Formation of immature and mature genomic RNA dimers in wild-type and protease-inactive HIV-1: Differential roles of the Gag polyprotein, nucleocapsid proteins NCp15, NCp9, NCp7, and the dimerization initiation site

Formation of immature genomic RNA (gRNA) dimers is exquisitely nucleocapsid (NC)-dependent in protease-inactive (PR-in) HIV-1. This establishes that Pr55gag/Pr160gag-pol has NC-dependent chaperone activity within intact HIV-1. Mutations in the proximal zinc finger and the linker of the NC sequence of Pr55gag/Pr160gag-pol abolish gRNA dimerization in PR-in HIV-1. In wild type, where the NC of Pr55gag is processed into progressively smaller proteins termed NCp15 (NCp7-p1-p6), NCp9 (NCp7-p1) and NCp7, formation of immature dimers is much swifter than in PR-in HIV-1. NCp7 and NCp15 direct this rapid accumulation. NCp9 is sluggish in this process, but it stimulates the transition from immature to mature gRNA dimer as well as NCp7 and much better than NCp15. The amino-terminus, proximal zinc finger, linker, and distal zinc finger of NCp7 contribute to this maturation event in intact HIV-1. The DIS is a dimerization initiation site for all immature gRNA dimers, irrespective of their mechanism of formation.     

Mapping of nucleocapsid residues important for HIV-1 genomic RNA dimerization and packaging

Retroviral genomic RNA (gRNA) dimerization appears essential for viral infectivity, and the nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) facilitates HIV-1 gRNA dimerization. To identify the relevant and dispensable positions of NC, 34 of its 55 residues were mutated, individually or in small groups, in a panel of 40 HIV-1 mutants prepared by site-directed mutagenesis. It was found that the amino-terminus, the proximal zinc finger, the linker, and the distal zinc finger of NC each contributed roughly equally to efficient HIV-1 gRNA dimerization. The N-terminal and linker segments appeared to play predominantly electrostatic and steric roles, respectively. Mutating the hydrophobic patch of either zinc finger, or substituting alanines for their glycine doublet, was as disabling as deleting the corresponding finger. Replacing the CysX(2)CysX(4)HisX(4)Cys motif of either finger by CysX(2)CysX(4)CysX(4)Cys or CysX(2)CysX(4)HisX(4)His, interchanging the zinc fingers or, replacing one zinc finger by a copy of the other one, had generally intermediate effects; among these mutations, the His23-->Cys substitution in the N-terminal zinc finger had the mildest effect. The charge of NC could be increased or decreased by up to 18%, that of the linker could be reduced by 75% or increased by 50%, and one or two electric charges could be added or subtracted from either zinc finger, without affecting gRNA dimerization. Shortening, lengthening, or making hydrophobic the linker was as disabling as deleting the N-terminal or the C-terminal zinc finger, but a neutral and polar linker was innocuous. The present work multiplies by 4 and by 33 the number of retroviral and lentiviral NC mutations known to inhibit gRNA dimerization, respectively. It shows the first evidence that gRNA dimerization can be inhibited by: 1) mutations in the N-terminus or the linker of retroviral NC; 2) mutations in the proximal zinc finger of lentiviral NC; 3) mutations in the hydrophobic patch or the conserved glycines of the proximal or the distal retroviral zinc finger. Some NC mutations impaired gRNA dimerization more than mutations inactivating the viral protease, indicating that gRNA dimerization may be stimulated by the NC component of the Gag polyprotein. Most, but not all, mutations inhibited gRNA packaging; some had a strong effect on virus assembly or stability.     

