern of Rev-responsive element (RRE)-containing mRNA, and attenuation of Gag p24 antigen production from HLfb rev(-) cells rescued by exogenous Rev. Co-transfection of a DDX1 expression vector with HIV-1 significantly increased viral production. DDX1 binding to Rev, as well as to the RRE, strongly suggest that DDX1 affects Rev function through the Rev-RRE axis. Moreover, down-regulation of DDX1 altered the steady state subcellular distribution of Rev, from nuclear/nucleolar to cytoplasmic dominance. These findings indicate that DDX1 is a critical cellular co-factor for Rev function, which maintains the proper subcellular distribution of this lentiviral regulatory protein. Therefore, alterations in DDX1-Rev interactions could induce HIV-1 persistence and targeting DDX1 may lead to rationally designed and novel anti-HIV-1 strategies and therapeutics

Current Peptide and Protein Candidates Challenging HIV Therapy beyond the Vaccine Era

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Koollawat Chupradit

2017-09-01

Full Text Available Human immunodeficiency virus (HIV is a causative agent of acquired immune deficiency syndrome (AIDS. Highly active antiretroviral therapy (HAART can slow down the replication of HIV-1, leading to an improvement in the survival of HIV-1-infected patients. However, drug toxicities and poor drug administration has led to the emergence of a drug-resistant strain. HIV-1 immunotherapy has been continuously developed, but antibody therapy and HIV vaccines take time to improve its efficiency and have limitations. HIV-1-specific chimeric antigen receptor (CAR-based immunotherapy founded on neutralizing antibodies is now being developed. In HIV-1 therapy, anti-HIV chimeric antigen receptors showed promising data in the suppression of HIV-1 replication; however, autologous transfusion is still a problem. This has led to the development of effective peptides and proteins for an alternative HIV-1 treatment. In this paper, we provide a comprehensive review of potent anti-HIV-1 peptides and proteins that reveal promising therapeutic activities. The inhibitory mechanisms of each therapeutic molecule in the different stages of the HIV-1 life cycle will be discussed herein.

The HIV-1 Tat protein modulates CD4 expression in human T cells through the induction of miR-222

Science.gov (United States)

Orecchini, Elisa; Doria, Margherita; Michienzi, Alessandro; Giuliani, Erica; Vassena, Lia; Ciafrè, Silvia Anna; Farace, Maria Giulia; Galardi, Silvia

2014-01-01

Several cellular microRNAs show substantial changes in expression during HIV-1 infection and their active role in the viral life cycle is progressively emerging. In the present study, we found that HIV-1 infection of Jurkat T cells significantly induces the expression of miR-222. We show that this induction depends on HIV-1 Tat protein, which is able to increase the transcriptional activity of NFkB on miR-222 promoter. Moreover, we demonstrate that miR-222 directly targets CD4, a key receptor for HIV-1, thus reducing its expression. We propose that Tat, by inducing miR-222 expression, complements the CD4 downregulation activity exerted by other viral proteins (i.e., Nef, Vpu, and Env), and we suggest that this represents a novel mechanism through which HIV-1 efficiently represses CD4 expression in infected cells. PMID:24717285

NC1 domain of type VII collagen binds to the beta3 chain of laminin 5 via a unique subdomain within the fibronectin-like repeats.

Science.gov (United States)

Chen, M; Marinkovich, M P; Jones, J C; O'Toole, E A; Li, Y Y; Woodley, D T

1999-02-01

Type VII collagen, the major component of anchoring fibrils, consists of a central collagenous triple-helical domain flanked by two noncollagenous, globular domains, NC1 and NC2. Approximately 50% of the molecular mass of the molecule is consumed by the NC1 domain. We previously demonstrated that NC1 binds to various extracellular matrix components including a complex of laminin 5 and laminin 6 (Chen et al, 1997a). In this study, we examined the interaction of NC1 with laminin 5 (a component of anchoring filaments). Both authentic and purified recombinant NC1 bound to human and rat laminin 5 as measured by enzyme-linked immunosorbant assay and by binding of 125I-radiolabeled NC1 to laminin 5-coated wells, but not to laminin 1 or albumin. NC1 bound predominantly to the beta3 chain of laminin 5, but also to the gamma2 chain when examined by a protein overlay assay. The binding of 125I-NC1 to laminin 5 was inhibited by a 50-fold excess of unlabeled NC1 or de-glycosylated NC1, as well as a polyclonal antibody to laminin 5 or a monoclonal antibody to the beta3 chain. In contrast, the NC1-laminin 5 interaction was not affected by a monoclonal antibody to the alpha3 chain. Using NC1 deletion mutant recombinant proteins, a 285 AA (residues 760-1045) subdomain of NC1 was identified as the binding site for laminin 5. IgG from an epidermolysis bullosa acquisita serum containing autoantibodies to epitopes within NC1 that colocalized with the laminin 5 binding site inhibited the binding of NC1 to laminin 5. Thus, perturbation of the NC1-laminin 5 interaction may contribute to the pathogenesis of epidermolysis bullosa acquisita.

HIV-1 uncoating: connection to nuclear entry and regulation by host proteins

Energy Technology Data Exchange (ETDEWEB)

Ambrose, Zandrea, E-mail: zaa4@pitt.edu [Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261 (United States); Aiken, Christopher [Department of Pathology, Microbiology and Immunology, Vanderbilt University, School of Medicine, Nashville, TN 37232 (United States)

2014-04-15

The RNA genome of human immunodeficiency virus type 1 (HIV-1) is enclosed by a capsid shell that dissociates within the cell in a multistep process known as uncoating, which influences completion of reverse transcription of the viral genome. Double-stranded viral DNA is imported into the nucleus for integration into the host genome, a hallmark of retroviral infection. Reverse transcription, nuclear entry, and integration are coordinated by a capsid uncoating process that is regulated by cellular proteins. Although uncoating is not well understood, recent studies have revealed insights into the process, particularly with respect to nuclear import pathways and protection of the viral genome from DNA sensors. Understanding uncoating will be valuable toward developing novel antiretroviral therapies for HIV-infected individuals.

HIV-1 vaccines

Science.gov (United States)

Excler, Jean-Louis; Robb, Merlin L; Kim, Jerome H

2014-01-01

The development of a safe and effective preventive HIV-1 vaccine remains a public health priority. Despite scientific difficulties and disappointing results, HIV-1 vaccine clinical development has, for the first time, established proof-of-concept efficacy against HIV-1 acquisition and identified vaccine-associated immune correlates of risk. The correlate of risk analysis showed that IgG antibodies against the gp120 V2 loop correlated with decreased risk of HIV infection, while Env-specific IgA directly correlated with increased risk. The development of vaccine strategies such as improved envelope proteins formulated with potent adjuvants and DNA and vectors expressing mosaics, or conserved sequences, capable of eliciting greater breadth and depth of potentially relevant immune responses including neutralizing and non-neutralizing antibodies, CD4+ and CD8+ cell-mediated immune responses, mucosal immune responses, and immunological memory, is now proceeding quickly. Additional human efficacy trials combined with other prevention modalities along with sustained funding and international collaboration remain key to bring an HIV-1 vaccine to licensure. PMID:24637946

Structural Study of a New HIV-1 Entry Inhibitor and Interaction with the HIV-1 Fusion Peptide in Dodecylphosphocholine Micelles.

Science.gov (United States)

Pérez, Yolanda; Gómara, Maria José; Yuste, Eloísa; Gómez-Gutierrez, Patricia; Pérez, Juan Jesús; Haro, Isabel

2017-08-25

Previous studies support the hypothesis that the envelope GB virus C (GBV-C) E1 protein interferes the HIV-1 entry and that a peptide, derived from the region 139-156 of this protein, has been defined as a novel HIV-1 entry inhibitor. In this work, we firstly focus on the characterization of the structural features of this peptide, which are determinant for its anti-HIV-1 activity and secondly, on the study of its interaction with the proposed viral target (i.e., the HIV-1 fusion peptide). We report the structure of the peptide determined by NMR spectroscopy in dodecylphosphocholine (DPC) micelles solved by using restrained molecular dynamics calculations. The acquisition of different NMR experiments in DPC micelles (i.e., peptide-peptide titration, diffusion NMR spectroscopy, and addition of paramagnetic relaxation agents) allows a proposal of an inhibition mechanism. We conclude that a 18-mer peptide from the non-pathogenic E1 GBV-C protein, with a helix-turn-helix structure inhibits HIV-1 by binding to the HIV-1 fusion peptide at the membrane level, thereby interfering with those domains in the HIV-1, which are critical for stabilizing the six-helix bundle formation in a membranous environment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformational preferences of a chimeric peptide HIV-1 immunogen from the C4-V3 domains of gp120 envelope protein of HIV-1 CAN0A based on solution NMR: comparison to a related immunogenic peptide from HIV-1 RF.

Science.gov (United States)

Vu, H M; de Lorimier, R; Moody, M A; Haynes, B F; Spicer, L D

1996-04-23

A critical problem to overcome on HIV vaccine design is the variability among HIV strains. One strategy to solve this problem is the construction of multicomponent immunogens reflective of common HIV motifs. Currently, it is not known if these motifs should be based primarily on amino acid sequence or higher-order structure of the viral proteins of a combination of the two. In this paper, we report NMR-derived solution conformations for a sympathetic peptide taken from the C4 and V3 domains of HIV-1 CAN0A gp120 envelope protein. This peptide, designated T1-SP10CAN0(A), is compared to a recently reported C4-V3 peptide. T1-SP10RF(A) from the HIV-1 RF strain [de Lorimier et al. (1994) Biochemistry 33, 2055-2062], in terms of conformational features and immune responses in mice [Haynes et al. (1995) AIDS Res. Hum. Retroviruses 11, 211-221]. The T1 segment of 16 amino acids from the gp120 C4 domain is identical in both peptides and exhibits nascent helical character. The SP10 region, taken from the gp120 V3 loop, differs from that of T1-SP10RF(A) in both sequence and conformations. A reverse turn is observed at the conserved GPGX sequence. The rest of the Sp10 domain is extended with the exception of the last three residues which show evidence for a helical arrangement. Modeling of the turn region of the T1-SP10CAN0(A) peptide shows exposure of a continuous apolar stretch of side chains similar to that reported in the crystal structure of a V3 peptide from HIV-1 MN complexed with a monoclonal antibody [Rini et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6325-6329]. this hydrophobic patch is interrupted by a charged Lys residue in the T1-SP10RF(A) peptide. This observation suggests that the HIV-1 CAN0A and HIV-1 RF C4-V3 peptides can induce widely different anti-HIV antibodies. consistent with immunogenic results.

ORF Alignment: NC_003888 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003888 gi|21219041 >1pv1A 14 282 20 256 6e-05 ... emb|CAE53384.1| hypothetical protein [Actinoplanes... teichomyceticus] emb|CAG15045.1| ... hypothetical protein [Actinoplanes teichomyce

ORF Alignment: NC_003306 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003306 gi|17938860 >1pv1A 14 282 20 256 6e-05 ... emb|CAE53384.1| hypothetical protein [Actinoplanes... teichomyceticus] emb|CAG15045.1| ... hypothetical protein [Actinoplanes teichomyce

ORF Alignment: NC_003064 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003064 gi|16119505 >1pv1A 14 282 20 256 6e-05 ... emb|CAE53384.1| hypothetical protein [Actinoplanes... teichomyceticus] emb|CAG15045.1| ... hypothetical protein [Actinoplanes teichomyce

Discovery of natural mouse serum derived HIV-1 entry inhibitor(s).

Science.gov (United States)

Wei, M; Chen, Y; Xi, J; Ru, S; Ji, M; Zhang, D; Fang, Q; Tang, B

Among rationally designed human immunodeficiency virus 1 (HIV-1) inhibitors, diverse natural factors have showed as potent anti-HIV activity in human blood. We have discovered that the boiled supernatant of healthy mouse serum could suppress HIV-1 entry, and exhibited reduced inhibitory activity after trypsin digestion. Further analysis demonstrated that only the fraction containing 10-25 K proteins could inhibit HIV-1 mediated cell-cell fusion. These results suggest that the 10-25 K protein(s) is novel natural HIV-1 entry inhibitor(s). Our findings provide important information about novel natural HIV entry inhibitors in mouse serum.

Systematic Protein-Protein Docking and Molecular Dynamics Studies of HIV-1 gp120 and CD4: Insights for New Drug Development

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M. Rizman-Idid

2011-12-01

Full Text Available Background and the purpose of the study: The interactions between HIV-1 gp120 and mutated CD4 proteins were investigated in order to identify a lead structure for therapy based on competitive blocking of the HIV binding receptor for human T-cells. Crystal structures of HIV gp120-CD4 complexes reveal a close interaction of the virus receptor with CD4 Phe43, which is embedded in a pocket of the virus protein.Methods: This study applies computer simulations to determine the best binding of amino acid 43 CD4 mutants to HIV gp120. Besides natural CD4, three mutants carrying alternate aromatic residues His, Trp and Tyr at position 43 were investigated. Several docking programs were applied on isolated proteins based on selected crystal structures of gp120-CD4 complexes, as well as a 5 ns molecular dynamics study on the protein complexes. The initial structures were minimized in Gromacs to avoid crystal packing effects, and then subjected to docking experiments using AutoDock4, FireDock, ClusPro and ZDock. In molecular dynamics, the Gibbs free binding energy was calculated for the gp120-CD4 complexes. The docking outputs were analyzed on energy within the respective docking software.Results and conclusion: Visualization and hydrogen bonding analysis were performed using the Swiss-PdbViewer. Strong binding to HIV gp120 can be achieved with an extended aromatic group (Trp. However, the sterical demand of the interaction affects the binding kinetics. In conclusion, a ligand for an efficient blocking of HIV gp120 should involve an extended but conformational flexible aromatic group, i.e. a biphenyl. A docking study on biphenylalanine-43 confirms this expectation

Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

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Elisabeth Humphris-Narayanan

Full Text Available Predicting which mutations proteins tolerate while maintaining their structure and function has important applications for modeling fundamental properties of proteins and their evolution; it also drives progress in protein design. Here we develop a computational model to predict the tolerated sequence space of HIV-1 protease reachable by single mutations. We assess the model by comparison to the observed variability in more than 50,000 HIV-1 protease sequences, one of the most comprehensive datasets on tolerated sequence space. We then extend the model to a second protein, reverse transcriptase. The model integrates multiple structural and functional constraints acting on a protein and uses ensembles of protein conformations. We find the model correctly captures a considerable fraction of protease and reverse-transcriptase mutational tolerance and shows comparable accuracy using either experimentally determined or computationally generated structural ensembles. Predictions of tolerated sequence space afforded by the model provide insights into stability-function tradeoffs in the emergence of resistance mutations and into strengths and limitations of the computational model.

Immunization of dogs with a canine herpesvirus vector expressing Neospora caninum surface protein, NcSRS2.

Science.gov (United States)

Nishikawa, Y; Ikeda, H; Fukumoto, S; Xuan, X; Nagasawa, H; Otsuka, H; Mikami, T

2000-10-01

In order to develop a vaccine against Neospora caninum in dogs, we constructed recombinant canine herpesvirus (CHV) expressing N. caninum surface protein, NcSRS2. Indirect immunofluorescence indicated that the antigenic structure of the recombinant NcSRS2 was similar to the authentic parasite protein. The dogs immunised with recombinant virus produced IgG antibody to N. caninum, and their sera recognised the parasite protein on Western blot. The dogs inoculated with recombinant virus showed no clinical symptoms and infectious CHV was not recovered from the dogs, suggesting that recombinant CHV expressing N. caninum proteins may lead to a vaccine against neosporosis in dogs.

Thermodynamic characterization of the peptide assembly inhibitor binding to HIV-1 capsid protein

Czech Academy of Sciences Publication Activity Database

Kožíšek, Milan; Durčák, Jindřich; Konvalinka, Jan

2013-01-01

Roč. 10, Suppl. 1 (2013), S37-S37 ISSN 1742-4690. [Frontiers of Retrovirology: Complex retorviruses, retroelements and their hosts. 16.09.2013-18.09.2013, Cambridge] R&D Projects: GA ČR GA13-19561S Institutional support: RVO:61388963 Keywords : HIV -1 capsid protein * CAI Subject RIV: EE - Microbiology, Virology http://www.retrovirology.com/content/10/S1/P108

Mapping the binding interface between an HIV-1 inhibiting intrabody and the viral protein Rev.

