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1.
Retrovirology ; 17(1): 17, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32615983

ABSTRACT

BACKGROUND: Heterosexual transmission remains the main route of HIV-1 transmission and female genital tract (FGT) inflammation increases the risk of infection. However, the mechanism(s) by which inflammation facilitates infection is not fully understood. In rhesus macaques challenged with simian immunodeficiency virus, dendritic cell (DC) mediated recruitment of CD4+ T cells to the FGT was critical for infection. The aim of this study was to delineate the mechanisms underlying DC-mediated HIV infection by comparing chemokine and pro-inflammatory cytokine production in response to transmitted founder (TF) and chronic infection (CI) Envelope (Env) pseudotyped viruses (PSV). RESULTS: Monocyte-derived DCs (MDDCs) were stimulated with PSV and recombinant gp140 representing matched TF and CI pairs of four individuals and cytokine secretion measured by multiplex immuno-assay. We found that 4/9 Env induced robust MDDC inflammatory responses and of those, three were cloned from TFs. Overall, TF Env induced MDDCs from healthy donors to secrete higher concentrations of inflammatory cytokines and chemokines than those from CI, suggesting TF Env were better inducers of inflammation. Assessing the signalling pathway associated with inflammatory cytokines, we found that PSV of matched TF and CI variants and a gp140 clone activated ERK and JNK to similar levels. Recombinant soluble DC-SIGN inhibited cytokine release and activation of ERK by PSV, suggesting that Env-DC-SIGN binding was partly involved in MDDC stimulation. Therefore, Env clones might differentially stimulate MDDC immune responses via alternative, yet unidentified signalling pathways. CONCLUSION: Overall, this could suggest that the genetics of the virus itself influences inflammatory responses during HIV infection. In the absence of pre-existing infections, induction of greater inflammatory response by TFs might favour virus survival within the healthy FGT by driving an influx of target cells to sites of infection while suppressing immune responses via IL-10.


Subject(s)
Dendritic Cells/immunology , HIV Infections/virology , HIV-1/physiology , Cell Adhesion Molecules/metabolism , Chemokines/metabolism , Cytokines/metabolism , Female , Humans , Lectins, C-Type/metabolism , Mitogen-Activated Protein Kinase Kinases/metabolism , Monocytes/immunology , Receptors, Cell Surface/metabolism , Signal Transduction , env Gene Products, Human Immunodeficiency Virus/genetics , env Gene Products, Human Immunodeficiency Virus/metabolism
2.
PLoS One ; 15(1): e0227533, 2020.
Article in English | MEDLINE | ID: mdl-31978062

ABSTRACT

Envelope (Env) phenotype(s) that provide transmitted founders (TF) with a selective advantage during HIV-1 transmission would be the ideal target for preventative therapy. We generated Env clones from four individuals infected with a single virus and one participant infected with multiple variants at transmission and compared phenotype with matched Envs from chronic infection (CI). When we determined whether pseudovirus (PSV) of the five TF and thirteen matched CI Env clones differed in their ability to 1) enter TZM-bl cells, 2) bind DC-SIGN, and 3) trans-infect CD4+ cells there was no association between time post-infection and variation in Env phenotype. However, when we compared the ability of PSV to induce monocyte-derived dendritic cells (MDDCs) to secrete Interleukin-10 (IL-10), we found that only TF Envs from single variant transmission cases induced MDDCs to secrete either higher or similar levels of IL-10 as the CI clones. Furthermore, interaction between MDDC DC-SIGN and Env was required for secretion of IL-10. When variants were grouped according to time post-infection, TF PSV induced the release of higher levels of IL-10 than their CI counterparts although this relationship varied across MDDC donors. The selection of variants during transmission is therefore likely a complex event dependent on both virus and host genetics. Our findings suggest that, potentially due to overall variation in N-glycosylation across variants, nuanced differences in binding of TF Env to DC-SIGN might trigger alternative DC immune responses (IRs) in the female genital tract (FGT) that favour HIV-1 survival and facilitate transmission.