The T12I mutation within the SP1 region of Gag restricts packaging of spliced viral RNA into human immunodeficiency virus type 1 with mutated RNA packaging signals and mutated nucleocapsid sequence

Specific packaging of human immunodeficiency virus type 1 (HIV-1) RNA is attributable to the high affinity of nucleocapsid (NC) sequence of Gag for the cis-acting RNA packaging signals located within the 5' un-translated region (5' UTR). Interestingly, we have previously reported that the T12I mutation (named MP2) within SP1 of Gag prevented incorporation of spliced viral RNA into mutated viruses that lacked the stem-loop 1 (SL1) RNA element (also named dimerization initiation site, DIS), suggesting a role for the SP1 sequence in viral RNA packaging. In this study, we have further tested this activity of MP2 in the context of a variety of mutations that affect viral RNA incorporation. The results showed that MP2 was able to effectively restrict packaging of spliced viral RNA into viruses containing either NC mutations R10A and K11A or mutated 5' UTR sequence, such as DeltaGU3 that lacked the 112-GUCUGUUGUGUG-123 sequence of U5, D1 that was deleted of a 27 nt fragment immediately downstream of the primer binding site (PBS), Delta(306-325) that had the SL3 RNA element removed and MD2 that was missing the 328-GGAG-331 sequence. As a result, MP2 contributed increased infectivity to the related viruses. Therefore, the MP2 mutation demonstrates a distinct role in HIV-1 RNA packaging that is neither pertained to the specific viral RNA packaging signal nor to the NC sequence.     

HIV-1核心蛋白p24在大肠杆菌中的表达与纯化

探索进一步提高ＨＩＶ－１Ｐ２４ｇａｇ蛋白在大肠杆菌中的表达效率,增加产物的纯化手段。方法：通过改造原核表达载体ＰＢＶ２２０和ｐＥＴ２８,构建了一种通用型温控原核表达载体ｐＶＶ５,将ＨＩＶ－１ｇａｇ基因的１１４８－１８５７编码序列,插入到ｐＶＶ５ｂ和ｐＥＴ２８ｂ的相应位点中,构建了重组表达质粒,ｐＥＧ１ｂ和ｐＥＧ７ｂ,转化到大肠杆菌中进行表达,产物利用ＩＭＡＣ金属螯合层析柱进行纯经,纯化的表达产物用     

Moloney murine leukemia virus genomic RNA packaged in the absence of a full complement of wild type nucleocapsid protein

The current model for MLV genomic RNA (gRNA) packaging predicts that of the thousands of Gag proteins in a budding virion, only a small number (≤1%) may be necessary to recruit gRNA. Here, we examined the threshold limits of functional Gag required to package gRNA using wild-type (WT) and packaging deficient mutant nucleocapsid (NC) phenotypically mixed virions. Although gRNA packaging was severely diminished for the NC mutant, the residual encapsidated RNA dimer displayed motility on gels, thermostability, and integrity that was indistinguishable from that of WT. In phenotypically mixed virions, gRNA encapsidation recovered to within approximately two-fold of WT levels when the amount of WT NC was 5-10% of the total. Our results demonstrate that NC's roles in gRNA dimerization and packaging are genetically separable. Additionally, MLV gRNA packaging does not require 100% WT NC, but the amount of functional NC required is greater than the predicted minimum.     

Mutations in VP2 and VP1 capsid proteins increase infectivity and mouse lethality of enterovirus 71 by virus binding and RNA accumulation enhancement

Enterovirus 71 (EV71) is a major cause of hand-foot-and-mouth disease. EV71 infection occasionally associates with severe neurological sequelae such as brainstem encephalitis or poliovirus-like paralysis. We demonstrated that mouse-adapted strain increases infectivity, resulting in higher cytotoxicity of neuron cells and mortality to neonatal mice than a non-adapted strain. Results pointed to EV71 capsid region determining viral infectivity and mouse lethality. Mutant virus with lysine to methionine substitution at VP2₁₄₉ (VP2_149M) or glutamine to glutamic acid substitution at VP1₁₄₅ (VP1_145E) showed greater viral titers and apoptosis. Synergistic effect of VP2_149M and VP1_145E double mutations enhanced viral binding and RNA accumulation in infected Neuro-2a cells. The dual substitution mutants markedly reduced value of 50% lethal dose in neonatal mice infection, indicating they raised mouse lethality in vivo. In sum, VP2_149M and VP1_145E mutations cooperatively promote viral binding and RNA accumulation of EV71, contributing to viral infectivity in vitro and mouse lethality in vivo.     