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Thomas Vercruysse

Full Text Available HIV-1 Rev is the key protein in the nucleocytoplasmic export and expression of the late viral mRNAs. An important aspect for its function is its ability to multimerize on these mRNAs. We have recently identified a llama single-domain antibody (Nb190 as the first inhibitor targeting the Rev multimerization function in cells. This nanobody is a potent intracellular antibody that efficiently inhibits HIV-1 viral production. In order to gain insight into the Nb190-Rev interaction interface, we performed mutational and docking studies to map the interface between the nanobody paratope and the Rev epitope. Alanine mutants of the hyper-variable domains of Nb190 and the Rev multimerization domains were evaluated in different assays measuring Nb190-Rev interaction or viral production. Seven residues within Nb190 and five Rev residues are demonstrated to be crucial for epitope recognition. These experimental data were used to perform docking experiments and map the Nb190-Rev structural interface. This Nb190-Rev interaction model can guide further studies of the Nb190 effect on HIV-1 Rev function and could serve as starting point for the rational development of smaller entities binding to the Nb190 epitope, aimed at interfering with protein-protein interactions of the Rev N-terminal domain.

Biochemistry and biophysics of HIV-1 gp41 - membrane interactions and implications for HIV-1 envelope protein mediated viral-cell fusion and fusion inhibitor design.

Science.gov (United States)

Cai, Lifeng; Gochin, Miriam; Liu, Keliang

2011-12-01

Human immunodeficiency virus type 1 (HIV-1), the pathogen of acquired immunodeficiency syndrome (AIDS), causes ~2 millions death every year and still defies an effective vaccine. HIV-1 infects host cells through envelope protein - mediated virus-cell fusion. The transmembrane subunit of envelope protein, gp41, is the molecular machinery which facilitates fusion. Its ectodomain contains several distinguishing functional domains, fusion peptide (FP), Nterminal heptad repeat (NHR), C-terminal heptad repeat (CHR) and membrane proximal extracellular region (MPER). During the fusion process, FP inserts into the host cell membrane, and an extended gp41 prehairpin conformation bridges the viral and cell membranes through MPER and FP respectively. Subsequent conformational change of the unstable prehairpin results in a coiled-coil 6-helix bundle (6HB) structure formed between NHR and CHR. The energetics of 6HB formation drives membrane apposition and fusion. Drugs targeting gp41 functional domains to prevent 6HB formation inhibit HIV-1 infection. T20 (enfuvirtide, Fuzeon) was approved by the US FDA in 2003 as the first fusion inhibitor. It is a 36-residue peptide from the gp41 CHR, and it inhibits 6HB formation by targeting NHR and lipids. Development of new fusion inhibitors, especially small molecule drugs, is encouraged to overcome the shortcomings of T20 as a peptide drug. Hydrophobic characteristics and membrane association are critical for gp41 function and mechanism of action. Research in gp41-membrane interactions, using peptides corresponding to specific functional domains, or constructs including several interactive domains, are reviewed here to get a better understanding of gp41 mediated virus-cell fusion that can inform or guide the design of new HIV-1 fusion inhibitors.

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002945 gi|31791180 >1ii8A 1 187 1 168 2e-14 ... ref|NP_853673.1| DNA REPLICATION A...D92865.1| ... DNA REPLICATION AND REPAIR PROTEIN RECF (SINGLE-STRAND ... DNA BINDING PROTEIN)

ORF Alignment: NC_004331 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004331 gi|23619306 >1wfiA 3 125 209 328 1e-34 ... ref|NP_705268.1| nuclear movement... protein, putative [Plasmodium falciparum 3D7] ... emb|CAD52505.1| nuclear movement protein, putativ

ORF Alignment: NC_003070 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003070 gi|15221381 >1bq00 2 77 15 90 4e-20 ... ref|NP_177004.1| gravity-responsive... protein / altered response to gravity protein ... (ARG1) [Arabidopsis thaliana] gb|AAD13758.1| Altere

ORF Alignment: NC_002696 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002696 gi|16124962 >1adn0 1 76 1 75 1e-17 ... ref|NP_419526.1| ada regulatory protein, internal deletion... [Caulobacter crescentus ... CB15] gb|AAK22694.1| ada regulatory protein, internal ... deletion... [Caulobacter crescentus CB15] pir||B87337 ada ... regulatory protein, internal deletion

The HIV-1 Vpu protein induces apoptosis in Drosophila via activation of JNK signaling.

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Christelle Marchal

Full Text Available The genome of the human immunodeficiency virus type 1 (HIV-1 encodes the canonical retroviral proteins, as well as additional accessory proteins that enhance the expression of viral genes, the infectivity of the virus and the production of virions. The accessory Viral Protein U (Vpu, in particular, enhances viral particle production, while also promoting apoptosis of HIV-infected human T lymphocytes. Some Vpu effects rely on its interaction with the ubiquitin-proteasome protein degradation system, but the mechanisms responsible for its pro-apoptotic effects in vivo are complex and remain largely to be elucidated.We took advantage of the Drosophila model to study the effects of Vpu activity in vivo. Expression of Vpu in the developing Drosophila wing provoked tissue loss due to caspase-dependent apoptosis. Moreover, Vpu induced expression of the pro-apoptotic gene reaper, known to down-regulate Inhibitor of Apoptosis Proteins (IAPs which are caspase-antagonizing E3 ubiquitin ligases. Indeed, Vpu also reduced accumulation of Drosophila IAP1 (DIAP1. Though our results demonstrate a physical interaction between Vpu and the proteasome-addressing SLIMB/β-TrCP protein, as in mammals, both SLIMB/βTrCP-dependent and -independent Vpu effects were observed in the Drosophila wing. Lastly, the pro-apoptotic effect of Vpu in this tissue was abrogated upon inactivation of the c-Jun N-terminal Kinase (JNK pathway. Our results in the fly thus provide the first functional evidence linking Vpu pro-apoptotic effects to activation of the conserved JNK pathway.

Human CNS cultures exposed to HIV-1 gp120 reproduce dendritic injuries of HIV-1-associated dementia

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Hammond Robert R

2004-05-01

Full Text Available Abstract HIV-1-associated dementia remains a common subacute to chronic central nervous system degeneration in adult and pediatric HIV-1 infected populations. A number of viral and host factors have been implicated including the HIV-1 120 kDa envelope glycoprotein (gp120. In human post-mortem studies using confocal scanning laser microscopy for microtubule-associated protein 2 and synaptophysin, neuronal dendritic pathology correlated with dementia. In the present study, primary human CNS cultures exposed to HIV-1 gp120 at 4 weeks in vitro suffered gliosis and dendritic damage analogous to that described in association with HIV-1-associated dementia.

Cyclophilin B enhances HIV-1 infection

Energy Technology Data Exchange (ETDEWEB)

DeBoer, Jason; Madson, Christian J. [Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE (United States); Belshan, Michael, E-mail: michaelbelshan@creighton.edu [Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE (United States); The Nebraska Center for Virology, University of Nebraska, Lincoln, NE (United States)

2016-02-15

Cyclophilin B (CypB) is a member of the immunophilin family and intracellular chaperone. It predominantly localizes to the ER, but also contains a nuclear localization signal and is secreted from cells. CypB has been shown to interact with the Gag protein of human immunodeficiency type 1 (HIV-1). Several proteomic and genetic studies identified it as a potential factor involved in HIV replication. Herein, we show that over-expression of CypB enhances HIV infection by increasing nuclear import of viral DNA. This enhancement was unaffected by cyclosporine treatment and requires the N-terminus of the protein. The N-terminus contains an ER leader sequence, putative nuclear localization signal, and is required for secretion. Deletion of the N-terminus resulted in mislocalization from the ER and suppression of HIV infection. Passive transfer experiments showed that secreted CypB did not impact HIV infection. Combined, these experiments show that intracellular CypB modulates a pathway of HIV nuclear import. - Highlights: • CypB has been identified in several proteomic studies of HIV-1 infection. • CypB expression is upregulated in activated and infected T-cells. • Over-expression of CypB enhances HIV nuclear import and infection. • The N-terminus of CypB is necessary for these effects.

Cyclophilin B enhances HIV-1 infection

International Nuclear Information System (INIS)

DeBoer, Jason; Madson, Christian J.; Belshan, Michael

2016-01-01

Cyclophilin B (CypB) is a member of the immunophilin family and intracellular chaperone. It predominantly localizes to the ER, but also contains a nuclear localization signal and is secreted from cells. CypB has been shown to interact with the Gag protein of human immunodeficiency type 1 (HIV-1). Several proteomic and genetic studies identified it as a potential factor involved in HIV replication. Herein, we show that over-expression of CypB enhances HIV infection by increasing nuclear import of viral DNA. This enhancement was unaffected by cyclosporine treatment and requires the N-terminus of the protein. The N-terminus contains an ER leader sequence, putative nuclear localization signal, and is required for secretion. Deletion of the N-terminus resulted in mislocalization from the ER and suppression of HIV infection. Passive transfer experiments showed that secreted CypB did not impact HIV infection. Combined, these experiments show that intracellular CypB modulates a pathway of HIV nuclear import. - Highlights: • CypB has been identified in several proteomic studies of HIV-1 infection. • CypB expression is upregulated in activated and infected T-cells. • Over-expression of CypB enhances HIV nuclear import and infection. • The N-terminus of CypB is necessary for these effects.

ORF Alignment: NC_000921 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000921 gi|15612352 >1mwmA 3 314 14 329 4e-45 ... ref|NP_224005.1| ROD SHAPE-DETERMINING... PROTEIN [Helicobacter pylori J99] ... gb|AAD06861.1| ROD SHAPE-DETERMINING PROTEIN ... [

ORF Alignment: NC_003071 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003071 gi|18403860 >1rl1A 4 90 215 300 7e-09 ... ref|NP_705268.1| nuclear movement... protein, putative [Plasmodium falciparum 3D7] ... emb|CAD52505.1| nuclear movement protein, putative

Picomolar dichotomous activity of gnidimacrin against HIV-1.

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Li Huang

Full Text Available Highly active antiretroviral therapy (HAART has offered a promising approach for controlling HIV-1 replication in infected individuals. However, with HARRT, HIV-1 is suppressed rather than eradicated due to persistence of HIV-1 in latent viral reservoirs. Thus, purging the virus from latent reservoirs is an important strategy toward eradicating HIV-1 infection. In this study, we discovered that the daphnane diterpene gnidimacrin, which was previously reported to have potent anti-cancer cell activity, activated HIV-1 replication and killed persistently-infected cells at picomolar concentrations. In addition to its potential to purge HIV-1 from latently infected cells, gnidimacrin potently inhibited a panel of HIV-1 R5 virus infection of peripheral blood mononuclear cells (PBMCs at an average concentration lower than 10 pM. In contrast, gnidimacrin only partially inhibited HIV-1 ×4 virus infection of PBMCs. The strong anti-HIV-1 R5 virus activity of gnidimacrin was correlated with its effect on down-regulation of the HIV-1 coreceptor CCR5. The anti-R5 virus activity of gnidimacrin was completely abrogated by a selective protein kinase C beta inhibitor enzastaurin, which suggests that protein kinase C beta plays a key role in the potent anti-HIV-1 activity of gnidimacrin in PBMCs. In summary, these results suggest that gnidimacrin could activate latent HIV-1, specifically kill HIV-1 persistently infected cells, and inhibit R5 viruses at picomolar concentrations.

Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism.

Science.gov (United States)

Moonsamy, Suri; Bhakat, Soumendranath; Soliman, Mahmoud E S

2015-01-01

The first account on the dynamic features of Nef or negative factor, a small myristoylated protein located in the cytoplasm believes to increase HIV-1 viral titer level, is reported herein. Due to its major role in HIV-1 pathogenicity, Nef protein is considered an emerging target in anti-HIV drug design and discovery process. In this study, comparative long-range all-atom molecular dynamics simulations were employed for apo and bound protein to unveil molecular mechanism of HIV-Nef dimerization and inhibition. Results clearly revealed that B9, a newly discovered Nef inhibitor, binds at the dimeric interface of Nef protein and caused significant separation between orthogonally opposed residues, namely Asp108, Leu112 and Gln104. Large differences in magnitudes were observed in the radius of gyration (∼1.5 Å), per-residue fluctuation (∼2 Å), C-alpha deviations (∼2 Å) which confirm a comparatively more flexible nature of apo conformation due to rapid dimeric association. Compared to the bound conformer, a more globally correlated motion in case of apo structure of HIV-Nef confirms the process of dimeric association. This clearly highlights the process of inhibition as a result of ligand binding. The difference in principal component analysis (PCA) scatter plot and per-residue mobility plot across first two normal modes further justifies the same findings. The in-depth dynamic analyses of Nef protein presented in this report would serve crucial in understanding its function and inhibition mechanisms. Information on inhibitor binding mode would also assist in designing of potential inhibitors against this important HIV target.

Higher Desolvation Energy Reduces Molecular Recognition in Multi-Drug Resistant HIV-1 Protease

Directory of Open Access Journals (Sweden)

Ladislau C. Kovari

2012-05-01

Full Text Available Designing HIV-1 protease inhibitors that overcome drug-resistance is still a challenging task. In this study, four clinical isolates of multi-drug resistant HIV-1 proteases that exhibit resistance to all the US FDA-approved HIV-1 protease inhibitors and also reduce the substrate recognition ability were examined. A multi-drug resistant HIV-1 protease isolate, MDR 769, was co-crystallized with the p2/NC substrate and the mutated CA/p2 substrate, CA/p2 P1’F. Both substrates display different levels of molecular recognition by the wild-type and multi-drug resistant HIV-1 protease. From the crystal structures, only limited differences can be identified between the wild-type and multi-drug resistant protease. Therefore, a wild-type HIV-1 protease and four multi-drug resistant HIV-1 proteases in complex with the two peptides were modeled based on the crystal structures and examined during a 10 ns-molecular dynamics simulation. The simulation results reveal that the multi-drug resistant HIV-1 proteases require higher desolvation energy to form complexes with the peptides. This result suggests that the desolvation of the HIV-1 protease active site is an important step of protease-ligand complex formation as well as drug resistance. Therefore, desolvation energy could be considered as a parameter in the evaluation of future HIV-1 protease inhibitor candidates.

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

1992-01-01

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

1992-12-31

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

ORF Alignment: NC_006905 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006905 gi|62179485 >1iwlA 1 182 23 204 2e-69 ... ref|YP_215902.1| periplasmic protein effects...ica ... subsp. enterica serovar Choleraesuis str. SC-B67] ... gb|AAX64821.1| periplasmic protein effects

ORF Alignment: NC_006300 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006300 gi|52425721 >1p3dA 1 463 15 477 e-153 ... ref|YP_088858.1| MurC protein [Ma...nnheimia succiniciproducens MBEL55E] gb|AAU38273.1| ... MurC protein [Mannheimia succiniciproducens M

ORF Alignment: NC_002940 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002940 gi|33151562 >1u07A 8 84 201 279 1e-08 ... gb|AAP95304.1| TobB energy transd...ucing protein [Haemophilus ducreyi 35000HP] ... ref|NP_872915.1| TobB energy transducing protein ...

Modulation of HIV-1 Gag NC/p1 cleavage efficiency affects protease inhibitor resistance and viral replicative capacity

Czech Academy of Sciences Publication Activity Database

Maarseveen van, N. M.; Andersson, Dan; Lepšík, Martin; Fun, A.; Schipper, P. J.; Jong de, D.; Boucher, Ch. A. B.; Nijhuis, M.

2012-01-01

Roč. 9, č. 29 (2012), s. 1-7 ISSN 1742-4690 EU Projects: European Commission(XE) 37693 - HIV PI RESISTANCE Grant - others:Dutch AIDS Fund(XE) 2006028; (NWO) VIDI(XE) 91796349 Institutional research plan: CEZ:AV0Z40550506 Keywords : HIV-1 * protease * Gag * resistance * cleavage Subject RIV: CE - Biochemistry Impact factor: 5.657, year: 2012

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

OpenAIRE

Budhiraja, Sona; Liu, Hongbing; Couturier, Jacob; Malovannaya, Anna; Qin, Jun; Lewis, Dorothy E.; Rice, Andrew P.

2015-01-01

By recruiting the host protein XPO1 (CRM1), the HIV-1 Rev protein mediates the nuclear export of incompletely spliced viral transcripts. We mined data from the recently described human nuclear complexome to identify a host protein, RBM14, which associates with XPO1 and Rev and is involved in Rev function. Using a Rev-dependent p24 reporter plasmid, we found that RBM14 depletion decreased Rev activity and Rev-mediated enhancement of the cytoplasmic levels of unspliced viral transcripts. RBM14 ...