Subject(s)
Dendritic Cells/metabolism , Dendritic Cells/virology , Genetic Variation , HIV-1/genetics , HIV-1/physiology , Interleukin-10/metabolism , env Gene Products, Human Immunodeficiency Virus/genetics , Cell Adhesion Molecules/metabolism , Dendritic Cells/immunology , Female , Glycosylation , HEK293 Cells , HIV-1/immunology , Humans , Lectins, C-Type/metabolism , Phenotype , Receptors, Cell Surface/metabolism , Vaccines, DNA/immunology , Virus Internalization , env Gene Products, Human Immunodeficiency Virus/metabolism
3.
BMC Res Notes ; 12(1): 340, 2019 Jun 17.
Article in English | MEDLINE | ID: mdl-31208438

ABSTRACT

OBJECTIVE: As part of a larger study to understand how Envelope N-glycosylation influences HIV-1 pathogenesis, we selected a participant infected with a single Subtype C variant and determined whether deletion of specific potential N-glycan sites (PNGs) impacted Envelope function longitudinally. RESULTS: We deleted five PNGs previously linked to HIV-1 transmission of two matched Envelope clones representing variants at 5 and 173 weeks post-infection. The transmitted founder (TF) had significantly better pseudovirus entry efficiency than the chronic infection (CI) variant. Deletion of all PNGs significantly reduced TF entry efficiency, binding to dendritic cell-specific intracellular adhesion molecule 3 grabbing non-integrin (DC-SIGN) receptor and trans-infection. However, mutational analysis did not affect the phenotype of the CI Envelope to the same extent. Notably, deletion of the PNGs at N241 and N448 had no effect on CI Envelope function, suggesting that some PNGs might only be important during acute infection. Therefore, vaccines that elicit antibodies against N-glycans important for TF Envelope function could drive the loss of PNGs during immune escape, abrogating viral replication. Conversely, changes in N-glycosylation might have no effect on some variants, reducing vaccine efficacy. This finding highlights the need for further investigation into the role of Envelope N-glycosylation in HIV-1 pathogenesis.


Subject(s)
Dendritic Cells/immunology , HIV Infections/immunology , HIV-1/immunology , env Gene Products, Human Immunodeficiency Virus/immunology , Amino Acid Sequence , Binding Sites/genetics , Binding Sites/immunology , Cell Adhesion Molecules/genetics , Cell Adhesion Molecules/immunology , Cell Adhesion Molecules/metabolism , Cell Line, Tumor , Cells, Cultured , Dendritic Cells/cytology , Dendritic Cells/metabolism , Disease Progression , Female , Glycosylation , HEK293 Cells , HIV Infections/transmission , HIV Infections/virology , HIV-1/genetics , HIV-1/pathogenicity , Humans , Lectins, C-Type/genetics , Lectins, C-Type/immunology , Lectins, C-Type/metabolism , Receptors, Cell Surface/genetics , Receptors, Cell Surface/immunology , Receptors, Cell Surface/metabolism , Sequence Deletion/immunology , Virus Replication/genetics , Virus Replication/immunology , env Gene Products, Human Immunodeficiency Virus/genetics , env Gene Products, Human Immunodeficiency Virus/metabolism
4.
Cell Host Microbe ; 24(4): 593-599.e3, 2018 10 10.
Article in English | MEDLINE | ID: mdl-30269971

ABSTRACT

Eliciting antibodies that neutralize a broad range of circulating HIV strains (broadly neutralizing antibodies [bnAbs]) represents a key priority for vaccine development. HIV superinfection (re-infection with a second strain following an established infection) has been associated with neutralization breadth, and can provide insights into how the immune system responds to sequential exposure to distinct HIV envelope glycoproteins (Env). Characterizing the neutralizing antibody (nAb) responses in four superinfected women revealed that superinfection does not boost memory nAb responses primed by the first infection or promote nAb responses to epitopes conserved in both infecting viruses. While one superinfected individual developed potent bnAbs, superinfection was likely not the driver as the nAb response did not target an epitope conserved in both viruses. Rather, sequential exposure led to nAbs specific to each Env but did not promote bnAb development. Thus, sequential immunization with heterologous Envs may not be sufficient to focus the immune response onto conserved epitopes.


Subject(s)
HIV Antibodies/immunology , HIV Infections/virology , HIV-1/immunology , RNA, Viral/immunology , Superinfection/virology , Adult , Anti-HIV Agents/therapeutic use , Antibodies, Neutralizing/immunology , Female , HEK293 Cells , HIV Envelope Protein gp120/genetics , HIV Envelope Protein gp120/immunology , HIV Infections/blood , HIV Infections/complications , HIV Infections/drug therapy , HIV-1/drug effects , HIV-1/genetics , Humans , Middle Aged , Peptide Fragments/genetics , Peptide Fragments/immunology , RNA, Viral/blood , RNA, Viral/genetics , Superinfection/blood , Superinfection/complications , Superinfection/drug therapy , Tenofovir/therapeutic use
5.
Ann Clin Microbiol Antimicrob ; 15: 16, 2016 Mar 11.
Article in English | MEDLINE | ID: mdl-26968525