Human immunodeficiency virus type 1 capsid protein is a substrate of the retroviral proteinase while integrase is resistant toward proteolysis

The capsid protein of human immunodeficiency virus type 1 was observed to undergo proteolytic cleavage in vitro when viral lysate was incubated in the presence of dithiothreitol at acidic pH. Purified HIV-1 capsid protein was also found to be a substrate of the viral proteinase in a pH-dependent manner; acidic pH (<7) was necessary for cleavage, and decreasing the pH toward 4 increased the degree of processing. Based on N-terminal sequencing of the cleavage products, the capsid protein was found to be cleaved at two sites, between residues 77 and 78 as well as between residues 189 and 190. Oligopeptides representing these cleavage sites were also cleaved at the expected peptide bonds. The presence of cyclophilin A decreased the degree of capsid protein processing. Unlike the capsid protein, integrase was found to be resistant toward proteolysis in good agreement with its presence in the preintegration complex.     

Epstein-Barr Virus load and immune activation in Human Immunodeficiency Virus type 1-infected patients

Background

Patients infected with HIV-1 are at high risk of developing Epstein-Barr Virus (EBV)-related diseases. Chronic immune activation is a hallmark of HIV-1 pathogenesis and may play a role in B-cell stimulation and expansion of EBV-infected cells.

Objectives

The aim of the study was to define the relationship between parameters of immune activation and EBV load in HIV-1-infected subjects.

Study design

A total of 156 HIV-1-infected patients were studied. EBV types 1 and 2 were quantified on peripheral blood mononuclear cells by multiplex real-time PCR. Plasma levels of cytokines and lipopolysaccharide (LPS) were determined by immunoenzymatic assays. B-cell activation was analyzed by flow cytometry.

Results

EBV-DNA was detected in 114 patients, and in all but 3 was EBV type 1. The median [interquartile] EBV-DNA load was 43[1-151] copies/10⁵ PBMC. EBV-DNA load was higher in patients with detectable HIV-1 plasma viremia, despite good immunological status (CD4 > 500 cells/μl), than in patients with undetectable HIV-1 plasma viremia regardless of immunological status (46[5-136] copies/10⁵ cells vs 17[1-56] copies/10⁵ cells, p = 0.008). Patients with high EBV-DNA load (>median value) had higher levels of LPS and proinflammatory cytokines (IL-6, IL-10 and TNF-α) than patients with low EBV load. Furthermore, percentages of activated B-cells correlated with EBV-DNA load (r_s = 0.754; p < 0.001).

Conclusions

Overall, these findings indicate a strong association between HIV-1 viremia, markers of immune activation and EBV load and suggest that persistence of HIV-1 viremia and immune activation, regardless of peripheral CD4 cell depletion/repopulation, may favor expansion of EBV-infected cells and onset of EBV-related malignancies.     

Distribution of the Human Immunodeficiency Virus Coreceptors CXCR4 and CCR5 on Leukocytes of Persons with Human Immunodeficiency Virus Type 1 Infection and Pulmonary Tuberculosis: Implications for Pathogenesis

Expression of CXCR4 was significantly reduced from normal on all cell subsets of persons with pulmonary tuberculosis (TB group), with HIV-1 infection (HIV group), and those with both infections (HIV/TB group), except for on monocytes in the HIV group. The reductions were most notable in the two TB groups. Interestingly, the duration of antituberculosis treatment was significantly negatively correlated with the expression of CXCR4 on CD4⁺ and CD8⁺CD45RO⁺ cells, monocytes and NK cells, viral load, and proportions of CD38-expressing CD8⁺ lymphocytes, in HIV/TB patients. By contrast, CCR5 expression on most cell subsets analyzed was increased in all the disease groups, except for on monocytes in the two TB groups. There was no change in CCR5 expression on CD4⁺ cells when based on the disease groupings. However, higher proportions of CD4⁺CD45RA⁺ and CD8⁺ lymphocytes as well as B cells expressing CCR5 correlated with advancing HIV-1 disease, as did decreased proportions of CXCR4-expressing CD4⁺CD45RA⁺ cells.     