Cloning, Expression and Purification of the Recombinant HIV-1 Tat-Nef Fusion Protein in Prokaryotic Expression System

Directory of Open Access Journals (Sweden)

Somayeh Kadkhodayan

2016-07-01

Full Text Available Abstract Background: Nef is one of the HIV-1 critical proteins, because it is essential for viral replication and AIDS disease progression and induction of immune response against it can partially inhibit viral infection. Moreover, a domain of the HIV-1 Trans-Activator of Transcription (Tat, 48-60 aa could act as a cell penetrating peptide (CPP. In current study, cloning and expression of Tat-Nef fusion protein was performed in E. coli for the first time. The protein expression was confirmed by western blot analysis and was purified using reverse staining method. Materials and Methods: In this experimental study, primarily, cloning of Tat-Nef fusion gene was done in pGEX6p2 expression vector. Then, the expression of Tat-Nef recombinat protein in E.coli BL21 (DE3 strain was performed by using IPTG inducer. The protein expression was confirmed by SDS-PAGE and western blotting using anti-Nef monoclonal antibody. Then, the recombinant fusion protein was purified from gel using reverse staining method. Results: The results of PCR analysis and enzyme digestion showed a clear band of ~ 726 bp in agarose gel indicating the correct Tat-Nef fusion cloning in pGEX6p2 prokaryotic expression vector. In addition, a 54 kDa band of Tat-Nef on SDS-PAGE revealed Tat-Nef protein expression that western blot analysis using anti-Nef monoclonal antibody confirmed it. Conclusion: The purified Tat-Nef recombinant fusion protein will be used as an antigen for protein vaccine design against HIV infection.

HIV-1 Nef binds with human GCC185 protein and regulates mannose 6 phosphate receptor recycling

Energy Technology Data Exchange (ETDEWEB)

Kumar, Manjeet; Kaur, Supinder; Nazir, Aamir; Tripathi, Raj Kamal, E-mail: rajkamalcdri@gmail.com

2016-05-20

HIV-1 Nef modulates cellular function that enhances viral replication in vivo which culminate into AIDS pathogenesis. With no enzymatic activity, Nef regulates cellular function through host protein interaction. Interestingly, trans-cellular introduction of recombinant Nef protein in Caenorhabditis elegans results in AIDS like pathogenesis which might share common pathophysiology because the gene sequence of C. elegans and humans share considerable homology. Therefore employing C. elegans based initial screen complemented with sequence based homology search we identified GCC185 as novel host protein interacting with HIV-1 Nef. The detailed molecular characterization revealed N-terminal EEEE{sub 65} acidic domain of Nef as key region for interaction. GCC185 is a tethering protein that binds with Rab9 transport vesicles. Our results show that Nef-GCC185 interaction disrupts Rab9 interaction resulting in delocalization of CI-MPR (cation independent Mannose 6 phosphate receptor) resulting in elevated secretion of hexosaminidase. In agreement with this, our studies identified novel host GCC185 protein that interacts with Nef EEEE65 acidic domain interfering GCC185-Rab9 vesicle membrane fusion responsible for retrograde vesicular transport of CI-MPR from late endosomes to TGN. In light of existing report suggesting critical role of Nef-GCC185 interaction reveals valuable mechanistic insights affecting specific protein transport pathway in docking of late endosome derived Rab9 bearing transport vesicle at TGN elucidating role of Nef during viral pathogenesis. -- Highlights: •Nef, an accessory protein of HIV-1 interacts with host factor and culminates into AIDS pathogenesis. •Using Caenorhabditis elegans based screen system, novel Nef interacting cellular protein GCC185 was identified. •Molecular characterization of Nef and human protein GCC185 revealed Nef EEEE{sub 65} key region interacted with full length GCC185. •Nef impeded the GCC185-Rab 9 interaction and

HDAC inhibition induces HIV-1 protein and enables immune-based clearance following latency reversal

DEFF Research Database (Denmark)

Wu, Guoxin; Swanson, Michael; Talla, Aarthi

2017-01-01

Promising therapeutic approaches for eradicating HIV include transcriptional activation of provirus from latently infected cells using latency-reversing agents (LRAs) and immune-mediated clearance to purge reservoirs. Accurate detection of cells capable of producing viral antigens and virions......, and the measurement of clearance of infected cells, is essential to assessing therapeutic efficacy. Here, we apply enhanced methodology extending the sensitivity limits for the rapid detection of subfemtomolar HIV gag p24 capsid protein in CD4+ T cells from ART-suppressed HIV+ individuals, and we show viral protein...... induction following treatment with LRAs. Importantly, we demonstrate that clinical administration of histone deacetylase inhibitors (HDACis; vorinostat and panobinostat) induced HIV gag p24, and ex vivo stimulation produced sufficient viral antigen to elicit immune-mediated cell killing using anti-gp120/CD3...

ORF Alignment: NC_005070 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005070 gi|33865578 >1f39A 4 97 54 143 4e-22 ... ref|NP_897137.1| putative SOS mutagenesis... protein UmuD [Synechococcus sp. WH 8102] ... emb|CAE07559.1| putative SOS mutagenesis protein

ORF Alignment: NC_002678 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002678 gi|13472874 >1b4uB 49 289 86 299 5e-14 ... ref|NP_104441.1| encapsulation p...rotein CapA [Mesorhizobium loti MAFF303099] ... dbj|BAB50227.1| encapsulation protein; CapA ...

ORF Alignment: NC_006177 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006177 gi|51893967 >1b4uB 49 289 86 299 5e-14 ... ref|NP_104441.1| encapsulation p...rotein CapA [Mesorhizobium loti MAFF303099] ... dbj|BAB50227.1| encapsulation protein; CapA ...

ORF Alignment: NC_002967 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002967 gi|42528039 >1b4uB 49 289 86 299 5e-14 ... ref|NP_104441.1| encapsulation p...rotein CapA [Mesorhizobium loti MAFF303099] ... dbj|BAB50227.1| encapsulation protein; CapA ...

HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function.

Science.gov (United States)

Kesby, James P; Najera, Julia A; Romoli, Benedetto; Fang, Yiding; Basova, Liana; Birmingham, Amanda; Marcondes, Maria Cecilia G; Dulcis, Davide; Semenova, Svetlana

2017-10-01

Methamphetamine abuse is common among humans with immunodeficiency virus (HIV). The HIV-1 regulatory protein TAT induces dysfunction of mesolimbic dopaminergic systems which may result in impaired reward processes and contribute to methamphetamine abuse. These studies investigated the impact of TAT expression on methamphetamine-induced locomotor sensitization, underlying changes in dopamine function and adenosine receptors in mesolimbic brain areas and neuroinflammation (microgliosis). Transgenic mice with doxycycline-induced TAT protein expression in the brain were tested for locomotor activity in response to repeated methamphetamine injections and methamphetamine challenge after a 7-day abstinence period. Dopamine function in the nucleus accumbens (Acb) was determined using high performance liquid chromatography. Expression of dopamine and/or adenosine A receptors (ADORA) in the Acb and caudate putamen (CPu) was assessed using RT-PCR and immunohistochemistry analyses. Microarrays with pathway analyses assessed dopamine and adenosine signaling in the CPu. Activity-dependent neurotransmitter switching of a reserve pool of non-dopaminergic neurons to a dopaminergic phenotype in the ventral tegmental area (VTA) was determined by immunohistochemistry and quantified with stereology. TAT expression enhanced methamphetamine-induced sensitization. TAT expression alone decreased striatal dopamine (D1, D2, D4, D5) and ADORA1A receptor expression, while increasing ADORA2A receptors expression. Moreover, TAT expression combined with methamphetamine exposure was associated with increased adenosine A receptors (ADORA1A) expression and increased recruitment of dopamine neurons in the VTA. TAT expression and methamphetamine exposure induced microglia activation with the largest effect after combined exposure. Our findings suggest that dopamine-adenosine receptor interactions and reserve pool neuronal recruitment may represent potential targets to develop new treatments for

ORF Alignment: NC_003071 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003071 gi|42569531 >1wd2A 1 58 290 342 7e-13 ... gb|AAD32294.1| similar to Ariadne... protein from Drosophila [Arabidopsis thaliana] ... emb|CAD52893.1| ARIADNE-like protein ARI11 [Arabi...dopsis ... thaliana] pir||A84725 similar to Ariadne protein from ... Drosophila [imported] - A

ORF Alignment: NC_000915 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000915 gi|15645437 >1r9lA 6 291 286 549 7e-39 ... gb|AAD07866.1| osmoprotection pr...otein (proWX) [Helicobacter pylori 26695] ... pir||B64622 osmoprotection protein - Helicobacter pylor...i ... (strain 26695) ref|NP_207611.1| osmoprotection protein ... (proWX) [Helicobacter pylori

The C-terminal sequence of IFITM1 regulates its anti-HIV-1 activity.

Directory of Open Access Journals (Sweden)

Rui Jia

Full Text Available The interferon-inducible transmembrane (IFITM proteins inhibit a wide range of viruses. We previously reported the inhibition of human immunodeficiency virus type 1 (HIV-1 strain BH10 by human IFITM1, 2 and 3. It is unknown whether other HIV-1 strains are similarly inhibited by IFITMs and whether there exists viral countermeasure to overcome IFITM inhibition. We report here that the HIV-1 NL4-3 strain (HIV-1NL4-3 is not restricted by IFITM1 and its viral envelope glycoprotein is partly responsible for this insensitivity. However, HIV-1NL4-3 is profoundly inhibited by an IFITM1 mutant, known as Δ(117-125, which is deleted of 9 amino acids at the C-terminus. In contrast to the wild type IFITM1, which does not affect HIV-1 entry, the Δ(117-125 mutant diminishes HIV-1NL4-3 entry by 3-fold. This inhibition correlates with the predominant localization of Δ(117-125 to the plasma membrane where HIV-1 entry occurs. In spite of strong conservation of IFITM1 among most species, mouse IFITM1 is 19 amino acids shorter at its C-terminus as compared to human IFITM1 and, like the human IFITM1 mutant Δ(117-125, mouse IFITM1 also inhibits HIV-1 entry. This is the first report illustrating the role of viral envelope protein in overcoming IFITM1 restriction. The results also demonstrate the importance of the C-terminal region of IFITM1 in modulating the antiviral function through controlling protein subcellular localization.

Cyclophilin B enhances HIV-1 infection.

Science.gov (United States)

DeBoer, Jason; Madson, Christian J; Belshan, Michael

2016-02-01

Cyclophilin B (CypB) is a member of the immunophilin family and intracellular chaperone. It predominantly localizes to the ER, but also contains a nuclear localization signal and is secreted from cells. CypB has been shown to interact with the Gag protein of human immunodeficiency type 1 (HIV-1). Several proteomic and genetic studies identified it as a potential factor involved in HIV replication. Herein, we show that over-expression of CypB enhances HIV infection by increasing nuclear import of viral DNA. This enhancement was unaffected by cyclosporine treatment and requires the N-terminus of the protein. The N-terminus contains an ER leader sequence, putative nuclear localization signal, and is required for secretion. Deletion of the N-terminus resulted in mislocalization from the ER and suppression of HIV infection. Passive transfer experiments showed that secreted CypB did not impact HIV infection. Combined, these experiments show that intracellular CypB modulates a pathway of HIV nuclear import. Copyright © 2015 Elsevier Inc. All rights reserved.

HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

Directory of Open Access Journals (Sweden)

Santiago Guerrero

2015-01-01

Full Text Available Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1 uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.

ORF Alignment: NC_006142 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006142 gi|51473766 >1xvqA 17 163 40 196 7e-07 ... ref|YP_067523.1| Sco2-like prote...in [Rickettsia typhi str. Wilmington] gb|AAU04041.1| ... Sco2-like protein [Rickettsia typhi str. Wil

Induction of HIV neutralizing antibodies against the MPER of the HIV envelope protein by HA/gp41 chimeric protein-based DNA and VLP vaccines.

Directory of Open Access Journals (Sweden)

Ling Ye

Full Text Available Several conserved neutralizing epitopes have been identified in the HIV Env protein and among these, the MPER of gp41 has received great attention and is widely recognized as a promising target. However, little success has been achieved in eliciting MPER-specific HIV neutralizing antibodies by a number of different vaccine strategies. We investigated the ability of HA/gp41 chimeric protein-based vaccines, which were designed to enhance the exposure of the MPER in its native conformation, to induce MPER-specific HIV neutralizing antibodies. In characterization of the HA/gp41 chimeric protein, we found that by mutating an unpaired Cys residue (Cys-14 in its HA1 subunit to a Ser residue, the modified chimeric protein HA-C14S/gp41 showed increased reactivity to a conformation-sensitive monoclonal antibody against HA and formed more stable trimers in VLPs. On the other hand, HA-C14S/gp41 and HA/gp41 chimeric proteins expressed on the cell surfaces exhibited similar reactivity to monoclonal antibodies 2F5 and 4E10. Immunization of guinea pigs using the HA-C14S/gp41 DNA or VLP vaccines induced antibodies against the HIV gp41 as well as to a peptide corresponding to a segment of MPER at higher levels than immunization by standard HIV VLPs. Further, sera from vaccinated guinea pigs were found to exhibit HIV neutralizing activities. Moreover, sera from guinea pigs vaccinated by HA-C14S/gp41 DNA and VLP vaccines but not the standard HIV VLPs, were found to neutralize HIV pseudovirions containing a SIV-4E10 chimeric Env protein. The virus neutralization could be blocked by a MPER-specific peptide, thus demonstrating induction of MPER-specific HIV neutralizing antibodies by this novel vaccine strategy. These results show that induction of MPER-specific HIV neutralizing antibodies can be achieved through a rationally designed vaccine strategy.

ORF Alignment: NC_002696 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002696 gi|16124962 >1mgtA 4 167 79 239 2e-25 ... ref|NP_419526.1| ada regulatory protein, internal deletion... [Caulobacter crescentus ... CB15] gb|AAK22694.1| ada regulatory protein, internal ... deletio...n [Caulobacter crescentus CB15] pir||B87337 ada ... regulatory protein, internal deletion

ORF Alignment: NC_000918 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000918 gi|15606868 >1tg6E 33 200 25 196 8e-08 ... ref|NP_214248.1| nodulation competitiveness... protein NfeD [Aquifex aeolicus VF5] ... gb|AAC07639.1| nodulation competitiveness protein... NfeD ... [Aquifex aeolicus VF5] pir||H70456 nodulation ... competitiveness protein NfeD - Aqu

ORF Alignment: NC_000917 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000917 gi|11498586 >1b0uA 5 258 11 250 4e-55 ... ref|NP_069814.1| osmoprotection p...rotein (proV) [Archaeoglobus fulgidus DSM 4304] ... gb|AAB90260.1| osmoprotection protein (proV) ... ... ... [Archaeoglobus fulgidus DSM 4304] pir||E69372 ... osmoprotection protein (proV) homolog - Arch

Extracellular histones identified in crocodile blood inhibit in-vitro HIV-1 infection.

Science.gov (United States)

Kozlowski, Hannah N; Lai, Eric T L; Havugimana, Pierre C; White, Carl; Emili, Andrew; Sakac, Darinka; Binnington, Beth; Neschadim, Anton; McCarthy, Stephen D S; Branch, Donald R

2016-08-24

It has been reported that crocodile blood contains potent antibacterial and antiviral properties. However, its effects on HIV-1 infection remain unknown. We obtained blood from saltwater crocodiles to examine whether serum or plasma could inhibit HIV-1 infection. We purified plasma fractions then used liquid chromatography-mass spectrometry to identify the inhibitory protein factor(s). We then analyzed the ability of recombinant proteins to recapitulate HIV-1 inhibition and determine their mechanism of action. Crocodylus porosus plasma was tested for inhibition of Jurkat T-cell HIV-1 infection. Inhibitor(s) were purified by reverse-phase chromatography then identified by protein liquid chromatography-mass spectrometry. Anti-HIV-1 activity of purified plasma or recombinant proteins were measured by p24 enzyme-linked immunosorbent assay and luciferase readouts, and mechanism of action was determined by measuring HIV-1 RNA, cDNA and transcription (using 1G5 cells). Crocodile plasma contains potent inhibitors of HIV-1IIIB infection, which were identified as histones. Recombinant human histones H1 and H2A significantly reduced HIV-1JR-FL infection (IC50 of 0.79 and 0.45 μmol/l, respectively), whereas H4 enhanced JR-FL luciferase activity. The inhibitory effects of crocodile plasma, recombinant H1 or recombinant H2A on HIV-1 infection were during or post-viral transcription. Circulating histones in crocodile blood, possibly released by neutrophil extracellular traps, are significant inhibitors of HIV-1 infection in-vitro. Extracellular recombinant histones have different effects on HIV-1 transcription and protein expression and are downregulated in HIV-1 patients. Circulating histones may be a novel resistance factor during HIV-1 infection, and peptide versions should be explored as future HIV-1 therapeutics that modulate viral transcription.

Human serum protein and C-reactive protein levels among HIV ...

African Journals Online (AJOL)

Human serum protein and C-reactive protein levels were determined among HIV patients visiting St Camillus Hospital, Uromi, Edo State, Nigeria, between January to March, 2013. Fifty (50) HIV patients (20 males; 30 females) and 50 control subjects (24 males; 26 females) were enrolled for this study. The clinical status of ...