ABSTRACT

Bacterial vaginosis (BV) is the most common vaginal disorder affecting women of reproductive age and is associated with increased risk of sexually transmitted infections such as human immunodeficiency syndrome (HIV-1). Sub-Saharan Africa has the highest BV and HIV-1 burden and yet very few studies have focused on understanding the aetiology of BV and its association with HIV in this region. It has been suggested that we need to accurately diagnose and treat BV to lower the risk of HIV infection globally. However, effective diagnosis requires knowledge of what constitutes a "healthy" cervicovaginal microbiome and current studies indicate that Lactobacillus crispatus might not be the only commensal protective against BV: healthy women from different countries and ethnicities harbour alternative commensals. Microbiotas associated with BV have also shown global variation, further complicating effective diagnosis via culture-based assays as some species are difficult to grow. Antibiotics and probiotics have been suggested to be key in controlling BV infection, but the efficacy of this treatment might rely on reconstituting endogenous commensals while targeting a specific species of BV-associated bacteria (BVAB). Alternatively, therapy could inhibit essential BV bacterial growth factors e.g. sialidases or provide anti-microbial compounds e.g. lactic acid associated with a healthy cervicovaginal microbiome. But without global investigation into the mechanism of BV pathogenesis and its association with HIV, selection of such compounds could be limited to Caucasian women from certain regions. To confirm this suggestion and guide future therapy we require standardised diagnostic assays and research methodologies. This review will focus on research papers that describe the global variation of BV aetiology and how this influences the identification of determinants of BV pathogenesis and potential probiotic and antimicrobial therapy.


Subject(s)
Anti-Bacterial Agents/administration & dosage , HIV Infections/prevention & control , Probiotics/administration & dosage , Vaginosis, Bacterial/prevention & control , Africa South of the Sahara/epidemiology , Female , HIV Infections/etiology , Humans , Lactobacillus/physiology , Vaginosis, Bacterial/complications , Vaginosis, Bacterial/microbiology
6.
AIDS Res Hum Retroviruses ; 32(3): 303-10, 2016 Mar.
Article in English | MEDLINE | ID: mdl-25905681

ABSTRACT

Mutations in functionally constrained sites of the HIV envelope (Env) can affect entry efficiency and are potential targets for vaccine and drug design. We investigated Du151, a dual-infected individual with rapid disease progression. At her death 19 months postinfection (mpi), she was infected with a recombinant variant, which outgrew both parental viruses. We aimed to determine whether the recombinant virus had enhanced Env entry efficiency compared to the parental viruses and to identify the functional determinant. We generated 15 env clones at 1, 2, 8, and 19 mpi. Pseudovirus carrying a recombinant Env clone (PSV clone), C18 (19 mpi), had significantly higher entry efficiency compared to the parents, suggesting that the recombinant virus had enhanced fitness. To identify the functional determinant, we compared two recombinant PSV clones (C18 and C63)-differing in entry efficiency (2-fold) and by four and three amino acids in gp120 and gp41, respectively. The increased entry efficiency of a C18-gp41 PSV chimera indicated that the three amino acids in the C18 gp41 region were involved (K658, G671, and F717). Site-directed mutagenesis of the three amino acids of C63 showed that a single amino acid mutation, R658K, increased pseudovirion entry efficiency. The introduction of R658 into two PSV clones (C1 and C18) decreased their entry efficiency, suggesting that R658 carries a fitness cost. Thus, our data suggest that a recombinant virus emerged at 19 mpi with enhanced Env entry efficiency. Therefore, K658 in gp41 could in part be a contributing factor to the increased viral load and rapid disease progression of Du151.


Subject(s)
HIV Infections/pathology , HIV Infections/virology , HIV-1/genetics , HIV-1/physiology , Recombination, Genetic , Virus Internalization , env Gene Products, Human Immunodeficiency Virus/genetics , DNA Mutational Analysis , Disease Progression , Female , HIV-1/isolation & purification , Humans , Mutagenesis, Site-Directed , Mutant Proteins/genetics , Viral Load
7.
J Infect Dis ; 212(6): 904-8, 2015 Sep 15.
Article in English | MEDLINE | ID: mdl-25754982

ABSTRACT

The relevance of superinfection as a model to identify correlates of protection against human immunodeficiency virus (HIV) depends on whether the superinfecting transmission resembles primary infection, which has not been established. Here, we characterize the genetic bottleneck in superinfected individuals for the first time. In all 3 cases, superinfection produced a spike in viral load and could be traced to a single, C-C chemokine receptor 5-tropic founder virus with shorter, less glycosylated variable regions than matched chronic viruses. These features are consistent with primary HIV transmission and provide support for the use of superinfection as a model to address correlates of protection against HIV.