Evidence for Selection of more Adapted Human Immunodeficiency Virus Type 1 Recombinant Strains in a Dually Infected Transfusion Recipient

Human immunodeficiency virus type-1 (HIV-1) genetic diversity is one of the remarkable characteristics of these viruses, and the mechanisms involved in the selective forces driving HIV-1 evolution are of great interest. Samples from hosts infected with multiple distinct strains represent a valuable in vivo resource to investigate the role of recombination in the natural evolution of HIV-1. This work describes a detailed study regarding the evolution of the envelope gene (env) (C2-V5 region) in a dually infected child who received blood transfusions simultaneously from two distinct HIV-1 infected donors. In this study, we were able to directly compare the data obtained from the dually infected recipient with data obtained from two other singly HIV-1 infected children who had received blood transfusion from each of the two donors. Sequences from the singly infected children clustered into two distinct groups, each related to the respective donor-derived sequence by phylogenetic analysis, and hence were consistent with the epidemiological data. In the case of the dually infected child, a high degree of recombination between the two donor-derived sequences was observed at the C2-V3 region, whereas in the V4-V5 region selection of only one derived donor sequence was seen. Measurement of nonsynonymous versus synonymous substitution rates at each region revealed that negative selection was the main evolutionary force acting on the viral population of the dually infected child, regardless of the genetic mechanism by which each region evolved. Based on direct comparison with data obtained for the two singly infected children we propose that the higher amount of viral diversity observed in HIV-1 multi-infection events, as in the case of the dually infected patient, might contribute to maximizing selective advantage and possibly minimizing immune response. We conclude that recombination shaped by selective forces may increase the adaptive potential of HIV-1.     

Bluetongue Virus and Double-Stranded RNA Increase Human Vascular Permeability: Role of p38 MAPK

Endothelial cell (EC) involvement in viral hemorrhagic fevers has been clearly established. However, virally activated mechanisms leading to endothelial activation and dysfunction are not well understood. Several different potential mechanisms such as direct viral infection, alterations in procoagulant/anticoagulant balance, and increased cytokine production have been suggested. We utilized a model of EC barrier dysfunction and vascular endothelial leakage to explore the effect of bluetongue virus (BTV), a hemorrhagic fever virus of ruminants, on human lung endothelial cell barrier properties. Infection of human lung EC with BTV induced a significant and dose-dependent decrease in trans-endothelial electrical resistance (TER). Furthermore, decreases in TER occurred in conjunction with cytoskeletal rearrangement, suggesting a direct mechanism for viral infection-mediated endothelial barrier disruption. Interestingly, double-stranded RNA (dsRNA) mimicked the effects of BTV on endothelial barrier properties. Both BTV- and dsRNA-induced endothelial barrier dysfunction was blocked by treatment with a pharmacological inhibitor of p38 MAPK. The induction of vascular permeability by dsRNA treatment or BTV infection was concomitent with induction of inflammatory cytokines. Taken together, our data suggest that the presence of dsRNA during viral infections and subsequent activation of p38 MAPK is a potential molecular pathway for viral induction of hemorrhagic fevers. Collectively, our data suggest that inhibition of p38 MAPK may be a possible therapeutic approach to alter viral-induced acute hemorrhagic diseases.     

Improved methods for quantification of human immunodeficiency virus type 1 RNA and hepatitis C virus RNA in blood using spin column technology and chemiluminescent assays of PCR products

The quantification of human immunodeficiency virus type 1 (HIV-1) RNA or hepatitis C virus (HCV) RNA has been facilitated by adapting a spin column procedure for sample preparation and the use of chemiluminescent detection of polymerase chain reaction (PCR) products in microtiter plate format. All materials were commercially available and relatively inexpensive. By making a single dilution prior to amplification, concentrations of 500 copies to 2.5 million HIV-1 1 RNA copies per mL and 1,000 copies to 50 million HCV RNA copies per mL could be determined on 140-μL samples. Between-run imprecision employing the improved procedure for HIV-1 RNA was 23%. Correlation of HIV-1 RNA concentrations obtained using chemiluminescent detection with values obtained by colorimetric assay of PCR products was 0.98. Correlation of HCV RNA concentration determined by the spin column-chemiluminescent assay procedure with those obtained by branched DNA methodology was 0.91. Spin columns could be used with serum or plasma containing acid-citrate-dextrose or heparin anticoagulant, but heparinized samples required treatment with heparinase prior to amplification. J Med Virol 51:56–63, 1997. © 1997 Wiley-Liss, Inc.     