ORF Sequence: NC_005027 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005027 gi|32471017 >gi|32471017|ref|NP_864010.1| hypothetical protein-transmemb...HALISRLRIWGRETLTEMPSWLVSMVVHLTLLLVLALIGRSTSKVGQIELLFRQSSESSSMELAEFTIAAAAPLESFERSMEEERIATTQLVSIDVIDAEAEMFSLVP

ORF Sequence: NC_002942 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002942 gi|52840424 >gi|52840424|ref|YP_094223.1| probable transmembrane protein...EYKRAQKQTFVMFFKGSLKGLVTTAPVTYRGVKIGEVKVIEITENKEHSKVLIPVYVQFFVERTYGFSQDPIHLLIDNGYVANITKPNLLTGVAEIELIKPTPAVKYKQTYYHSYPVFPTHNSAEKYTSME

ORF Sequence: NC_005027 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005027 gi|32476407 >gi|32476407|ref|NP_869401.1| hypothetical protein-transmemb...IYPDDRPGWIDQPIVNDGKDYSLVVTAGPSGSMEEADELIGVYARGAVQSYVDELVSEQEWATEPEMIPLDIDWIRDELVVRRYEGVVQVGDEQQFEKAILIRIEPEDKKVFETAIADMKLKERLAATGIVILGGFSLLVGGSIVLGGLASRQKQPTAAA

Hyperthermia stimulates HIV-1 replication.

Directory of Open Access Journals (Sweden)

Ferdinand Roesch

Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

ORF Alignment: NC_002528 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002528 gi|15617004 >1etoB 1 98 1 98 1e-23 ... ref|NP_240217.1| factor-for-inversion... ... DNA-binding protein fis dbj|BAB13103.1| ... factor-for-inversion stimulation protein [Buchnera ... ... aphidicola str. APS (Acyrthosiphon pisum)] pir||G84976 ... factor-for-inversion

ORF Alignment: NC_006300 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006300 gi|52425669 >4uagA 6 428 2 453 3e-46 ... ref|YP_088806.1| MurC protein [Man...nheimia succiniciproducens MBEL55E] gb|AAU38221.1| ... MurC protein [Mannheimia succiniciproducens MB

ORF Alignment: NC_000912 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000912 gi|13507986 >1txoB 6 236 9 257 6e-28 ... gb|AAB96233.1| protein phoshatase ...iae ... M129] pir||S73911 protein phoshatase 2C homolog ptc1 - ... Mycoplasma pneumoniae (stra... ... ref|NP_109935.1| protein phoshatase 2C homolog; similar ... to Swiss-Prot Accession Number P3518

HIV Genome-Wide Protein Associations: a Review of 30 Years of Research

Science.gov (United States)

2016-01-01

SUMMARY The HIV genome encodes a small number of viral proteins (i.e., 16), invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. As a known example, the HIV envelope glycoprotein GP120 is closely associated with GP41 for viral entry. From a genome-wide perspective, a hypothesis can be worked out to determine whether 16 HIV proteins could develop 120 possible pairwise associations either by physical interactions or by functional associations mediated via HIV or host molecules. Here, we present the first systematic review of experimental evidence on HIV genome-wide protein associations using a large body of publications accumulated over the past 3 decades. Of 120 possible pairwise associations between 16 HIV proteins, at least 34 physical interactions and 17 functional associations have been identified. To achieve efficient viral replication and infection, HIV protein associations play essential roles (e.g., cleavage, inhibition, and activation) during the HIV life cycle. In either a dispensable or an indispensable manner, each HIV protein collaborates with another viral protein to accomplish specific activities that precisely take place at the proper stages of the HIV life cycle. In addition, HIV genome-wide protein associations have an impact on anti-HIV inhibitors due to the extensive cross talk between drug-inhibited proteins and other HIV proteins. Overall, this study presents for the first time a comprehensive overview of HIV genome-wide protein associations, highlighting meticulous collaborations between all viral proteins during the HIV life cycle. PMID:27357278

ORF Alignment: NC_003047 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003047 gi|15964777 >1v4aA 24 435 49 467 e-101 ... emb|CAC45596.1| PUTATIVE GLUTAMATE-AMMONIA...-LIGASE ADENYLYLTRANSFERASE PROTEIN ... [Sinorhizobium meliloti] ref|NP_385130.1| PUTATIVE ... GLUTAMATE-AMMO...NIA-LIGASE ADENYLYLTRANSFERASE PROTEIN ... [Sinorhizobium meliloti 1021] sp|

ORF Alignment: NC_003911 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003911 gi|56698296 >1eljA 1 332 19 332 1e-06 ... gb|AAV96699.1| polyamine ABC trasnporte...snporter, periplasmic polyamine-binding protein ... [Silicibacter pomeroyi D...r, periplasmic polyamine-binding protein ... [Silicibacter pomeroyi DSS-3] ref|YP_168669.1| polyamine ... ABC tra

ORF Alignment: NC_004547 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004547 gi|50121570 >1iwlA 1 182 22 203 1e-59 ... ref|YP_050737.1| outer-membrane lipoproteins...oproteins carrier protein [Erwinia ... carotovora subsp. atroseptica SCRI104... carrier protein [Erwinia carotovora ... subsp. atroseptica SCRI1043] emb|CAG75546.1| ... outer-membrane lip

Neurocognitive function in HIV infected patients on antiretroviral therapy.

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Alan Winston

Full Text Available To describe factors associated with neurocognitive (NC function in HIV-positive patients on stable combination antiretroviral therapy.We undertook a cross-sectional analysis assessing NC data obtained at baseline in patients entering the Protease-Inhibitor-Monotherapy-Versus-Ongoing-Triple therapy (PIVOT trial.NC testing comprised of 5 domains. Raw results were z-transformed using standard and demographically adjusted normative datasets (ND. Global z-scores (NPZ-5 were derived from averaging the 5 domains and percentage of subjects with test scores >1 standard deviation (SD below population means in at least two domains (abnormal Frascati score calculated. Patient characteristics associated with NC results were assessed using multivariable linear regression.Of the 587 patients in PIVOT, 557 had full NC results and were included. 77% were male, 68% Caucasian and 28% of Black ethnicity. Mean (SD baseline and nadir CD4+ lymphocyte counts were 553(217 and 177(117 cells/µL, respectively, and HIV RNA was <50 copies/mL in all. Median (IQR NPZ-5 score was -0.5 (-1.2/-0 overall, and -0.3 (-0.7/0.1 and -1.4 (-2/-0.8 in subjects of Caucasian and Black ethnicity, respectively. Abnormal Frascati scores using the standard-ND were observed in 51%, 38%, and 81%, respectively, of subjects overall, Caucasian and Black ethnicity (p<0.001, but in 62% and 69% of Caucasian and Black subjects using demographically adjusted-ND (p = 0.20. In the multivariate analysis, only Black ethnicity was associated with poorer NPZ-5 scores (P<0.001.In this large group of HIV-infected subjects with viral load suppression, ethnicity but not HIV-disease factors is closely associated with NC results. The prevalence of abnormal results is highly dependent on control datasets utilised.ClinicalTrials.gov, NCT01230580.

ORF Alignment: NC_004851 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004851 gi|31983537 >1mwmA 1 315 2 316 e-100 ... ref|NP_858328.1| plasmid stable inheritance... protein [Shigella flexneri 2a str. 301] ... gb|AAL72301.1| plasmid stable inheritance prote...7.1| plasmid stable ... inheritance protein [Shigella flexneri] ref|NP_085...361.1| ... plasmid stable inheritance protein [Shigella flexneri] ... Length = 315 ... Query: 2 ...

Identification of a human protein-derived HIV-1 fusion inhibitor targeting the gp41 fusion core structure.

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Lijun Chao

Full Text Available The HIV-1 envelope glycoprotein (Env gp41 plays a crucial role in the viral fusion process. The peptides derived from the C-terminal heptad repeat (CHR of gp41 are potent HIV fusion inhibitors. However, the activity of these anti-HIV-1 peptides in vivo may be attenuated by their induction of anti-gp41 antibodies. Thus, it is essential to identify antiviral peptides or proteins with low, or no, immunogenicity to humans. Here, we found that the C-terminal fragment (aa 462-521 of the human POB1 (the partner of RalBP1, designated C60, is an HIV-1 fusion inhibitor. It bound to N36, the peptide derived from the N-terminal heptad repeat (NHR of gp41, and to the six-helix bundle (6-HB formed by N36 and C34, a CHR-peptide, but it did not bind to C34. Unlike the CHR-peptides, C60 did not block gp41 6-HB formation. Rather, results suggest that C60 inhibits HIV-1 fusion by binding to the 6-HB, in particular, the residues in the gp41 NHR domain that are exposed on the surface of 6-HB. Since 6-HB plays a crucial role in the late stage of fusion between the viral envelope and endosomal membrane during the endocytic process of HIV-1, C60 may serve as a host restriction factor to suppress HIV-1 entry into CD4+ T lymphocytes. Taken together, it can be concluded from these results that C60 can be used as a lead for the development of anti-HIV-1 therapeutics or microbicides for the treatment and prevention of HIV-1 infection, as well as a molecular probe to study the fusogenic mechanism of HIV-1.

Creation of chimeric human/rabbit APOBEC1 with HIV-1 restriction and DNA mutation activities

Science.gov (United States)

Ikeda, Terumasa; Ong, Eugene Boon Beng; Watanabe, Nobumoto; Sakaguchi, Nobuo; Maeda, Kazuhiko; Koito, Atsushi

2016-01-01

APOBEC1 (A1) proteins from lagomorphs and rodents have deaminase-dependent restriction activity against HIV-1, whereas human A1 exerts a negligible effect. To investigate these differences in the restriction of HIV-1 by A1 proteins, a series of chimeric proteins combining rabbit and human A1s was constructed. Homology models of the A1s indicated that their activities derive from functional domains that likely act in tandem through a dimeric interface. The C-terminal region containing the leucine-rich motif and the dimerization domains of rabbit A1 is important for its anti-HIV-1 activity. The A1 chimeras with strong anti-HIV-1 activity were incorporated into virions more efficiently than those without anti-HIV-1 activity, and exhibited potent DNA-mutator activity. Therefore, the C-terminal region of rabbit A1 is involved in both its packaging into the HIV-1 virion and its deamination activity against both viral cDNA and genomic RNA. This study identifies the novel molecular mechanism underlying the target specificity of A1.

A single gp120 residue can affect HIV-1 tropism in macaques.

Directory of Open Access Journals (Sweden)

Gregory Q Del Prete

2017-09-01

Full Text Available Species-dependent variation in proteins that aid or limit virus replication determines the ability of lentiviruses to jump between host species. Identifying and overcoming these differences facilitates the development of animal models for HIV-1, including models based on chimeric SIVs that express HIV-1 envelope (Env glycoproteins, (SHIVs and simian-tropic HIV-1 (stHIV strains. Here, we demonstrate that the inherently poor ability of most HIV-1 Env proteins to use macaque CD4 as a receptor is improved during adaptation by virus passage in macaques. We identify a single amino acid, A281, in HIV-1 Env that consistently changes during adaptation in macaques and affects the ability of HIV-1 Env to use macaque CD4. Importantly, mutations at A281 do not markedly affect HIV-1 Env neutralization properties. Our findings should facilitate the design of HIV-1 Env proteins for use in non-human primate models and thus expedite the development of clinically relevant reagents for testing interventions against HIV-1.

ORF Sequence: NC_002162 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002162 gi|13358063 >gi|13358063|ref|NP_078337.1| hypothetical protein UU500 [Ureap...MGNHTWDHPDIFEILTTKTNIIRPYNIINTHQYHLVGSGSRVFYCNKKMIRVTNLLGNSIDMKGLQTNPFESLDKIIAFNEAPIHIVDFHAETTSEKNALFLDFKSKL

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000962 gi|57116873 >1dkgA 1 141 20 160 6e-40 ... gb|AAU86502.1| heat shock protein [Shigella boy...dii] gb|AAU86448.1| heat shock ... protein [Shigella boydii] gb|AAU86447.1| heat shock ... ... protein [Shigella boydii] gb|AAU86446.1| heat shock ... protein [Shigella boydii] gb|AAU86...445.1| heat shock ... protein [Shigella boydii] gb|AAU86444.1| heat shock ... ... protein [Shigella boydii] gb|AAU86443.1| heat shock ... protein [Shigella boydii] gb|AAU86

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002945 gi|31792677 >1dkgA 1 141 20 160 6e-40 ... gb|AAU86502.1| heat shock protein [Shigella boy...dii] gb|AAU86448.1| heat shock ... protein [Shigella boydii] gb|AAU86447.1| heat shock ... ... protein [Shigella boydii] gb|AAU86446.1| heat shock ... protein [Shigella boydii] gb|AAU86...445.1| heat shock ... protein [Shigella boydii] gb|AAU86444.1| heat shock ... ... protein [Shigella boydii] gb|AAU86443.1| heat shock ... protein [Shigella boydii] gb|AAU86

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002755 gi|15840943 >1dkgA 1 141 20 160 6e-40 ... gb|AAU86502.1| heat shock protein [Shigella boy...dii] gb|AAU86448.1| heat shock ... protein [Shigella boydii] gb|AAU86447.1| heat shock ... ... protein [Shigella boydii] gb|AAU86446.1| heat shock ... protein [Shigella boydii] gb|AAU86...445.1| heat shock ... protein [Shigella boydii] gb|AAU86444.1| heat shock ... ... protein [Shigella boydii] gb|AAU86443.1| heat shock ... protein [Shigella boydii] gb|AAU86

ORF Alignment: NC_000963 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000963 gi|15604438 >1xvqA 17 163 47 203 4e-07 ... ref|NP_220956.1| SCO2 PROTEIN PRECURSOR (sco2...) [Rickettsia prowazekii str. Madrid E] ... emb|CAA15032.1| SCO2 PROTEIN PRECURSOR (sco2...) ... [Rickettsia prowazekii] pir||F71663 sco2 protein ... precursor (sco2) RP587 - Rickettsia

ORF Alignment: NC_005090 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005090 gi|34557359 >1mwmA 3 314 11 322 5e-28 ... ref|NP_907174.1| PUTATIVE ROD SHAPE-DETERMINING... PROTEIN (FRAGMENT) [Wolinella ... succinogenes DSM 1740] emb|CAE10074.1| PUTATIVE ROD ... SHAPE-DETERMIN...ING PROTEIN (FRAGMENT) [Wolinella ... succinogenes] ... Length = 312 ...

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002755 gi|15839632 >1gmeA 4 129 9 136 2e-13 ... ref|NP_214765.1| HEAT SHOCK PROTEIN HSP (HEAT-STRESS... ... ref|NP_853922.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRESS-INDUCED RIBOSOME-BINDING PROTEIN A) ... ...] emb|CAD93121.1| HEAT ... SHOCK PROTEIN HSP (HEAT-STRESS-INDUCED RIBOSOME-BINDING ... PROTEIN...terium tuberculosis ... (strain H37RV) emb|CAA17343.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRE...SS-INDUCED RIBOSOME-BINDING PROTEIN A) ... [Mycobacterium tuberculosis H37Rv

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002945 gi|31791429 >1gmeA 4 129 9 136 2e-13 ... ref|NP_214765.1| HEAT SHOCK PROTEIN HSP (HEAT-STRESS... ... ref|NP_853922.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRESS-INDUCED RIBOSOME-BINDING PROTEIN A) ... ...] emb|CAD93121.1| HEAT ... SHOCK PROTEIN HSP (HEAT-STRESS-INDUCED RIBOSOME-BINDING ... PROTEIN...terium tuberculosis ... (strain H37RV) emb|CAA17343.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRE...SS-INDUCED RIBOSOME-BINDING PROTEIN A) ... [Mycobacterium tuberculosis H37Rv

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000962 gi|15607392 >1gmeA 4 129 9 136 2e-13 ... ref|NP_214765.1| HEAT SHOCK PROTEIN HSP (HEAT-STRESS... ... ref|NP_853922.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRESS-INDUCED RIBOSOME-BINDING PROTEIN A) ... ...] emb|CAD93121.1| HEAT ... SHOCK PROTEIN HSP (HEAT-STRESS-INDUCED RIBOSOME-BINDING ... PROTEIN...terium tuberculosis ... (strain H37RV) emb|CAA17343.1| HEAT SHOCK PROTEIN HSP ... (HEAT-STRE...SS-INDUCED RIBOSOME-BINDING PROTEIN A) ... [Mycobacterium tuberculosis H37Rv

ORF Sequence: NC_005027 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005027 gi|32475512 >gi|32475512|ref|NP_868506.1| hypothetical protein-signal peptide and transme...VLVGLLLPAVQAAREAARRMSCSNNIAQLTLATHNYEFSMEHLPPGTTNPTGPIVNTPNGEHISFLVRLLPYIEQQGTADDFDLTASVYAPANAKVRAYQISAFLCPS

Nucleocapsid promotes localization of HIV-1 gag to uropods that participate in virological synapses between T cells.