Subject(s)
HIV Infections/virology , HIV-1/genetics , Superinfection/virology , Cohort Studies , Consensus Sequence , DNA, Complementary/chemistry , Gene Products, env/chemistry , Genetic Variation , HIV Infections/immunology , HIV-1/classification , HIV-1/physiology , Humans , Longitudinal Studies , Phylogeny , RNA, Viral/genetics , Receptors, Chemokine , Retrospective Studies , Superinfection/immunology , Viral Load , Virus Attachment
8.
J Virol ; 86(24): 13423-33, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23015721

ABSTRACT

Certain immune-driven mutations in HIV-1, such as those arising in p24(Gag), decrease viral replicative capacity. However, the intersubtype differences in the replicative consequences of such mutations have not been explored. In HIV-1 subtype B, the p24(Gag) M250I mutation is a rare variant (0.6%) that is enriched among elite controllers (7.2%) (P = 0.0005) and appears to be a rare escape variant selected by HLA-B58 supertype alleles (P < 0.01). In contrast, in subtype C, it is a relatively common minor polymorphic variant (10 to 15%) whose appearance is not associated with a particular HLA allele. Using site-directed mutant viruses, we demonstrate that M250I reduces in vitro viral replicative capacity in both subtype B and subtype C sequences. However, whereas in subtype C downstream compensatory mutations at p24(Gag) codons 252 and 260 reduce the adverse effects of M250I, fitness costs in subtype B appear difficult to restore. Indeed, patient-derived subtype B sequences harboring M250I exhibited in vitro replicative defects, while those from subtype C did not. The structural implications of M250I were predicted by protein modeling to be greater in subtype B versus C, providing a potential explanation for its lower frequency and enhanced replicative defects in subtype B. In addition to accounting for genetic differences between HIV-1 subtypes, the design of cytotoxic-T-lymphocyte-based vaccines may need to account for differential effects of host-driven viral evolution on viral fitness.


Subject(s)
Genes, gag , HIV Core Protein p24/genetics , HIV-1/physiology , Mutation , Virus Replication/genetics , Amino Acid Sequence , Cohort Studies , HIV Core Protein p24/chemistry , HIV Infections/virology , Humans , Molecular Sequence Data , Mutagenesis, Site-Directed , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology, Amino Acid
9.
J Infect Dis ; 205(2): 194-203, 2012 Jan 15.
Article in English | MEDLINE | ID: mdl-22190580

ABSTRACT

BACKGROUND: The biggest challenge in human immunodeficiency virus type 1 (HIV-1) prevention in Africa is the high HIV-1 burden in young women. In macaques, proinflammatory cytokine production in the genital tract is necessary for target cell recruitment and establishment of simian immunodeficiency virus (SIV) infection following vaginal inoculation. The purpose of this study was to assess if genital inflammation during early HIV-1 infection predisposes women to rapid disease progression. METHODS: Inflammatory cytokine concentrations were measured in cervicovaginal lavage (CVL) from 49 women 6, 17, 30, and 55 weeks after HIV-1 infection and from 22 of these women before infection. Associations between genital inflammation and viral load set point and blood CD4 cell counts 12 months after infection were investigated. RESULTS: Elevated genital cytokine concentrations 6 and 17 weeks after HIV-1 infection were associated with higher viral load set points and, to a lesser extent, with CD4 depletion. CVL cytokine concentrations during early infection did not differ relative to preinfection but were elevated in women who had vaginal discharge, detectable HIV-1 RNA in their genital tracts, and lower blood CD4 counts. CONCLUSION: Genital inflammation during early HIV-1 infection was associated with higher viral load set point and CD4 depletion, which are markers of rapid disease progression. Strategies aimed at reducing genital inflammation during early HIV-1 infection may slow disease progression.


Subject(s)
Cytokines/metabolism , HIV Infections/virology , HIV-1/immunology , RNA, Viral/metabolism , Uterine Cervicitis/metabolism , Vaginitis/metabolism , Viral Load , Adolescent , Adult , CD4 Lymphocyte Count , Disease Progression , Female , HIV Infections/complications , HIV Infections/immunology , Humans , Logistic Models , Middle Aged , Statistics, Nonparametric , Time Factors , Uterine Cervicitis/complications , Uterine Cervicitis/virology , Vaginal Douching , Vaginitis/complications , Vaginitis/virology , Young Adult
10.
Virology ; 415(2): 107-13, 2011 Jul 05.
Article in English | MEDLINE | ID: mdl-21531432

ABSTRACT

The Mbeya region of Tanzania has a genetically complex HIV epidemic with multiple subtypes and recombinant forms circulating, together with a high frequency of dual infections with more than one subtype. This study aimed to determine whether this impacted the HIV-1 transmission bottleneck. A total of 210 env sequences from 22 participants were generated from recently infected women from Mbeya using the single genome amplification approach. Participants were infected with subtypes C (n=9), A (n=4), or D (n=1), and recombinants AC (n=4), CD (n=2), AD (n=1), or ACD (n=1). Sixteen participants (73%) were infected with a single variant; five (23%) with multiple variants; and one (4%) was dually infected. Thus the frequency of single variant infections was similar to cohorts located in genetically restricted subtype B or C epidemics, suggesting that multiple circulating subtypes and unique recombinant forms do not have a significant impact on the transmission bottleneck.