HIV-1 RNA被有效抑制下T细胞与外周血中HIV-1前病毒DNA

目的:考察HIV-1 RNA被有效抑制下T细胞与外周血中HIV-1前病毒DNA的相关性。方法:对云南地区90例确诊为AIDS,HAART持续治疗时间超过6个月,血浆HIV RNA<50 Copies/ml的患者进行研究,采用Spearmans秩和相关回顾性分析CD4+、CD3+、CD8+、CD4+CD28+、CD4+CD45RA+、CD4+CD45RO+、CD38+、CD8+CD38+T细胞的绝对计数和相对计数与外周血中HIV-1前病毒DNA的相关性,同时考察HIV-1前病毒DNA拷贝数与HAART持续治疗时间的相关性。将90例患者根据HAART后CD4+T细胞绝对计数分为A(CD4+<200 cells/μl)、B(200≤CD4+≤349 cells/μl)、C(CD4+≥350 cells/μl)3组,考察3组间T细胞亚群的差别。结果:HIV-1前病毒DNA的log拷贝数与CD4+CD45RA+T细胞绝对计数呈负相关(r=-0.231,P<0.05),与CD4+CD45RA+T细胞相对计数呈明显负相关(r=-0.270,P<0.01);与CD38+T细胞绝对计数呈正相关(r=0.250,P<0.05);与HAART持续治疗时间无相关性。B、C组的CD3+T细胞绝对计数明显高于A组(P<0.01);C组的CD8+T细胞绝对计数高于B组的(P<0.05);B、C组的CD4+CD28+T细胞绝对计数和相对计数明显高于A组(P<0.01),C组的CD4+CD28+T细胞绝对计数高于B组(P<0.05);B、C组的CD4+CD45RA+T细胞、CD4+CD45RO+T细胞绝对计数明显高于A组(P<0.01),C组的CD4+CD45RA+T细胞、CD4+CD45RO+T细胞绝对计数高于B组(P<0.05),B、C组的CD4+CD45RO+T细胞相对计数高于A组(P<0.05);B、C组的CD8+CD38+T细胞绝对计数低于A组(P<0.05),B组的CD8+CD38+T细胞相对计数低于A组(P<0.05);C组的CD38+T细胞绝对计数高于A组(P<0.05)。A、B、C组的HIV-1前病毒DNA的log拷贝数分别为3.561±0.297 9,3.605±0.277 6,3.434±0.289 1(copies/ml),3组间无显著性差异(P>0.05)。结论:经过HAART治疗后HIV-1前病毒DNA可能处于稳定状态,HIV-1前病毒DNA拷贝数只是某些T细胞亚群数量改变的原因之一。     

A second-site suppressor significantly improves the defective phenotype imposed by mutation of an aromatic residue in the N-terminal domain of the HIV-1 capsid protein

The HIV-1 capsid (CA) protein plays an important role in virus assembly and infectivity. Previously, we showed that Ala substitutions in the N-terminal residues Trp23 and Phe40 cause a severely defective phenotype. In searching for mutations at these positions that result in a non-lethal phenotype, we identified one candidate, W23F. Mutant virions contained aberrant cores, but unlike W23A, also displayed some infectivity in a single-round replication assay and delayed replication kinetics in MT-4 cells. Following long-term passage in MT-4 cells, two second-site mutations were isolated. In particular, the W23F/V26I mutation partially restored the wild-type phenotype, including production of particles with conical cores and wild-type replication kinetics in MT-4 cells. A structural model is proposed to explain the suppressor phenotype. These findings describe a novel occurrence, namely suppression of a mutation in a hydrophobic residue that is critical for maintaining the structural integrity of CA and proper core assembly.     