Science.gov (United States)

Llewellyn, G Nicholas; Hogue, Ian B; Grover, Jonathan R; Ono, Akira

2010-10-28

T cells adopt a polarized morphology in lymphoid organs, where cell-to-cell transmission of HIV-1 is likely frequent. However, despite the importance of understanding virus spread in vivo, little is known about the HIV-1 life cycle, particularly its late phase, in polarized T cells. Polarized T cells form two ends, the leading edge at the front and a protrusion called a uropod at the rear. Using multiple uropod markers, we observed that HIV-1 Gag localizes to the uropod in polarized T cells. Infected T cells formed contacts with uninfected target T cells preferentially via HIV-1 Gag-containing uropods compared to leading edges that lack plasma-membrane-associated Gag. Cell contacts enriched in Gag and CD4, which define the virological synapse (VS), are also enriched in uropod markers. These results indicate that Gag-laden uropods participate in the formation and/or structure of the VS, which likely plays a key role in cell-to-cell transmission of HIV-1. Consistent with this notion, a myosin light chain kinase inhibitor, which disrupts uropods, reduced virus particle transfer from infected T cells to target T cells. Mechanistically, we observed that Gag copatches with antibody-crosslinked uropod markers even in non-polarized cells, suggesting an association of Gag with uropod-specific microdomains that carry Gag to uropods. Finally, we determined that localization of Gag to the uropod depends on higher-order clustering driven by its NC domain. Taken together, these results support a model in which NC-dependent Gag accumulation to uropods establishes a preformed platform that later constitutes T-cell-T-cell contacts at which HIV-1 virus transfer occurs.

Nucleocapsid promotes localization of HIV-1 gag to uropods that participate in virological synapses between T cells.

Directory of Open Access Journals (Sweden)

G Nicholas Llewellyn

2010-10-01

Full Text Available T cells adopt a polarized morphology in lymphoid organs, where cell-to-cell transmission of HIV-1 is likely frequent. However, despite the importance of understanding virus spread in vivo, little is known about the HIV-1 life cycle, particularly its late phase, in polarized T cells. Polarized T cells form two ends, the leading edge at the front and a protrusion called a uropod at the rear. Using multiple uropod markers, we observed that HIV-1 Gag localizes to the uropod in polarized T cells. Infected T cells formed contacts with uninfected target T cells preferentially via HIV-1 Gag-containing uropods compared to leading edges that lack plasma-membrane-associated Gag. Cell contacts enriched in Gag and CD4, which define the virological synapse (VS, are also enriched in uropod markers. These results indicate that Gag-laden uropods participate in the formation and/or structure of the VS, which likely plays a key role in cell-to-cell transmission of HIV-1. Consistent with this notion, a myosin light chain kinase inhibitor, which disrupts uropods, reduced virus particle transfer from infected T cells to target T cells. Mechanistically, we observed that Gag copatches with antibody-crosslinked uropod markers even in non-polarized cells, suggesting an association of Gag with uropod-specific microdomains that carry Gag to uropods. Finally, we determined that localization of Gag to the uropod depends on higher-order clustering driven by its NC domain. Taken together, these results support a model in which NC-dependent Gag accumulation to uropods establishes a preformed platform that later constitutes T-cell-T-cell contacts at which HIV-1 virus transfer occurs.

Artificial 64-Residue HIV-1 Enhancer-Binding Peptide Is a Potent Inhibitor of Viral Replication in HIV-1-Infected Cells.

Science.gov (United States)

Oufir, Mouhssin; Bisset, Leslie R; Hoffmann, Stefan R K; Xue, Gongda; Klauser, Stephan; Bergamaschi, Bianca; Gervaix, Alain; Böni, Jürg; Schüpbach, Jörg; Gutte, Bernd

2011-01-01

An artificial HIV-1 enhancer-binding peptide was extended by nine consecutive arginine residues at the C-terminus and by the nuclear localization signal of SV40 large T antigen at the N-terminus. The resulting synthetic 64-residue peptide was found to bind to the two enhancers of the HIV-1 long terminal repeat, cross the plasma membrane and the nuclear envelope of human cells, and suppress the HIV-1 enhancer-controlled expression of a green fluorescent protein reporter gene. Moreover, HIV-1 replication is inhibited by this peptide in HIV-1-infected CEM-GFP cells as revealed by HIV-1 p24 ELISA and real-time RT-PCR of HIV-1 RNA. Rapid uptake of this intracellular stable and inhibitory peptide into the cells implies that this peptide may have the potential to attenuate HIV-1 replication in vivo.

ORF Alignment: NC_004431 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004431 gi|26249016 >1j9iA 1 68 1 68 1e-21 ... ref|NP_415092.1| DLP12 prophage; bacteriophage DNA packaging... protein [Escherichia ... coli K12] gb|AAC73661.1| bacteriophage DNA packaging... ... protein; DLP12 prophage; bacteriophage DNA packaging ... protein [Escherichia coli K12] pir... ... Escherichia coli (strain K-12) sp|P31062|NOHB_ECOLI ... Prophage QSR' DNA packaging protein NU...||F64788 DNA ... packaging protein homolog nohB, phage protein-related - ...

ORF Alignment: NC_000913 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000913 gi|16128543 >1j9iA 1 68 1 68 1e-21 ... ref|NP_415092.1| DLP12 prophage; bacteriophage DNA packaging... protein [Escherichia ... coli K12] gb|AAC73661.1| bacteriophage DNA packaging... ... protein; DLP12 prophage; bacteriophage DNA packaging ... protein [Escherichia coli K12] pir... ... Escherichia coli (strain K-12) sp|P31062|NOHB_ECOLI ... Prophage QSR' DNA packaging protein NU...||F64788 DNA ... packaging protein homolog nohB, phage protein-related - ...

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002755 gi|15839498 >1ixcA 2 291 3 298 1e-20 ... ref|NP_214631.1| OXIDATIVE STRESS ...RESPONSE REGULATORY PROTEIN OXYS [Mycobacterium ... tuberculosis H37Rv] ref|NP_853788.1| OXIDATIVE STRESS...ory protein - ... Mycobacterium tuberculosis (strain H37RV) ... emb|CAA17311.1| OXIDATIVE STRESS... RESPONSE REGULATORY ... PROTEIN OXYS [Mycobacterium tuberculosis H37Rv] ... emb|CAD92982.1| OXIDATIVE STRESS

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002945 gi|31791295 >1ixcA 2 291 3 298 1e-20 ... ref|NP_214631.1| OXIDATIVE STRESS ...RESPONSE REGULATORY PROTEIN OXYS [Mycobacterium ... tuberculosis H37Rv] ref|NP_853788.1| OXIDATIVE STRESS...ory protein - ... Mycobacterium tuberculosis (strain H37RV) ... emb|CAA17311.1| OXIDATIVE STRESS... RESPONSE REGULATORY ... PROTEIN OXYS [Mycobacterium tuberculosis H37Rv] ... emb|CAD92982.1| OXIDATIVE STRESS

Direct and dynamic detection of HIV-1 in living cells.

Directory of Open Access Journals (Sweden)

Jonas Helma

Full Text Available In basic and applied HIV research, reliable detection of viral components is crucial to monitor progression of infection. While it is routine to detect structural viral proteins in vitro for diagnostic purposes, it previously remained impossible to directly and dynamically visualize HIV in living cells without genetic modification of the virus. Here, we describe a novel fluorescent biosensor to dynamically trace HIV-1 morphogenesis in living cells. We generated a camelid single domain antibody that specifically binds the HIV-1 capsid protein (CA at subnanomolar affinity and fused it to fluorescent proteins. The resulting fluorescent chromobody specifically recognizes the CA-harbouring HIV-1 Gag precursor protein in living cells and is applicable in various advanced light microscopy systems. Confocal live cell microscopy and super-resolution microscopy allowed detection and dynamic tracing of individual virion assemblies at the plasma membrane. The analysis of subcellular binding kinetics showed cytoplasmic antigen recognition and incorporation into virion assembly sites. Finally, we demonstrate the use of this new reporter in automated image analysis, providing a robust tool for cell-based HIV research.

ORF Alignment: NC_006370 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available pothetical stbA Plasmid stable inheritance protein ... [Photobacterium profundum] ... Length = ... NC_006370 gi|54307287 >1mwmA 2 317 24 344 3e-96 ... ref|YP_128307.1| Hypothetical stbA Plasmid stable inherita...nce protein ... [Photobacterium profundum SS9] emb|CAG18505.1| ... Hy

ORF Alignment: NC_000913 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available outer ... membrane receptor for iron transport; outer membrane ... porin protein, putative ferris...porin protein, putative ferrisiderophore receptor ... [Escherichia coli K12] gb|AAC73892.1| putative ... NC_000913 gi|16128773 >1kmoA 12 661 63 760 6e-50 ... ref|NP_415326.1| outer membrane

ORF Alignment: NC_006834 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006834 gi|58582167 >1iwlA 2 180 70 254 2e-49 ... ref|YP_201183.1| outer-membrane lipoproteins... ... outer-membrane lipoproteins carrier protein precursor ... [Xanthomonas oryzae pv. oryzae KAC... carrier protein precursor [Xanthomonas ... oryzae pv. oryzae KACC10331] gb|AAW75798.1| ...

ORF Alignment: NC_004337 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004337 gi|56479866 >1u07A 1 90 153 242 2e-32 ... ref|NP_707161.2| membrane protein, energy... transducer [Shigella flexneri 2a str. 301] ... gb|AAN42868.2| membrane protein, energy trans...ducer ... [Shigella flexneri 2a str. 301] ref|NP_836946.1| ... membrane protein, energy transd...ucer [Shigella flexneri ... 2a str. 2457T] gb|AAP16753.1| membrane protein, energy

ORF Alignment: NC_002695 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002695 gi|15831006 >1u07A 1 90 153 242 2e-32 ... ref|NP_707161.2| membrane protein, energy... transducer [Shigella flexneri 2a str. 301] ... gb|AAN42868.2| membrane protein, energy trans...ducer ... [Shigella flexneri 2a str. 301] ref|NP_836946.1| ... membrane protein, energy transd...ucer [Shigella flexneri ... 2a str. 2457T] gb|AAP16753.1| membrane protein, energy

ORF Alignment: NC_004741 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004741 gi|30062775 >1u07A 1 90 153 242 2e-32 ... ref|NP_707161.2| membrane protein, energy... transducer [Shigella flexneri 2a str. 301] ... gb|AAN42868.2| membrane protein, energy trans...ducer ... [Shigella flexneri 2a str. 301] ref|NP_836946.1| ... membrane protein, energy transd...ucer [Shigella flexneri ... 2a str. 2457T] gb|AAP16753.1| membrane protein, energy

ORF Alignment: NC_000913 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000913 gi|16129213 >1u07A 1 90 153 242 2e-32 ... ref|NP_707161.2| membrane protein, energy... transducer [Shigella flexneri 2a str. 301] ... gb|AAN42868.2| membrane protein, energy trans...ducer ... [Shigella flexneri 2a str. 301] ref|NP_836946.1| ... membrane protein, energy transd...ucer [Shigella flexneri ... 2a str. 2457T] gb|AAP16753.1| membrane protein, energy

ORF Alignment: NC_004431 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004431 gi|26247582 >1u07A 1 90 153 242 2e-32 ... ref|NP_707161.2| membrane protein, energy... transducer [Shigella flexneri 2a str. 301] ... gb|AAN42868.2| membrane protein, energy trans...ducer ... [Shigella flexneri 2a str. 301] ref|NP_836946.1| ... membrane protein, energy transd...ucer [Shigella flexneri ... 2a str. 2457T] gb|AAP16753.1| membrane protein, energy

ORF Alignment: NC_004431 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004431 gi|26247437 >1j9iA 1 68 1 68 7e-21 ... ref|NP_753477.1| Prophage Qin DNA packaging... protein NU1 homolog [Escherichia coli ... CFT073] gb|AAN80037.1| Prophage Qin DNA packaging ... ...teriophage ... 21] pir||A49849 DNA-packaging protein Nu1 - phage 21 ...

ORF Sequence: NC_003279 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003279 gi|17507795 >gi|17507795|ref|NP_493043.1| putative protein, with at least 2 transme...YLNIQIADETTDLPVSIDRANVDMRIYRAFEMSMEKDIISLSTSNTSHAEISTPKSRKKKSRKLGLKNLEEVINSKYNSCQKQDNSMSIQ

ORF Sequence: NC_001141 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_001141 gi|6322114 >gi|6322114|ref|NP_012189.1| Part of a heptameric protein complex that regulates retro...grade Golgi-to-ER protein traffic in eukaryotic cells; coatomer forms the COP I ves

ORF Alignment: NC_002505 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002505 gi|15641120 >1iwlA 6 181 22 197 4e-50 ... gb|AAF94266.1| outer membrane lipoproteins...|F82241 outer membrane ... lipoproteins carrier protein VC1107 [imported] ... carrier protein [Vibrio cholerae O1 ... biovar eltor str. N16961] ref|NP_230752.1| outer ... membrane lipopro...teins carrier protein [Vibrio cholerae ... O1 biovar eltor str. N16961] pir|

Nef enhances HIV-1 infectivity via association with the virus assembly complex

International Nuclear Information System (INIS)

Qi Mingli; Aiken, Christopher

2008-01-01

The HIV-1 accessory protein Nef enhances virus infectivity by facilitating an early post-entry step of infection. Nef acts in the virus producer cell, leading to a beneficial modification to HIV-1 particles. Nef itself is incorporated into HIV-1 particles, where it is cleaved by the viral protease during virion maturation. To probe the role of virion-associated Nef in HIV-1 infection, we generated a fusion protein consisting of the host protein cyclophilin A (CypA) linked to the amino terminus of Nef. The resulting CypA-Nef protein enhanced the infectivity of Nef-defective HIV-1 particles and was specifically incorporated into the virions via association with Gag during particle assembly. Pharmacologic or genetic inhibition of CypA-Nef binding to Gag prevented incorporation of CypA-Nef into virions and inhibited infectivity enhancement. Our results indicate that infectivity enhancement by Nef requires its association with a component of the assembling HIV-1 particle

ORF Alignment: NC_002947 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available 1| ... acyl-CoA dehydrogenase, ferrulic acid biotransformation ... protein, putative [Pseudomo...ransformation protein, ... putative [Pseudomonas putida KT2440] gb|AAN68958.... NC_002947 gi|26990069 >1u8vA 9 432 4 458 7e-34 ... ref|NP_745494.1| acyl-CoA dehydrogenase, ferrulic acid biot

ORF Alignment: NC_003037 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003037 gi|16263035 >1nyoA 11 162 8 158 4e-30 ... ref|NP_435828.1| Nex18 Symbiotica...lly induced conserved protein [Sinorhizobium ... meliloti 1021] gb|AAK65240.1| Nex18 Symbiotically ... ... ... induced conserved protein [Sinorhizobium meliloti 1021] ... pir||F95334 Nex18 Symbiotically

ORF Alignment: NC_002758 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002758 gi|15923032 >1k55C 15 244 359 585 4e-64 ... ref|YP_039516.1| methicillin re...sistance protein MecR1 [Staphylococcus aureus subsp. ... aureus MRSA252] ref|YP_190061.1| methicillin...-resistance ... regulatory protein MecR1 [Staphylococcus epidermidis ... RP62A] gb|AAW53313.1| methic...rmidis RP62A] ... emb|CAG39069.1| methicillin resistance protein MecR1 ... [Staphylococcus aur...6.1| MecR1 protein [Staphylococcus sciuri] ... dbj|BAB56204.1| methicillin resistance protein ...

ORF Alignment: NC_002976 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002976 gi|57865867 >1k55C 15 244 359 585 4e-64 ... ref|YP_039516.1| methicillin re...sistance protein MecR1 [Staphylococcus aureus subsp. ... aureus MRSA252] ref|YP_190061.1| methicillin...-resistance ... regulatory protein MecR1 [Staphylococcus epidermidis ... RP62A] gb|AAW53313.1| methic...rmidis RP62A] ... emb|CAG39069.1| methicillin resistance protein MecR1 ... [Staphylococcus aur...6.1| MecR1 protein [Staphylococcus sciuri] ... dbj|BAB56204.1| methicillin resistance protein ...

ORF Alignment: NC_002952 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002952 gi|49482292 >1k55C 15 244 359 585 4e-64 ... ref|YP_039516.1| methicillin re...sistance protein MecR1 [Staphylococcus aureus subsp. ... aureus MRSA252] ref|YP_190061.1| methicillin...-resistance ... regulatory protein MecR1 [Staphylococcus epidermidis ... RP62A] gb|AAW53313.1| methic...rmidis RP62A] ... emb|CAG39069.1| methicillin resistance protein MecR1 ... [Staphylococcus aur...6.1| MecR1 protein [Staphylococcus sciuri] ... dbj|BAB56204.1| methicillin resistance protein ...