Subject(s)
HIV Infections/transmission , HIV Infections/virology , HIV-1/genetics , Recombination, Genetic , Cohort Studies , Female , HIV Infections/epidemiology , HIV-1/classification , HIV-1/isolation & purification , Humans , Molecular Sequence Data , Phylogeny , Tanzania/epidemiology
11.
AIDS Res Hum Retroviruses ; 27(11): 1167-72, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21198409

ABSTRACT

Previously, we determined the incidence of dual infections in a South African cohort and its association with higher viral setpoint. Ten years later, we compare the incidence and impact of dual infections at transmission on viral setpoint in a geographically similar cohort (n = 46) making use of both the heteroduplex mobility assay (HMA) and the more recent single genome amplification (SGA) approach. HIV incidence was lower in this cohort (7% compared to 18%), and we find a similar reduction in the number of dual infections (9% compared to 19%). Unlike the previous study, there was no association between either dual infection (n = 4) or multivariant transmission (n = 7) and disease progression. This study emphasized the importance of monitoring changes in the HIV epidemic as it may have important ramifications on our understanding of the natural history of disease.


Subject(s)
Coinfection/epidemiology , HIV Infections/complications , HIV Infections/epidemiology , Sex Work , Sexually Transmitted Diseases/complications , Sexually Transmitted Diseases/epidemiology , Adolescent , Adult , Cohort Studies , Disease Progression , Female , HIV Infections/diagnosis , HIV Infections/transmission , HIV-1/genetics , Heteroduplex Analysis , Humans , Incidence , Middle Aged , Molecular Sequence Data , Sequence Analysis, DNA , Sexually Transmitted Diseases/diagnosis , Sexually Transmitted Diseases/transmission , South Africa/epidemiology , Young Adult
12.
J Virol ; 84(22): 12018-29, 2010 Nov.
Article in English | MEDLINE | ID: mdl-20826686

ABSTRACT

Deciphering immune events during early stages of human immunodeficiency virus type 1 (HIV-1) infection is critical for understanding the course of disease. We characterized the hierarchy of HIV-1-specific T-cell gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay responses during acute subtype C infection in 53 individuals and associated temporal patterns of responses with disease progression in the first 12 months. There was a diverse pattern of T-cell recognition across the proteome, with the recognition of Nef being immunodominant as early as 3 weeks postinfection. Over the first 6 months, we found that there was a 23% chance of an increased response to Nef for every week postinfection (P = 0.0024), followed by a nonsignificant increase to Pol (4.6%) and Gag (3.2%). Responses to Env and regulatory proteins appeared to remain stable. Three temporal patterns of HIV-specific T-cell responses could be distinguished: persistent, lost, or new. The proportion of persistent T-cell responses was significantly lower (P = 0.0037) in individuals defined as rapid progressors than in those progressing slowly and who controlled viremia. Almost 90% of lost T-cell responses were coincidental with autologous viral epitope escape. Regression analysis between the time to fixed viral escape and lost T-cell responses (r = 0.61; P = 0.019) showed a mean delay of 14 weeks after viral escape. Collectively, T-cell epitope recognition is not a static event, and temporal patterns of IFN-γ-based responses exist. This is due partly to viral sequence variation but also to the recognition of invariant viral epitopes that leads to waves of persistent T-cell immunity, which appears to associate with slower disease progression in the first year of infection.