Genotypic and Phenotypic Evidence of Different Drug-Resistance Mutation Patterns between B and Non-B Subtype Isolates of Human Immunodeficiency Virus Type 1 found in Brazilian Patients Failing HAART

We have investigated the phenotypic and genotypic susceptibility of 14 HIV-1 strains isolated from individuals failing HAART therapy to protease inhibitors (PI). Proviral and plasma viral pol gene fragment were amplified, sequenced and subtyped. Nine samples clustered with protease subtype B reference strains and the remaining samples were classified as non-B subtype corresponding to subtype F (n=4) and subtype A (n=1). Although all patients were treated with similar PI drug regimen, the non-B subtype isolates did not present the L90M and I84V mutations and used mainly G48V and V82A/F to achieve drug resistance. A strong cross-resistance phenotype among all four PI was associated with the mutation L90M in the subtype-B isolates, and with G48V and V82A/F in the non-B counterparts. This observation revealed that the non-B viruses tested had specific genotypic characteristics contrasting with the subtype-B isolates.     

Role of distal zinc finger of nucleocapsid protein in genomic RNA dimerization of human immunodeficiency virus type 1; no role for the palindrome crowning the R-U5 hairpin

Genomic RNA isolated from HIV-1 variously mutated in nucleocapsid protein (NC) was characterized by nondenaturing gel electrophoresis. Mutations in the C-terminal, the N-terminal, and the linker regions had no effect on genomic RNA dimerization [they are R7R10K11S, P31L, R32G, S3(32-34), and K59L], while a C36S/C39S mutation in the distal zinc knuckle (Cys-His box or zinc finger) inhibited genome dimerization as much as disrupting the kissing-loop domain. The four mutations which inhibited tRNA(Lys3) genomic placement (i.e., the in vivo placement of tRNA(Lys3) on the primer binding site) had no effect on genome dimerization. Among five mutations which inhibited genome packaging, four had no effect on genome dimerization. Thus the N-terminal and linker regions of NC control genome packaging/tRNA(Lys3) placement (two processes which do not require mature NC) but have little influence on genome dimerization and 2-base extension of tRNA(Lys3) (two processes which are likely to require mature NC). It has been suggested, based on electron microscopy, that the AAGCUU82 palindrome crowning the R-U5 hairpin stimulates genomic RNA dimerization. To test this hypothesis, we deleted AGCU81 from wild-type viruses and from viruses bearing a disrupted kissing-loop hairpin or kissing-loop domain; in another mutant, we duplicated AGCU81. The loss of AGCU81 reduced dimerization by 2.5 +/- 4%; its duplication increased it by 3 +/- 6%. Dissociation temperature was left unchanged. We reach two conclusions. First, the palindrome crowning the R-U5 hairpin has no impact on HIV-1 genome dimerization. Second, genomic RNA dimerization is differentially influenced by NC sequence: it is Zn finger dependent but independent of the basic nature of the N-terminal and linker subdomains. We propose that the NC regions implicated in 2-base extension of tRNA(Lys3) are required for a second (maturation) step of tRNA placement. Genome dimerization and mature tRNA placement would then become two RNA-RNA interactions sharing similar NC sequence requirements.     

Suboptimal inhibition of protease activity in human immunodeficiency virus type 1: effects on virion morphogenesis and RNA maturation

Protease activity within nascently released human immunodeficiency virus type 1 (HIV-1) particles is responsible for the cleavage of the viral polyproteins Gag and Gag–Pol into their constituent parts, which results in the subsequent condensation of the mature conical core surrounding the viral genomic RNA. Concomitant with viral maturation is a conformational change in the packaged viral RNA from a loosely associated dimer into a more thermodynamically stable form. In this study we used suboptimal concentrations of two protease inhibitors, lopinavir and atazanavir, to study their effects on Gag polyprotein processing and on the properties of the RNA in treated virions. Analysis of the treated virions demonstrated that even with high levels of inhibition of viral infectivity (IC₉₀), most of the Gag and Gag–Pol polyproteins were processed, although slight but significant increases in processing intermediates of Gag were detected. Drug treatments also caused a significant increase in the proportion of viruses displaying either immature or aberrant mature morphologies. The aberrant mature particles were characterized by an electron-dense region at the viral periphery and an electron-lucent core structure in the viral center, possibly indicating exclusion of the genomic RNA from these viral cores. Intriguingly, drug treatments caused only a slight decrease in overall thermodynamic stability of the viral RNA dimer, suggesting that the dimeric viral RNA was able to mature in the absence of correct core condensation.