ORF Alignment: NC_002745 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002745 gi|15925746 >1k55C 15 244 359 585 4e-64 ... ref|YP_039516.1| methicillin re...sistance protein MecR1 [Staphylococcus aureus subsp. ... aureus MRSA252] ref|YP_190061.1| methicillin...-resistance ... regulatory protein MecR1 [Staphylococcus epidermidis ... RP62A] gb|AAW53313.1| methic...rmidis RP62A] ... emb|CAG39069.1| methicillin resistance protein MecR1 ... [Staphylococcus aur...6.1| MecR1 protein [Staphylococcus sciuri] ... dbj|BAB56204.1| methicillin resistance protein ...

Artificial 64-Residue HIV-1 Enhancer-Binding Peptide Is a Potent Inhibitor of Viral Replication in HIV-1-Infected Cells

Directory of Open Access Journals (Sweden)

Mouhssin Oufir

2011-01-01

Full Text Available An artificial HIV-1 enhancer-binding peptide was extended by nine consecutive arginine residues at the C-terminus and by the nuclear localization signal of SV40 large T antigen at the N-terminus. The resulting synthetic 64-residue peptide was found to bind to the two enhancers of the HIV-1 long terminal repeat, cross the plasma membrane and the nuclear envelope of human cells, and suppress the HIV-1 enhancer-controlled expression of a green fluorescent protein reporter gene. Moreover, HIV-1 replication is inhibited by this peptide in HIV-1-infected CEM-GFP cells as revealed by HIV-1 p24 ELISA and real-time RT-PCR of HIV-1 RNA. Rapid uptake of this intracellular stable and inhibitory peptide into the cells implies that this peptide may have the potential to attenuate HIV-1 replication in vivo.

Inhibition of human immunodeficiency virus type 1 (HIV-1) nuclear import via Vpr-Importin α interactions as a novel HIV-1 therapy

International Nuclear Information System (INIS)

Suzuki, Tatsunori; Yamamoto, Norio; Nonaka, Mizuho; Hashimoto, Yoshie; Matsuda, Go; Takeshima, Shin-nosuke; Matsuyama, Megumi; Igarashi, Tatsuhiko; Miura, Tomoyuki; Tanaka, Rie; Kato, Shingo; Aida, Yoko

2009-01-01

The development of multidrug-resistant viruses compromises the efficacy of anti-human immunodeficiency virus (HIV) therapy and limits treatment options. Therefore, new targets that can be used to develop novel antiviral agents need to be identified. One such target is the interaction between Vpr, one of the accessory gene products of HIV-1 and Importin α, which is crucial, not only for the nuclear import of Vpr, but also for HIV-1 replication in macrophages. We have identified a potential parent compound, hematoxylin, which suppresses Vpr-Importin α interaction, thereby inhibiting HIV-1 replication in a Vpr-dependent manner. Analysis by real-time PCR demonstrated that hematoxylin specifically inhibited nuclear import step of pre-integration complex. Thus, hematoxylin is a new anti-HIV-1 inhibitor that targets the nuclear import of HIV-1 via the Vpr-Importin α interaction, suggesting that a specific inhibitor of the interaction between viral protein and the cellular factor may provide a new strategy for HIV-1 therapy.

Alterations in the nuclear proteome of HIV-1 infected T-cells

International Nuclear Information System (INIS)

DeBoer, Jason; Jagadish, Teena; Haverland, Nicole A.; Madson, Christian J.; Ciborowski, Pawel; Belshan, Michael

2014-01-01

Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein–protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection. - Highlights: • We identify changes in the expression of nuclear proteins during HIV-1 infection. • 163 nuclear proteins were found differentially regulated during HIV-1 infection. • Bioinformatic analysis identified several nuclear pathways altered by HIV infection. • Candidate factors were validated in two independent cell lines

Alterations in the nuclear proteome of HIV-1 infected T-cells

Energy Technology Data Exchange (ETDEWEB)

DeBoer, Jason [Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178 (United States); Jagadish, Teena; Haverland, Nicole A. [Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198 (United States); Madson, Christian J. [Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178 (United States); Ciborowski, Pawel [Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198 (United States); The Nebraska Center for Virology, University of Nebraska, Lincoln 68583 (United States); Belshan, Michael, E-mail: michaelbelshan@creighton.edu [Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178 (United States); The Nebraska Center for Virology, University of Nebraska, Lincoln 68583 (United States)

2014-11-15

Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein–protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection. - Highlights: • We identify changes in the expression of nuclear proteins during HIV-1 infection. • 163 nuclear proteins were found differentially regulated during HIV-1 infection. • Bioinformatic analysis identified several nuclear pathways altered by HIV infection. • Candidate factors were validated in two independent cell lines.

Neuroinflammation and Behavior in HIV-1 Transgenic Rats Exposed to Chronic Adolescent Stress.

Science.gov (United States)

Rowson, Sydney A; Harrell, Constance S; Bekhbat, Mandakh; Gangavelli, Apoorva; Wu, Matthew J; Kelly, Sean D; Reddy, Renuka; Neigh, Gretchen N

2016-01-01

Highly active antiretroviral therapy (HAART) has improved prognosis for people living with HIV (PLWH) and dramatically reduced the incidence of AIDS. However, even when viral load is controlled, PLWH develop psychiatric and neurological disorders more frequently than those living without HIV. Adolescents with HIV are particularly susceptible to the development of psychiatric illnesses and neurocognitive impairments. While both psychiatric and neurocognitive disorders have been found to be exacerbated by stress, the extent to which chronic stress and HIV-1 viral proteins interact to impact behavior and relevant neuroinflammatory processes is unknown. Determination of the individual contributions of stress and HIV to neuropsychiatric disorders is heavily confounded in humans. In order to isolate the influence of HIV-1 proteins and chronic stress on behavior and neuroinflammation, we employed the HIV-1 transgenic (Tg) rat model, which expresses HIV-1 proteins with a gag and pol deletion, allowing for viral protein expression without viral replication. This Tg line has been characterized as a model of HAART-controlled HIV-1 infection due to the lack of viral replication but continued presence of HIV-1 proteins. We exposed male and female adolescent HIV-1 Tg rats to a mixed-modality chronic stress paradigm consisting of isolation, social defeat and restraint, and assessed behavior, cerebral vascularization, and neuroinflammatory endpoints. Stress, sex, and presence of the HIV-1 transgene impacted weight gain in adolescent rats. Female HIV-1 Tg rats showed decreases in central tendency during the light cycle in the open field regardless of stress exposure. Both male and female HIV-1 Tg rats exhibited decreased investigative behavior in the novel object recognition task, but no memory impairments. Adolescent stress had no effect on the tested behaviors. Microglia in female HIV-1 Tg rats exhibited a hyper-ramified structure, and gene expression of complement factor B was

ORF Sequence: NC_003909 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003909 gi|42782207 >gi|42782207|ref|NP_979454.1| BclA protein [Bacillus cereus ATCC 10987] MANRLNFTGP...LGCCGISGKTGPTGPTGPTGVTGSTGPTGPTGATGFTGPTGPTGATGPTGATGPTGATGPTGATGPTGATGPTGPTGPTGATGFTGPTGPTGATGPTGATGPTGATGP...TGATGPTGATGPTGATGPTGATGPTGATGPTGATGPTGATGFTGPTGPTGATGPTGATGPTGATGPTGATGPTGATGPTGATGSTGP

ORF Sequence: NC_003070 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003070 gi|18407972 >gi|18407972|ref|NP_564823.1| no apical meristem (NAM) famil...y protein [Arabidopsis thaliana] MQAEEIICRVSDEEIIENYLRPKINGETSSIPRYVVELAEELYTVEPWLLPRQTAPILNPGEWFYFGKRNRKYSN

HIV-1 Nef control of cell signalling molecules: multiple strategies

Indian Academy of Sciences (India)

HIV-1 has at its disposal numerous proteins encoded by its genome which provide the required arsenal to establish and maintain infection in its host for a considerable number of years. One of the most important and enigmatic of these proteins is Nef. The Nef protein of HIV-1 plays a fundamental role in the virus life cycle.

ORF Alignment: NC_002947 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002947 gi|26988182 >1rwrA 1 265 36 293 1e-50 ... ref|NP_743607.1| surface colonization... ... gb|AAN67071.1| surface colonization protein, putative ... [Pseudomonas putida KT2440] ...

ORF Alignment: NC_003995 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003995 gi|21402596 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_005945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005945 gi|49187443 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_003997 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003997 gi|30264621 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain prot...ein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP domain protein [Bacillus anthr...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_003888 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003888 gi|21220505 >1chkA 2 236 70 304 9e-83 ... ref|NP_626284.1| putative chitosan...ase (putative secreted protein) [Streptomyces ... coelicolor A3(2)] emb|CAB52859.1| putative chitosan...ase ... (putative secreted protein) [Streptomyces coelicolor ... A3(2)] pir||T34867 probable chitosan

ORF Alignment: NC_002162 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002162 gi|13357567 >1dd3A 1 106 4 99 2e-11 ... ref|NP_077841.1| ribosomal protein L7/L12 [Ureap...lasma parvum serovar 3 str. ATCC ... 700970] gb|AAF30416.1| ribosomal protein L7/L12 ... [Ureap...L12 ... pir||B82946 ribosomal protein L7/L12 UU011 [imported] - ... Ureap...XIKLVEAG 63 ... LTIEQFIAAIKEMSMLELNDLVKAIETEFGVS ... IKLVEAG Sbjct: 1 ... LTIEQFIAAIKEMSMLELNDLVKAIETEFGVSAAAPVAAAAAPVAAEAPTEVTIKLVEAG 60 ...

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003295 gi|17546366 >1bxdA 1 144 297 447 7e-18 ... emb|CAD15349.1| PROBABLE OXIDATIVE STRESS...PROTEIN ... [Ralstonia solanacearum] ref|NP_519768.1| PROBABLE ... OXIDATIVE STRESS RESISTANCE

ORF Alignment: NC_007530 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_007530 gi|47530092 >1m65A 4 232 339 570 1e-51 ... ref|YP_021441.1| php domain protein [Bacillus anthracis str. 'Ames Ancestor'] ... ref|NP_846998.1| PHP...acis ... str. Ames] ref|YP_030695.1| PHP domain protein [Bacillus ... anthracis str. Sterne] r.... A2012] ... gb|AAP28484.1| PHP domain protein [Bacillus anthracis ... str. Ames] gb|AAT33916.1| PHP... domain protein [Bacillus ... anthracis str. 'Ames Ancestor'] gb|AAT56746.1| PHP ... dom

ORF Alignment: NC_002655 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002655 gi|15800390 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

ORF Alignment: NC_004741 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004741 gi|30062138 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

ORF Alignment: NC_004431 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004431 gi|26246664 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

ORF Alignment: NC_002695 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002695 gi|15829972 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

ORF Alignment: NC_004337 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004337 gi|56479698 >1j3eA 1 115 2 116 2e-47 ... pdb|1IU3|F Chain F, Crystal Structure Of The E.Coli... ... Structure Of The E.Coli Seqa Protein Complexed With ... Hemimethylated Dna ... Length = ... Seqa Protein Complexed ... With Hemimethylated Dna pdb|1IU3|C Chain C, Crystal ...

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003295 gi|17546028 >1fjgR 2 71 22 91 5e-16 ... emb|CAD15011.1| PROBABLE PRIMOSOMAL REPLICATION... PROTEIN [Ralstonia solanacearum] ... ref|NP_519430.1| PROBABLE PRIMOSOMAL REPLICATION ...

ORF Alignment: NC_003304 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003304 gi|17935259 >1tjlA 17 141 10 134 5e-37 ... ref|NP_532049.1| dnaK deletion s...uppressor protein [Agrobacterium tumefaciens str. ... C58] gb|AAL42365.1| dnaK deletion suppressor pr...otein ... [Agrobacterium tumefaciens str. C58] pir||AG2743 dnaK ... deletion suppressor protei

ORF Alignment: NC_003062 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003062 gi|15888685 >1tjlA 17 141 10 134 5e-37 ... ref|NP_532049.1| dnaK deletion s...uppressor protein [Agrobacterium tumefaciens str. ... C58] gb|AAL42365.1| dnaK deletion suppressor pr...otein ... [Agrobacterium tumefaciens str. C58] pir||AG2743 dnaK ... deletion suppressor protei

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ASE AND NICOTINAMIDASE ... HYDROLASE (NICOTINE DEAMIDASE) [Ralstonia solanac...earum] ... ref|NP_519881.1| PROBABLE BIFUNCTIONAL PROTEIN: ... PYRAZINAMIDASE AND NICOTINAMIDAS...E HYDROLASE (NICOTINE ... DEAMIDASE) [Ralstonia solanacearum GMI1000] ... ... NC_003295 gi|17546479 >1j2rA 11 186 9 209 4e-27 ... emb|CAD15462.1| PROBABLE BIFUNCTIONAL PROTEIN: PYRAZINAMID

ORF Alignment: NC_002758 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002758 gi|15923033 >1sd4A 3 117 7 121 9e-28 ... dbj|BAB56205.1| methicillin resist...ance regulatory protein [Staphylococcus aureus ... subsp. aureus Mu50] sp|Q932L5|MECI_STAAM Methicill...in ... resistance regulatory protein mecI ref|NP_370567.1| ... methicillin resistance regulato

ORF Alignment: NC_004463 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004463 gi|27377041 >1xewY 1 130 1026 1153 2e-37 ... ref|NP_248653.1| chromosome segreta...tion protein (smc1) [Methanocaldococcus ... jannaschii DSM 2661] gb|AAB99663.1| chromosome ... segreta

ORF Alignment: NC_000909 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000909 gi|15669839 >1gxlA 2 204 475 685 1e-34 ... ref|NP_248653.1| chromosome segreta...tion protein (smc1) [Methanocaldococcus ... jannaschii DSM 2661] gb|AAB99663.1| chromosome ... segreta

ORF Alignment: NC_003237 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003237 gi|19075000 >1xewY 1 130 1026 1153 2e-37 ... ref|NP_248653.1| chromosome segreta...tion protein (smc1) [Methanocaldococcus ... jannaschii DSM 2661] gb|AAB99663.1| chromosome ... segreta

ORF Alignment: NC_000909 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000909 gi|15669839 >1xewY 1 130 1026 1153 2e-37 ... ref|NP_248653.1| chromosome segreta...tion protein (smc1) [Methanocaldococcus jannaschii ... DSM 2661] gb|AAB99663.1| chromosome segreta

ORF Alignment: NC_006348 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006348 gi|53725407 >1dlwA 1 115 25 145 1e-19 ... ref|YP_103467.1| protozoan/cyanob...acterial globin family protein [Burkholderia mallei ... ATCC 23344] gb|AAU49423.1| protozoan/cyanobac

ORF Alignment: NC_006350 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006350 gi|53718816 >1dlwA 1 115 25 145 1e-19 ... ref|YP_103467.1| protozoan/cyanob...acterial globin family protein [Burkholderia mallei ... ATCC 23344] gb|AAU49423.1| protozoan/cyanobac

ORF Sequence: NC_005363 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005363 gi|42523756 >gi|42523756|ref|NP_969136.1| membrane protein necessary for nodulation/competitivene...ss [Bdellovibrio bacteriovorus HD100] MKSLMLILFVSLLSVVAKADCTTAITINEAISASTSDYLERAEKR

ORF Sequence: NC_003078 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available etitiveness [Sinorhizobium meliloti 1021] MQLSACARRREAVRYRRRMARILILLFSLLSAFAFPVTPVP... NC_003078 gi|16264863 >gi|16264863|ref|NP_437655.1| probable membrane protein necessary for nodulation comp

ORF Sequence: NC_002678 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002678 gi|13471138 >gi|13471138|ref|NP_102707.1| transcriptional regulatory protein, nodulation competit...iveness determinant [Mesorhizobium loti MAFF303099] MTNESDTRSAELAELTADIVSAYVSNNPLPV

ORF Sequence: NC_003047 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003047 gi|15964332 >gi|15964332|ref|NP_384685.1| PROBABLE PYRAZINAMIDASE/NICOTINAMIDAS...E (INCLUDES: PYRAZINAMIDASE, NICOTINAMIDASE) PROTEIN [Sinorhizobium meliloti 1021] MADAARPDLREAMADEAL

ORF Alignment: NC_006085 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006085 gi|50842772 >1qr0A 1 205 2 202 3e-27 ... ref|YP_055999.1| biosurfactants pr...oduction protein [Propionibacterium acnes ... KPA171202] gb|AAT83041.1| biosurfactants production ...