Subject(s)
HIV Infections/immunology , HIV Infections/pathology , HIV-1/immunology , T-Lymphocytes/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Cohort Studies , Disease Progression , Female , Follow-Up Studies , HIV Infections/blood , HIV Infections/virology , HIV-1/classification , Humans , Interferon-gamma/blood , Interferon-gamma/immunology , Male , T-Lymphocytes/virology
13.
Curr Opin HIV AIDS ; 4(4): 247-52, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19532060

ABSTRACT

PURPOSE OF REVIEW: To provide an update on the origin of the HIV epidemic and insights into how the immune response is shaping virus evolution. RECENT FINDINGS: Characterization of archival samples showed that by the 1960s, HIV had already diverged within humans. It is now estimated that HIV has been in humans since at least the early 1900s. However, despite the potential for different divergent viruses to spread, surprisingly few viruses successfully expanded to cause the global epidemic. In approximately 80% of cases, productive infection is the result of infection with only a single virus or single virus-infected cell. After transmission, HIV evolves at a rapid rate driven by the immune pressure until the virus reaches a delicate survival balance: on one hand avoiding elimination through the development of cytotoxic T-cell immune escape mutations, and on the other sacrificing replication fitness as these mutations may come with a severe fitness cost to the virus. People infected with these 'attenuated' cytotoxic T-cell escape viruses can have a survival advantage. Cytotoxic T-cell responses are molding HIV diversity at a population level resulting in a loss of some of the common immune epitopes. SUMMARY: Insights into the origin of HIV and its evolution between populations and within individuals is essential to understanding HIV pathogenesis and imperative for the design of effective biomedical interventions such as vaccines.


Subject(s)
HIV Infections/virology , HIV-1/classification , HIV-1/genetics , RNA, Viral/genetics , Cluster Analysis , Evolution, Molecular , Genotype , HIV Infections/epidemiology , HIV Infections/immunology , HIV-1/immunology , HIV-1/isolation & purification , Humans , Molecular Epidemiology , Sequence Analysis, DNA
14.
Virol J ; 5: 160, 2008 Dec 23.
Article in English | MEDLINE | ID: mdl-19105834

ABSTRACT

BACKGROUND: Positive selection pressure acting on protein-coding sequences is usually inferred when the rate of nonsynonymous substitution is greater than the synonymous rate. However, purifying selection acting directly on the nucleotide sequence can lower the synonymous substitution rate. This could result in false inference of positive selection because when synonymous changes at some sites are under purifying selection, the average synonymous rate is an underestimate of the neutral rate of evolution. Even though HIV-1 coding sequences contain a number of regions that function at the nucleotide level, and are thus likely to be affected by purifying selection, studies of positive selection assume that synonymous substitutions can be used to estimate the neutral rate of evolution. RESULTS: We modelled site-to-site variation in the synonymous substitution rate across coding regions of the HIV-1 genome. Synonymous substitution rates were found to vary significantly within and between genes. Surprisingly, regions of the genome that encode proteins in more than one frame had significantly higher synonymous substitution rates than regions coding in a single frame. We found evidence of strong purifying selection pressure affecting synonymous mutations in fourteen regions with known functions. These included an exonic splicing enhancer, the rev-responsive element, the poly-purine tract and a transcription factor binding site. A further five highly conserved regions were located within known functional domains. We also found four conserved regions located in env and vpu which have not been characterized previously. CONCLUSION: We provide the coordinates of genomic regions with markedly lower synonymous substitution rates, which are putatively under the influence of strong purifying selection pressure at the nucleotide level as well as regions encoding proteins in more than one frame. These regions should be excluded from studies of positive selection acting on HIV-1 coding regions.


Subject(s)
HIV-1/genetics , Viral Matrix Proteins/genetics , Amino Acid Substitution , Base Sequence , Codon/genetics , Computer Simulation , DNA, Viral/genetics , Genes, Viral , Genetic Variation , Genome, Viral , Models, Genetic , Models, Statistical , Selection, Genetic , Sequence Alignment
15.
PLoS Pathog ; 4(3): e1000033, 2008 Mar 21.
Article in English | MEDLINE | ID: mdl-18369479

ABSTRACT

One of the most important genetic factors known to affect the rate of disease progression in HIV-infected individuals is the genotype at the Class I Human Leukocyte Antigen (HLA) locus, which determines the HIV peptides targeted by cytotoxic T-lymphocytes (CTLs). Individuals with HLA-B*57 or B*5801 alleles, for example, target functionally important parts of the Gag protein. Mutants that escape these CTL responses may have lower fitness than the wild-type and can be associated with slower disease progression. Transmission of the escape variant to individuals without these HLA alleles is associated with rapid reversion to wild-type. However, the question of whether infection with an escape mutant offers an advantage to newly infected hosts has not been addressed. Here we investigate the relationship between the genotypes of transmitted viruses and prognostic markers of disease progression and show that infection with HLA-B*57/B*5801 escape mutants is associated with lower viral load and higher CD4+ counts.