ORF Alignment: NC_000913 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000913 gi|16129507 >1j9iA 1 68 1 68 3e-21 ... ref|NP_416066.1| DNA packaging prote...in NU1 homolog from lambdoid prophage Qin ... [Escherichia coli K12] gb|AAC74621.1| DNA packaging ... ... ... protein NU1 homolog from lambdoid prophage Qin; Qin ... prophage; packaging protein NU1 [Escheri...chia coli K12] ... pir||G64909 DNA packaging protein homolog nohA, phage ... ... ... protein-related - Escherichia coli (strain K-12) ... sp|P31061|NOHA_ECOLI Prophage Qin DNA packaging

ORF Alignment: NC_004556 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004556 gi|28199002 >1j9iA 1 68 1 68 3e-21 ... ref|NP_416066.1| DNA packaging prote...in NU1 homolog from lambdoid prophage Qin ... [Escherichia coli K12] gb|AAC74621.1| DNA packaging ... ... ... protein NU1 homolog from lambdoid prophage Qin; Qin ... prophage; packaging protein NU1 [Escheri...chia coli K12] ... pir||G64909 DNA packaging protein homolog nohA, phage ... ... ... protein-related - Escherichia coli (strain K-12) ... sp|P31061|NOHA_ECOLI Prophage Qin DNA packaging

ORF Alignment: NC_006814 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006814 gi|58337071 >1j9iA 1 68 1 68 3e-21 ... ref|NP_416066.1| DNA packaging prote...in NU1 homolog from lambdoid prophage Qin ... [Escherichia coli K12] gb|AAC74621.1| DNA packaging ... ... ... protein NU1 homolog from lambdoid prophage Qin; Qin ... prophage; packaging protein NU1 [Escheri...chia coli K12] ... pir||G64909 DNA packaging protein homolog nohA, phage ... ... ... protein-related - Escherichia coli (strain K-12) ... sp|P31061|NOHA_ECOLI Prophage Qin DNA packaging

ORF Alignment: NC_005363 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005363 gi|42523916 >1a12A 35 375 64 376 3e-39 ... emb|CAE53335.1| putative RCC1 repeats protein [Actinoplan...es teichomyceticus] ... Length = 313 ... Query: 425 GVGFACALYDNNDLKCFGANDYGQLGD

ORF Alignment: NC_005090 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005090 gi|34558174 >1wcv1 4 239 4 244 2e-25 ... ref|NP_907989.1| SEPTUM SITE-DETERMINING...| SEPTUM ... SITE-DETERMINING PROTEIN MIND CELL DIVISION INHIBITOR ... MIND [Wolinella succino

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003295 gi|17547365 >1gkmA 3 497 10 504 e-143 ... emb|CAD16353.1| PROBABLE HISTIDINE AMMONIA...-LYASE (HISTIDASE) PROTEIN [Ralstonia ... solanacearum] ref|NP_520767.1| PROBABLE HISTIDINE ... AMMONIA

ORF Alignment: NC_003047 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003047 gi|15966456 >1gkmA 2 501 3 499 e-107 ... emb|CAC47282.1| PUTATIVE HISTIDINE AMMONIA...-LYASE PROTEIN [Sinorhizobium meliloti] ... ref|NP_386809.1| PUTATIVE HISTIDINE AMMONIA-LYASE

ORF Alignment: NC_004461 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004461 gi|27467672 >1pwgA 4 344 72 389 1e-36 ... ref|NP_764309.1| autolysis and me...thicillin resistant-related protein [Staphylococcus ... epidermidis ATCC 12228] gb|AAO04351.1| autolysis

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003295 gi|17548082 >1wcv1 2 241 2 249 7e-27 ... emb|CAD16862.1| PROBABLE SEPTUM SITE-DETERMINING... PROTEIN MIND [Ralstonia ... solanacearum] ref|NP_521484.1| PROBABLE SEPTUM ... SITE-DETERMINING

ORF Alignment: NC_005126 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005126 gi|37525549 >1iwlA 1 182 22 203 4e-57 ... ref|NP_928893.1| outer-membrane lipoproteins... ... emb|CAE13895.1| outer-membrane lipoproteins carrier ... protein precursor (P20) [Photorhabdus

ORF Alignment: NC_005966 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005966 gi|50085964 >1iwlA 2 180 37 230 6e-44 ... ref|YP_047474.1| outer-membrane lipoproteins... carrier protein [Acinetobacter sp. ... ADP1] emb|CAG69652.1| outer-membrane lipoproteins

ORF Alignment: NC_005085 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005085 gi|34497069 >1iwlA 2 178 25 203 1e-46 ... gb|AAQ59290.1| outer membrane lipoproteins... carrier protein [Chromobacterium ... violaceum ATCC 12472] ref|NP_901284.1| outer membrane ... lipoproteins

ORF Sequence: NC_006155 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available g protein (involved in environmental [Yersinia pseudotuberculosis IP 32953] MTKTDYLMRLRKCTTIDTLERVIEKNKYELSDDELELFYSAADHRLAELTMNKLYDKIPPTVWQHVK ... NC_006155 gi|51595328 >gi|51595328|ref|YP_069519.1| hemolysin expression modulatin

ORF Sequence: NC_002162 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002162 gi|13357802 >gi|13357802|ref|NP_078076.1| ribosomal protein L24 [Ureapla...sma parvum serovar 3 str. ATCC 700970] MNRIKKGDTVVVISGKNKNKSGVVIQVNPKEQTALVEGVNKIKRHQKKDQTHEQSGIIEKEAPIRLCKLALVDPKGKDKGKATKVKYLLKDNKKVRVARKSGSELDVNKK

ORF Alignment: NC_003236 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003236 gi|19074669 >1jmcA 1 238 213 445 1e-62 ... emb|CAD25779.1| DNA REPLICATION ...FACTOR A PROTEIN 1 [Encephalitozoon cuniculi GB-M1] ... ref|NP_586175.1| DNA REPLICATION FACTOR A PRO

ORF Alignment: NC_006834 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006834 gi|58581923 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_004757 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004757 gi|30250333 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_004572 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004572 gi|28493349 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_005966 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005966 gi|50085709 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_003919 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003919 gi|21242823 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_003116 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003116 gi|15793872 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_006085 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006085 gi|50842381 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_006513 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006513 gi|56478742 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_004551 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004551 gi|28572541 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_003112 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003112 gi|15676600 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_006369 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006369 gi|54293610 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_002488 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002488 gi|15837680 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_002946 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002946 gi|59800726 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_005085 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005085 gi|34495926 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_006368 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006368 gi|54296649 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_002977 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002977 gi|53803220 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_002942 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002942 gi|52840863 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_003869 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003869 gi|20807422 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

ORF Alignment: NC_006361 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006361 gi|54024866 >1jmvA 2 140 154 297 6e-16 ... ref|YP_227183.1| UNIVERSAL STRESS...icum ATCC 13032] ... emb|CAF20967.1| UNIVERSAL STRESS PROTEIN FAMILY ... [Corynebacterium glut

ORF Alignment: NC_003450 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003450 gi|19554128 >1jmvA 2 140 154 297 6e-16 ... ref|YP_227183.1| UNIVERSAL STRESS...icum ATCC 13032] ... emb|CAF20967.1| UNIVERSAL STRESS PROTEIN FAMILY ... [Corynebacterium glut

ORF Alignment: NC_003911 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003911 gi|56696447 >1dlwA 19 115 21 125 4e-12 ... gb|AAV94850.1| protozoan/cyanoba...cterial globin family protein [Silicibacter ... pomeroyi DSS-3] ref|YP_166804.1| ... protozoan

ORF Alignment: NC_002977 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002977 gi|53804116 >1dlwA 19 113 26 120 5e-13 ... gb|AAU92168.1| protozoan/cyanoba...cterial globin family protein [Methylococcus ... capsulatus str. Bath] ref|YP_114018.1| ... protozoa

ORF Alignment: NC_003296 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003296 gi|17548586 >1gkmA 10 504 26 526 e-118 ... ref|NP_521926.1| PROBABLE HISTIDINE AMMONIA...-LYASE PROTEIN [Ralstonia solanacearum ... GMI1000] emb|CAD17516.1| PROBABLE HISTIDINE ... AMMONIA

ORF Alignment: NC_003902 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003902 gi|21231422 >1iwlA 2 180 23 207 3e-47 ... ref|NP_637339.1| outer-membrane lipoproteins... ... gb|AAM41263.1| outer-membrane lipoproteins carrier ... protein precursor [Xanthomonas campest

ORF Alignment: NC_004459 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004459 gi|27364633 >1etoB 1 98 1 98 7e-29 ... ref|YP_131497.1| putative factor-for-inversion... stimulation protein [Photobacterium ... profundum SS9] emb|CAG21695.1| putative ... factor-for-inversion

ORF Alignment: NC_004603 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004603 gi|28899659 >1etoB 1 98 1 98 7e-29 ... ref|YP_131497.1| putative factor-for-inversion... stimulation protein [Photobacterium ... profundum SS9] emb|CAG21695.1| putative ... factor-for-inversion

ORF Alignment: NC_004061 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004061 gi|21672661 >1etoB 1 98 1 99 3e-23 ... ref|NP_660728.1| factor-for-inversion... stimulation protein [Buchnera aphidicola ... str. Sg (Schizaphis graminum)] gb|AAM67939.1| ... factor-for-inversion

ORF Alignment: NC_005139 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005139 gi|37681323 >1etoB 1 98 1 98 7e-29 ... ref|YP_131497.1| putative factor-for-inversion... stimulation protein [Photobacterium ... profundum SS9] emb|CAG21695.1| putative ... factor-for-inversion

ORF Alignment: NC_006370 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006370 gi|54310477 >1etoB 1 98 1 98 7e-29 ... ref|YP_131497.1| putative factor-for-inversion... stimulation protein [Photobacterium ... profundum SS9] emb|CAG21695.1| putative ... factor-for-inversion

ORF Alignment: NC_000909 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000909 gi|15669839 >1ii8A 3 194 4 202 2e-10 ... ref|NP_248653.1| chromosome segreta...tion protein (smc1) [Methanocaldococcus ... jannaschii DSM 2661] gb|AAB99663.1| chromosome ... segreta

ORF Alignment: NC_005090 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005090 gi|34556511 >1mwmA 3 314 14 327 1e-46 ... ref|NP_906326.1| PUTATIVE ROD SHAPE-DETERMINING... PROTEIN [Wolinella succinogenes DSM ... 1740] emb|CAE09226.1| PUTATIVE ROD SHAPE-DETERMINING

ORF Alignment: NC_003921 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003921 gi|21264212 >1m1fA 1 109 2 110 1e-34 ... gb|AAM39231.1| plasmid stable inheritance... protein K [Xanthomonas axonopodis pv. ... citri str. 306] ref|NP_644713.1| plasmid stable ... inheritance

Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

Science.gov (United States)

Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

2012-11-02

HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

ORF Alignment: NC_005296 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005296 gi|39936343 >1bxwA 4 170 45 261 3e-15 ... ref|YP_222291.1| Omp31-1, outer m...embrane protein, 31 kDa [Brucella abortus biovar 1 ... str. 9-941] gb|AAX74930.1| Omp31-1, outer mem...brane ... protein, 31 kDa [Brucella abortus biovar 1 str. 9-941] ... gb|AAS84568.1| Omp31b [

ORF Alignment: NC_005945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005945 gi|49184136 >1dlwA 1 115 7 124 8e-22 ... ref|YP_017820.1| protozoan/cyanoba...cterial globin family protein [Bacillus anthracis ... str. 'Ames Ancestor'] ref|NP_843684.1| ... protozoa...n/cyanobacterial globin family protein [Bacillus ... anthracis str. Ames] ref|YP_027388.1| ... protozoa...racis str. ... A2012] gb|AAP25170.1| protozoan/cyanobacterial globin ... family protein [Bacil...lus anthracis str. Ames] ... gb|AAT30295.1| protozoan/cyanobacterial globi

ORF Alignment: NC_007530 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_007530 gi|47526471 >1dlwA 1 115 7 124 8e-22 ... ref|YP_017820.1| protozoan/cyanoba...cterial globin family protein [Bacillus anthracis ... str. 'Ames Ancestor'] ref|NP_843684.1| ... protozoa...n/cyanobacterial globin family protein [Bacillus ... anthracis str. Ames] ref|YP_027388.1| ... protozoa...racis str. ... A2012] gb|AAP25170.1| protozoan/cyanobacterial globin ... family protein [Bacil...lus anthracis str. Ames] ... gb|AAT30295.1| protozoan/cyanobacterial globi

ORF Alignment: NC_003997 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003997 gi|30261307 >1dlwA 1 115 7 124 8e-22 ... ref|YP_017820.1| protozoan/cyanoba...cterial globin family protein [Bacillus anthracis ... str. 'Ames Ancestor'] ref|NP_843684.1| ... protozoa...n/cyanobacterial globin family protein [Bacillus ... anthracis str. Ames] ref|YP_027388.1| ... protozoa...racis str. ... A2012] gb|AAP25170.1| protozoan/cyanobacterial globin ... family protein [Bacil...lus anthracis str. Ames] ... gb|AAT30295.1| protozoan/cyanobacterial globi

ORF Alignment: NC_003995 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003995 gi|21399119 >1dlwA 1 115 7 124 8e-22 ... ref|YP_017820.1| protozoan/cyanoba...cterial globin family protein [Bacillus anthracis ... str. 'Ames Ancestor'] ref|NP_843684.1| ... protozoa...n/cyanobacterial globin family protein [Bacillus ... anthracis str. Ames] ref|YP_027388.1| ... protozoa...racis str. ... A2012] gb|AAP25170.1| protozoan/cyanobacterial globin ... family protein [Bacil...lus anthracis str. Ames] ... gb|AAT30295.1| protozoan/cyanobacterial globi

ORF Alignment: NC_002976 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002976 gi|57866545 >1dlwA 19 115 47 146 6e-19 ... ref|YP_188173.1| protozoan/cyano...bacterial globin family protein [Staphylococcus ... epidermidis RP62A] gb|AAW53991.1| ... protozoa

ORF Alignment: NC_002951 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002951 gi|57650195 >1dlwA 19 115 21 120 3e-19 ... ref|YP_185875.1| protozoan/cyano...bacterial globin family protein [Staphylococcus ... aureus subsp. aureus COL] gb|AAW36475.1| ... protozoa

ORF Alignment: NC_003295 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003295 gi|17544778 >1mwmA 4 314 14 329 3e-49 ... emb|CAD13587.1| PROBABLE ROD SHAPE-DETERMINING... PROTEIN [Ralstonia solanacearum] ... ref|NP_518180.1| PROBABLE ROD SHAPE-DETERMINING PR

ORF Alignment: NC_004603 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004603 gi|28897880 >1iwlA 4 181 30 207 4e-54 ... ref|NP_797485.1| outer membrane lipoproteins... carrier protein [Vibrio ... parahaemolyticus RIMD 2210633] dbj|BAC59369.1| outer ... membrane lipoproteins

ORF Alignment: NC_005139 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005139 gi|37679507 >1iwlA 4 181 20 197 6e-54 ... ref|NP_934116.1| outer membrane lipoproteins...tein ... carrier protein precursor dbj|BAC94087.1| outer membrane ... lipoproteins carrier pro

ORF Alignment: NC_003919 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003919 gi|21242752 >1iwlA 2 180 23 207 3e-47 ... gb|AAM36870.1| outer-membrane lipoproteins... ... outer-membrane lipoproteins carrier protein precursor ... [Xanthomonas axonopodis pv. citr

ORF Alignment: NC_006370 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006370 gi|54308356 >1iwlA 4 181 22 199 2e-52 ... ref|YP_129376.1| hypothetical outer membrane lipoproteins... ... hypothetical outer membrane lipoproteins carrier protein ... [Photobacterium profundum] ... L

ORF Alignment: NC_003921 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003921 gi|21264213 >1ub4C 1 63 1 63 4e-10 ... gb|AAM39232.1| plasmid stable inheritance... protein I [Xanthomonas axonopodis pv. ... citri str. 306] ref|NP_644714.1| plasmid stable ... inheritance

ORF Alignment: NC_003317 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003317 gi|17987645 >1j1vA 4 94 20 109 8e-10 ... gb|AAL52543.1| CHROMOSOMAL REPLICATION... INITIATOR PROTEIN DNAA [Brucella melitensis ... 16M] ref|NP_540279.1| CHROMOSOMAL REPLICATION IN

ORF Alignment: NC_002952 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002952 gi|49483221 >1pwgA 4 329 74 373 1e-38 ... ref|YP_040445.1| autolysis and me...thicillin resistant-related protein [Staphylococcus ... aureus subsp. aureus MRSA252] emb|CAG40034.1| autolysis

ORF Alignment: NC_004578 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004578 gi|28871348 >1dlwA 1 114 25 138 3e-25 ... ref|NP_793967.1| protozoan/cyanob...acterial globin family protein [Pseudomonas ... syringae pv. tomato str. DC3000] gb|AAO57662.1| ... protozoa

Antibodies to the HIV-1 Tat protein correlated with nonprogression to AIDS: a rationale for the use of Tat toxoid as an HIV-1 vaccine.

Science.gov (United States)

Zagury, J F; Sill, A; Blattner, W; Lachgar, A; Le Buanec, H; Richardson, M; Rappaport, J; Hendel, H; Bizzini, B; Gringeri, A; Carcagno, M; Criscuolo, M; Burny, A; Gallo, R C; Zagury, D

1998-01-01

To investigate which immune parameters, such as antibodies against HIV-1 specificities, or viral parameters, such as p24 antigenemia, are predictive of disease progression. We performed studies on serum collected from individuals exhibiting two extremes of disease evolution--67 fast progressors (FP) and 182 nonprogressors (NP)--at their enrollment. After a 1- to 2-year clinical follow-up of 104 nonprogressors after their enrollment, we could determine the best serologic predictors for disease progression. We investigated levels of antibodies to tetanus toxoid and to HIV antigens including Env, Gag, Nef, and Tat proteins, as well as p24 antigenemia, viremia, CD4 cell count, and interferon-alpha (IFN-alpha) titers in FPs and NPs, and we correlated these data with clinical and biologic signs of progression. p24 Antigenemia, a marker of viral replication, and anti-Tat antibodies were highly and inversely correlated in both groups (P < .001). Furthermore, anti-p24 antibodies and low serum IFN-alpha levels were correlated to the NP versus the FP cohort. Finally, among NPs, only antibodies to Tat and not to the other HIV specificities (Env, Nef, Gag) were significantly predictive of clinical stability during their follow-up. Antibodies toward HIV-1 Tat, which are inversely correlated to p24 antigenemia, appear as a critical marker for a lack of disease progression. This study strongly suggests that rising anti-Tat antibodies through active immunization may be beneficial in AIDS vaccine development to control viral replication.

DJ1 Expression Downregulates in Neuroblastoma Cells (SK-N-MC Chronically Exposed to HIV-1 and Cocaine.

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Upal eRoy

2015-07-01

Full Text Available Background: HIV-associated neurological disorder (HAND has long been recognized as a consequence of Human Immunodeficiency Virus (HIV infection in the brain. The pathology of HAND gets more complicated with the recreational drug use such as cocaine. Recent studies have suggested multiple genetic influences involved in the pathology of addiction and HAND but only a fraction of the entire genetic risk has been investigated so far. In this regard, role of DJ1 protein (a gene linked to autosomal recessive early-onset Parkinson’s disease in regulating dopamine transmission and reactive oxygen species (ROS production in neuronal cells will be worth investigating in HIV-1 and cocaine exposed microenvironment. Being a very abundant protein in the brain, DJ1 could serve as a potential marker for early detection of HIV-1 and/or cocaine related neurological disorder.Methods: In vitro analysis was done to observe the effect of HIV-1 and/or cocaine on DJ1 protein expression in neuroblastoma cells (SK-N-MC. Gene expression and protein analysis of DJ1 was done on the HIV infected and/or cocaine treated SK-N-MC and compared to untreated cells using real time PCR, Western Blot and flow cytometry.Results: Gene expression and protein analysis indicated that there was a significant decrease in DJ1 expression in SK-N-MC chronically exposed to HIV-1 and/or cocaine.Conclusion: This is the first study to establish that DJ1 expression level in the neuronal cells significantly decreased in presence of HIV-1and/or cocaine indicating oxidative stress level of dopamine neurons.

ORF Alignment: NC_002758 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002758 gi|15924047 >1pwgA 4 329 74 373 1e-38 ... emb|CAG42767.1| autolysis and methic...autolysis ... and methicillin resistant-related protein ... [Staphylococcus aureus subsp. aure...us Mu50] ... ref|NP_374176.1| FmtA, autolysis and methicillin ... r...esistant-related protein [Staphylococcus aureus subsp. ... aureus N315] dbj|BAB94805.1| autolysis and methic...rain N315) ... ref|YP_043117.1| autolysis and methicillin ... resistant-related protein [Staph

ORF Alignment: NC_002951 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002951 gi|57650250 >1pwgA 4 329 74 373 1e-38 ... emb|CAG42767.1| autolysis and methic...autolysis ... and methicillin resistant-related protein ... [Staphylococcus aureus subsp. aure...us Mu50] ... ref|NP_374176.1| FmtA, autolysis and methicillin ... r...esistant-related protein [Staphylococcus aureus subsp. ... aureus N315] dbj|BAB94805.1| autolysis and methic...rain N315) ... ref|YP_043117.1| autolysis and methicillin ... resistant-related protein [Staph

ORF Alignment: NC_002953 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002953 gi|49485896 >1pwgA 4 329 74 373 1e-38 ... emb|CAG42767.1| autolysis and methic...autolysis ... and methicillin resistant-related protein ... [Staphylococcus aureus subsp. aure...us Mu50] ... ref|NP_374176.1| FmtA, autolysis and methicillin ... r...esistant-related protein [Staphylococcus aureus subsp. ... aureus N315] dbj|BAB94805.1| autolysis and methic...rain N315) ... ref|YP_043117.1| autolysis and methicillin ... resistant-related protein [Staph

ORF Alignment: NC_003923 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003923 gi|21282669 >1pwgA 4 329 74 373 1e-38 ... emb|CAG42767.1| autolysis and methic...autolysis ... and methicillin resistant-related protein ... [Staphylococcus aureus subsp. aure...us Mu50] ... ref|NP_374176.1| FmtA, autolysis and methicillin ... r...esistant-related protein [Staphylococcus aureus subsp. ... aureus N315] dbj|BAB94805.1| autolysis and methic...rain N315) ... ref|YP_043117.1| autolysis and methicillin ... resistant-related protein [Staph

ORF Alignment: NC_002745 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002745 gi|15926643 >1pwgA 4 329 74 373 1e-38 ... emb|CAG42767.1| autolysis and methic...autolysis ... and methicillin resistant-related protein ... [Staphylococcus aureus subsp. aure...us Mu50] ... ref|NP_374176.1| FmtA, autolysis and methicillin ... r...esistant-related protein [Staphylococcus aureus subsp. ... aureus N315] dbj|BAB94805.1| autolysis and methic...rain N315) ... ref|YP_043117.1| autolysis and methicillin ... resistant-related protein [Staph

ORF Alignment: NC_006155 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006155 gi|51595742 >1iwlA 1 181 22 202 2e-59 ... ref|YP_069933.1| putative outer-membrane lipoproteins...tis KIM] ... ref|NP_404970.1| putative outer-membrane lipoproteins ... ... ... carrier protein [Yersinia pestis CO92] emb|CAC90206.1| ... putative outer-membrane lipoproteins c...arrier protein ... [Yersinia pestis CO92] emb|CAH20642.1| putative ... outer-membrane lipoproteins...8 probable ... outer-membrane lipoproteins carrier protein lolA ... [imported] - Yersinia pest

ORF Alignment: NC_004088 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004088 gi|22126675 >1iwlA 1 181 22 202 2e-59 ... ref|YP_069933.1| putative outer-membrane lipoproteins...tis KIM] ... ref|NP_404970.1| putative outer-membrane lipoproteins ... ... ... carrier protein [Yersinia pestis CO92] emb|CAC90206.1| ... putative outer-membrane lipoproteins c...arrier protein ... [Yersinia pestis CO92] emb|CAH20642.1| putative ... outer-membrane lipoproteins...8 probable ... outer-membrane lipoproteins carrier protein lolA ... [imported] - Yersinia pest

ORF Alignment: NC_003143 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003143 gi|16121657 >1iwlA 1 181 22 202 2e-59 ... ref|YP_069933.1| putative outer-membrane lipoproteins...tis KIM] ... ref|NP_404970.1| putative outer-membrane lipoproteins ... ... ... carrier protein [Yersinia pestis CO92] emb|CAC90206.1| ... putative outer-membrane lipoproteins c...arrier protein ... [Yersinia pestis CO92] emb|CAH20642.1| putative ... outer-membrane lipoproteins...8 probable ... outer-membrane lipoproteins carrier protein lolA ... [imported] - Yersinia pest

ORF Alignment: NC_005810 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005810 gi|45441043 >1iwlA 1 181 22 202 2e-59 ... ref|YP_069933.1| putative outer-membrane lipoproteins...tis KIM] ... ref|NP_404970.1| putative outer-membrane lipoproteins ... ... ... carrier protein [Yersinia pestis CO92] emb|CAC90206.1| ... putative outer-membrane lipoproteins c...arrier protein ... [Yersinia pestis CO92] emb|CAH20642.1| putative ... outer-membrane lipoproteins...8 probable ... outer-membrane lipoproteins carrier protein lolA ... [imported] - Yersinia pest

ORF Alignment: NC_003236 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003236 gi|19074669 >1l1oC 2 175 456 623 1e-43 ... emb|CAD25779.1| DNA REPLICATION ...FACTOR A PROTEIN 1 [Encephalitozoon cuniculi GB-M1] ... ref|NP_586175.1| DNA REPLICATION FACTOR A PRO

ORF Sequence: NC_003283 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003283 gi|17563066 >gi|17563066|ref|NP_506462.1| putative protein family member, with a transme...mbrane domain (5O433) [Caenorhabditis elegans] MWNLVSPIHISSKFSMEMAEVNVVAVPEENRQTYLETDNDRLVMAIIWLIMPPMAVFFKCRGCTKHVFINFLLYLLLVLPAYKHATWFCFVKGREFEAEDGFVRAR

ORF Sequence: NC_003280 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003280 gi|17535455 >gi|17535455|ref|NP_495314.1| putative endoplasmic reticulum protein, with a transme...mbrane domain (2G788) [Caenorhabditis elegans] MTDVRFIIWNCIALLVALMMALTSIIILSDAPHNSME

Gag mutations strongly contribute to HIV-1 resistance to protease inhibitors in highly drug-experienced patients besides compensating for fitness loss.

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Elisabeth Dam

2009-03-01

Full Text Available Human immunodeficiency virus type 1 (HIV-1 resistance to protease inhibitors (PI results from mutations in the viral protease (PR that reduce PI binding but also decrease viral replicative capacity (RC. Additional mutations compensating for the RC loss subsequently accumulate within PR and in Gag substrate cleavage sites. We examined the respective contribution of mutations in PR and Gag to PI resistance and RC and their interdependence using a panel of HIV-1 molecular clones carrying different sequences from six patients who had failed multiple lines of treatment. Mutations in Gag strongly and directly contributed to PI resistance besides compensating for fitness loss. This effect was essentially carried by the C-terminal region of Gag (containing NC-SP2-p6 with little or no contribution from MA, CA, and SP1. The effect of Gag on resistance depended on the presence of cleavage site mutations A431V or I437V in NC-SP2-p6 and correlated with processing of the NC/SP2 cleavage site. By contrast, reverting the A431V or I437V mutation in these highly evolved sequences had little effect on RC. Mutations in the NC-SP2-p6 region of Gag can be dually selected as compensatory and as direct PI resistance mutations, with cleavage at the NC-SP2 site behaving as a rate-limiting step in PI resistance. Further compensatory mutations render viral RC independent of the A431V or I437V mutations while their effect on resistance persists.

Increasing cerebrospinal fluid chemokine concentrations despite undetectable cerebrospinal fluid HIV RNA in HIV-1-infected patients receiving antiretroviral therapy

NARCIS (Netherlands)

Gisolf, E. H.; van Praag, R. M.; Jurriaans, S.; Portegies, P.; Goudsmit, J.; Danner, S. A.; Lange, J. M.; Prins, J. M.

2000-01-01

Only limited data on cerebrospinal fluid (CSF) HIV-1 RNA responses and markers of local inflammation in CSF during antiretroviral therapy are available. HIV-RNA, soluble tumor necrosis factor (TNF)-receptor (sTNFr)-II, monocyte chemoattractant protein (MCP)-1, and interferon-gamma-inducible protein

ORF Alignment: NC_004605 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004605 gi|28900808 >1l3wA 6 536 1265 1798 3e-11 ... ref|NP_800463.1| putative biofilm...-associated surface protein [Vibrio parahaemolyticus ... RIMD 2210633] dbj|BAC62296.1| putative biofilm

ORF Alignment: NC_002952 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_002952 gi|49483165 >1dlwA 19 115 21 120 3e-19 ... ref|YP_040389.1| protozoan/cyano...bacterial globin family protein [Staphylococcus ... aureus subsp. aureus MRSA252] emb|CAG39975.1| ... protozoa

ORF Alignment: NC_006348 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006348 gi|53726032 >1iwlA 3 178 47 236 2e-42 ... ref|YP_109199.1| probable outer-membrane lipoproteins... ATCC 23344] ... emb|CAH36611.1| probable outer-membrane lipoproteins ... carrier protein [Bur

ORF Alignment: NC_006840 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006840 gi|59711513 >1iwlA 4 181 21 198 9e-49 ... ref|YP_204289.1| outer-membrane lipoproteins... carrier protein [Vibrio fischeri ES114] ... gb|AAW85401.1| outer-membrane lipoproteins ca

ORF Alignment: NC_006350 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006350 gi|53720213 >1iwlA 3 178 47 236 2e-42 ... ref|YP_109199.1| probable outer-membrane lipoproteins... ATCC 23344] ... emb|CAH36611.1| probable outer-membrane lipoproteins ... carrier protein [Bur

ORF Sequence: NC_001139 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_001139 gi|6321518 >gi|6321518|ref|NP_011595.1| Protein of unknown function; deletion... mutant has synthetic fitness defect with an sgs1 deletion mutant; Slx9p [Saccharomyces cerevisiae] MVA

ORF Alignment: NC_003236 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003236 gi|19074669 >1ewiA 5 113 54 161 1e-18 ... emb|CAD25779.1| DNA REPLICATION F...ACTOR A PROTEIN 1 [Encephalitozoon cuniculi GB-M1] ... ref|NP_586175.1| DNA REPLICATION FACTOR A PROT

ORF Alignment: NC_003070 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_003070 gi|18397761 >1wocC 2 96 2 97 5e-15 ... ref|YP_063428.1| ssb1 [Campylobacter... ... gb|EAL55921.1| single-strand binding protein, putative ... [Campylobacter coli RM2228] gb|AAR29517.1| ssb1

ORF Alignment: NC_005861 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_005861 gi|46446610 >1f39A 5 95 55 141 1e-16 ... ref|YP_007975.1| probable SOS mutagenesis... and repair protein UmuD [Parachlamydia sp. ... UWE25] emb|CAF23700.1| probable SOS mutagenesis

ORF Alignment: NC_006582 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_006582 gi|56962048 >1sd4A 2 99 6 103 1e-24 ... ref|YP_173770.1| methicillin resist...ance regulatory protein MecI [Bacillus clausii ... KSM-K16] dbj|BAD62809.1| methicillin resistance ...

ORF Alignment: NC_004463 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_004463 gi|27380945 >1tjlA 26 141 1 116 7e-32 ... ref|NP_772474.1| dnaK deletion su...ppressor protein [Bradyrhizobium japonicum USDA ... 110] dbj|BAC51099.1| dnaK deletion suppressor pro

ORF Alignment: NC_000117 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000117 gi|15605545 >1u7nA 1 327 4 316 2e-67 ... ref|NP_220331.1| FA/Phospholipid Synthesis... Protein [Chlamydia trachomatis D/UW-3/CX] ... gb|AAC68407.1| FA/Phospholipid Synthesis Prote

ORF Alignment: NC_000963 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_000963 gi|15604602 >1mwmA 4 314 14 327 1e-47 ... ref|NP_221120.1| ROD SHAPE-DETERMINING... PROTEIN MREB (mreB) [Rickettsia prowazekii ... str. Madrid E] emb|CAA15196.1| ROD SHAPE-DETERMINING

HIV-specific probabilistic models of protein evolution.

Directory of Open Access Journals (Sweden)

David C Nickle

2007-06-01

Full Text Available Comparative sequence analyses, including such fundamental bioinformatics techniques as similarity searching, sequence alignment and phylogenetic inference, have become a mainstay for researchers studying type 1 Human Immunodeficiency Virus (HIV-1 genome structure and evolution. Implicit in comparative analyses is an underlying model of evolution, and the chosen model can significantly affect the results. In general, evolutionary models describe the probabilities of replacing one amino acid character with another over a period of time. Most widely used evolutionary models for protein sequences have been derived from curated alignments of hundreds of proteins, usually based on mammalian genomes. It is unclear to what extent these empirical models are generalizable to a very different organism, such as HIV-1-the most extensively sequenced organism in existence. We developed a maximum likelihood model fitting procedure to a collection of HIV-1 alignments sampled from different viral genes, and inferred two empirical substitution models, suitable for describing between-and within-host evolution. Our procedure pools the information from multiple sequence alignments, and provided software implementation can be run efficiently in parallel on a computer cluster. We describe how the inferred substitution models can be used to generate scoring matrices suitable for alignment and similarity searches. Our models had a consistently superior fit relative to the best existing models and to parameter-rich data-driven models when benchmarked on independent HIV-1 alignments, demonstrating evolutionary biases in amino-acid substitution that are unique to HIV, and that are not captured by the existing models. The scoring matrices derived from the models showed a marked difference from common amino-acid scoring matrices. The use of an appropriate evolutionary model recovered a known viral transmission history, whereas a poorly chosen model introduced phylogenetic