Subject(s)
Antigens, CD/immunology , HIV Infections/immunology , HIV-1/immunology , HLA-B Antigens/immunology , Mutation , Organic Cation Transport Proteins/immunology , gag Gene Products, Human Immunodeficiency Virus/immunology , Antigens, CD/genetics , CD4 Lymphocyte Count , Cohort Studies , Disease Progression , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/immunology , Female , Genetic Predisposition to Disease , Genotype , HIV Infections/transmission , HIV Infections/virology , HIV-1/genetics , HLA-B Antigens/genetics , Humans , Immunodominant Epitopes/genetics , Immunodominant Epitopes/immunology , Organic Cation Transport Proteins/genetics , Survival Rate , T-Lymphocytes, Cytotoxic/immunology , gag Gene Products, Human Immunodeficiency Virus/genetics
16.
Biol Chem ; 387(8): 1043-51, 2006 Aug.
Article in English | MEDLINE | ID: mdl-16895474

ABSTRACT

Angiotensin-converting enzyme (ACE) exists as two isoforms: somatic ACE (sACE), comprised of two homologous N and C domains, and testis ACE (tACE), comprised of the C domain only. The N and C domains are both active, but show differences in substrate and inhibitor specificity. While both isoforms are shed from the cell surface via a sheddase-mediated cleavage, tACE is shed much more efficiently than sACE. To delineate the regions of tACE that are important in catalytic activity, intracellular processing, and regulated ectodomain shedding, regions of the tACE sequence were replaced with the corresponding N-domain sequence. The resultant chimeras C1-163Ndom-ACE, C417-579Ndom-ACE, and C583-623Ndom-ACE were processed to the cell surface of transfected Chinese hamster ovary (CHO) cells, and were cleaved at the identical site as that of tACE. They also showed acquisition of N-domain-like catalytic properties. Homology modelling of the chimeric proteins revealed structural changes in regions required for tACE-specific catalytic activity. In contrast, C164-416Ndom-ACE and C191-214Ndom-ACE demonstrated defective intracellular processing and were neither enzymatically active nor shed. Therefore, critical elements within region D164-V416 and more specifically I191-T214 are required for the processing, cell-surface targeting, and enzyme activity of tACE, and cannot be substituted for by the homologous N-domain sequence.


Subject(s)
Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/metabolism , Animals , CHO Cells , Catalysis , Catalytic Domain , Cricetinae , Enzyme Activation/physiology , Isoenzymes/biosynthesis , Isoenzymes/chemistry , Isoenzymes/metabolism , Kinetics , Male , Peptidyl-Dipeptidase A/genetics , Protein Conformation , Protein Structure, Tertiary , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Structure-Activity Relationship , Substrate Specificity , Testis/enzymology
17.
Virology ; 351(1): 18-28, 2006 Jul 20.
Article in English | MEDLINE | ID: mdl-16647097

ABSTRACT

Pim kinases are proto-oncogenes that are upregulated in a number of B cell cancers, including Epstein-Barr Virus (EBV) associated Burkitt's lymphoma. They have also been shown to be upregulated in Kaposi sarcoma-associated herpes virus (KSHV) infected primary B cells. Most cells in KSHV-associated tumors are latently infected and express only a small subset of viral genes, with KSHV latency associated nuclear antigen (LANA) being constitutively expressed. LANA regulates the transcription of a large number of cellular and viral genes. Here, we show that LANA upregulates transcription from the Pim-1 promoter (pPim-1) and map this activation to a region in the promoter located within the sequence (-681 to +37). We show that LANA expressing cells can proliferate faster and are better protected from drug induced apoptosis. Since transition through cell cycle check points and anti-apoptosis are functions associated with Pim-1, it is likely that higher Pim-1 expression in cells expressing LANA is responsible, at least in part, for this effect. A Pim-1 phosphorylation site was also identified within the amino-terminal domain of LANA. Using in vitro kinase assays, we confirmed that LANA was indeed a Pim-1 substrate, and the failure of Pim-1 to phosphorylate LANA mutated at SS205/6RR identified this site as the specific serine residues phosphorylated by Pim-1. This report provides valuable insight into yet another cellular signaling pathway subverted by KSHV LANA and suggests a contribution to KSHV related oncogenesis.


Subject(s)
Antigens, Viral/metabolism , Herpesvirus 8, Human/genetics , Herpesvirus 8, Human/metabolism , Nuclear Proteins/metabolism , Proto-Oncogene Proteins c-pim-1/metabolism , Up-Regulation , Antigens, Viral/genetics , Apoptosis , B-Lymphocytes/metabolism , Cell Line , Cell Proliferation , Epithelial Cells/metabolism , Humans , Nuclear Proteins/genetics , Phosphorylation , Promoter Regions, Genetic , Proto-Oncogene Proteins c-pim-1/genetics , Signal Transduction , Substrate Specificity , Transcription, Genetic
18.
Biochem J ; 389(Pt 3): 739-44, 2005 Aug 01.
Article in English | MEDLINE | ID: mdl-15813703

ABSTRACT

sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test this, we constructed two mutants: CNdom-ACE and CCdom-ACE. CNdom-ACE was shed less efficiently than sACE, whereas CCdom-ACE was shed as efficiently as tACE. Notably, cleavage occurred both within the stalk and the interdomain bridge in both mutants, suggesting that a sheddase recognition motif resides within the C domain and is capable of directly cleaving at both positions. Analysis of the catalytic properties of the mutants and comparison with sACE and tACE revealed that the k(cat) for sACE and CNdom-ACE was less than or equal to the sum of the kcat values for tACE and the N-domain, suggesting negative co-operativity, whereas the kcat value for the CCdom-ACE suggested positive co-operativity between the two domains. Taken together, the results provide support for (i) the existence of a sheddase recognition motif in the C domain and (ii) molecular flexibility of the N and C domains in sACE, resulting in occlusion of the C-domain recognition motif by the N domain as well as close contact of the two domains during hydrolysis of peptide substrates.


Subject(s)
Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/metabolism , Animals , CHO Cells , Catalytic Domain , Cricetinae , Gene Expression , Mutation , Protein Structure, Tertiary
19.
J Proteome Res ; 4(2): 258-67, 2005.
Article in English | MEDLINE | ID: mdl-15822901

ABSTRACT

ACE chimeric proteins and N domain monoclonal antibodies (mAbs) were used to determine the influence of the N domain, and particular regions thereof, on the rate of ACE ectodomain shedding. Somatic ACE (having both N and C domains) was shed at a rate of 20%/24 h. Deletion of the C domain of somatic ACE generated an N domain construct (ACEDeltaC) which demonstrated the lowest rate of shedding (12%). However, deletion of the N domain of somatic ACE (ACEDeltaN) dramatically increased shedding (212%). Testicular ACE (tACE) having 36 amino acid residues (heavily O-glycosylated) at the N-terminus of the C domain shows a 4-fold decrease in the rate of shedding (49%) compared to that of ACEDeltaN. When the N-terminal region of the C domain was replaced with the corresponding homologous 141 amino acids of the N domain (N-delACE) the rate of shedding of the ACEDeltaN was only slightly decreased (174%), but shedding was still 3.5-fold more efficient than wild-type testicular ACE. Monoclonal antibodies specific for distinct, but overlapping, N-domain epitopes altered the rate of ACE shedding. The mAb 3G8 decreased the rate of shedding by 30%, whereas mAbs 9B9 and 3A5 stimulated ACE shedding 2- to 4-fold. Epitope mapping of these mAbs in conjunction with a homology model of ACE N domain structure, localized a region in the N-domain that may play a role in determining the relatively low rate of shedding of somatic ACE from the cell surface.


Subject(s)
Antibodies, Monoclonal/immunology , Amino Acid Sequence , Animals , Base Sequence , CHO Cells , Cricetinae , DNA Primers , Enzyme-Linked Immunosorbent Assay , Epitope Mapping , Humans , Models, Molecular , Molecular Sequence Data , Primates , Sequence Homology, Amino Acid
20.
Biochem Biophys Res Commun ; 297(5): 1225-30, 2002 Oct 11.
Article in English | MEDLINE | ID: mdl-12372418

ABSTRACT

Numerous cytokines, receptors, and ectoenzymes, including angiotensin I-converting enzyme (ACE), are shed from the cell surface by limited proteolysis at the juxtamembrane stalk region. The membrane-proximal C domain of ACE has been implicated in sheddase-substrate recognition. We mapped the functional boundaries of the testis ACE ectodomain (identical to the C domain of somatic ACE) by progressive deletions from the N- and C-termini and analysing the effects on catalytic activity, stability, and shedding in transfected cells. We found that deletions extending beyond Leu37 at the N-terminus and Trp616 at the C-terminus abolished catalytic activity and shedding, either by disturbing the ectodomain conformation or by inhibiting maturation and surface expression. Based on these data and on sequence alignments, we propose that the boundaries of the ACE ectodomain are Asp40 at the N-terminus and Gly615 at the C-terminus.


Subject(s)
Peptidyl-Dipeptidase A/chemistry , Testis/metabolism , Amino Acid Sequence , Animals , Blotting, Western , CHO Cells , Catalysis , Cricetinae , Gene Deletion , Glycine/chemistry , Humans , Kinetics , Male , Microscopy, Confocal , Molecular Sequence Data , Mutation , Protein Binding , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Transfection
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