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Journal of Virology, February 2007, p. 1528-1533, Vol. 81, No. 3
0022-538X/07/$08.00+0 doi:10.1128/JVI.01596-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan,1 Departments of Molecular and Cellular Biology,2 Functional Morphology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601, Japan,3 International Laboratory of Advanced Molecular Medicine Incorporated, Level 16, Shiroyama Hills, 4-3-1 Toranomon, Minato-ku, Tokyo 105-6016, Japan,4 National Institute of Health, Ministry of Public Health, 88/7 Soi Bamrasnaradura, Tivanond Road, Nonthaburi 11000, Thailand,5 TB/HIV Research Project, RIT-JATA, 1050 Satarn Payabarn Road, Muang District, Chiang Rai 57000, Thailand6
Received 26 July 2006/ Accepted 5 November 2006
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In this study, we focused on the drug user (DU) cohort study conducted in northern Thailand wherein current epidemiological surveys have revealed a dramatic decrease in seroprevalence and incidence rate of HIV-1 infection in spite of unchanged behaviors among DUs (9). A total of 421 cases (HIV-1 seronegative, n = 320; seropositive, n = 101) in the DU cohort were enrolled with written informed consent from January 1999 to November 2000 and followed up (every 6 months) until November 2003 (Fig. 1A). Eight cases among 320 seronegative DUs had seroconverted, whereas the other 312 cases remained seronegative throughout the study. All enrollment samples were stored, and subsequently diagnostic and PCR tests for HIV-1 were performed in separate laboratories in Thailand to eliminate the possibility of cross-contamination. Duplicate follow-up specimens were also assayed for HIV-1 gag p17 by PCR test and sequencing (7, 15); a cytokine enzyme-linked immunospot assay kit (U-CyTech, The Netherlands) (10) was used to detect human gamma interferon responses by using overlapping (20 mer) whole Gag peptides designed from a CRF01_AE clinical isolate. Furthermore, gag p17 gene-containing fragments were cloned and sequenced. The nucleotide sequence alignment adjacent to nucleotide position 75 (+426) of the gag p17 gene of HIV-1 clones from each seronegative DU subject is shown in Fig. 1C. A mutant molecular clone, G6, containing an A426G mutation was constructed from a replication-competent HIV-1 molecular clone, G5, based on isolate 92TH022 (11).
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FIG. 1. Results of initial screening and phylogenetic analysis of the HIV-1 gag p17 gene. (A) Schematic diagram of this study. Serological studies were carried out with 421 DUs in Chiang Rai, Thailand. HIV-1 DNA PCR analysis was performed with 312 patients who were subsequently followed and who remained seronegative. The human gamma interferon enzyme-linked immunospot assay (IFN- ELISPOT) was performed with four seronegative but HIV-1 gag gene-positive DU cases and 23 randomly selected seronegative HIV-1 gag gene-negative DU cases to determine the anti-HIV-1 cytotoxic T-lymphocyte (CTL) responses. (B) Phylogenetic tree of the gag p17 gene. The neighbor-joining method was applied to obtain a phylogenetic tree with nucleotide sequences from HIV-1-seronegative but gag gene-positive DUs (underlined) and seropositive DUs infected with CRF01_AE in the same cohort (7) (indicated by #) together with the reference sequences from the Los Alamos National Laboratory HIV, including representatives of all group M clades and CRF01_AE (database available at http://www.hiv.lanl.gov/content/index).The infectious molecular clone G5 was constructed from isolate 92TH022 (11; Codon Usage Database at http://kazusa.or.jp/codon/; GenBank release 151.0) that was obtained in northern Thailand. (C) Sequence alignment of the gag p17 gene segment surrounding the nucleotide position 75 (+426). The consensus HIV-1 gag p17 sequences of seronegative and seropositive DU cases in the same cohort (Los Alamos National Laboratory HIV database) were obtained from the sequence comparison. The deterministic nucleotide sequence that distinguishes seronegative and seropositive cases was found at nucleotide position 75 (+426) of the gag p17 gene (boxed). Pos, seropositive; Neg, seronegative.
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Whereas most of the samples (308 cases) were negative for HIV-1 DNA by PCR, we identified four cases (MC873, MC943, MC3201, and MC4001) positive for the HIV-1 gag p17 gene (Fig. 1A). Although these four cases appeared healthy without any detectable HIV-1 antigens, antibodies, viral load, or reduction of CD4+ T lymphocytes, two of these four cases were found repeatedly positive for anti-HIV-1 cytotoxic T-lymphocyte responses. These four cases were followed up until November 2003, and no seroconversion was detected (data not shown).
The DNA fragment containing the gag p17 gene from these seronegative cases was amplified, cloned, and sequenced for further analyses. We found that the nucleotide sequences obtained from the above-mentioned four seronegative DU cases appeared to belong to the same group of CRF01_AE reference strains (Fig. 1B), suggesting their possible exposure to CRF01_AE which is prevalent in northern Thailand (Los Alamos National Laboratory HIV database available at http://www.hiv.lanl.gov/content/index).We found that the sequences of three out of four seronegative cases conform a tight cluster together with MC1001, obtained from a seropositive DU in our cohort (7), and 92TH022. MC4001 conformed to an isolated cluster together with MC69, a seropositive DU and long-term nonprogressors living in the same village. To clarify the cause of lack of seroconversion in these DU cases, we inspected the genetic differences between HIV-1 sequences of seropositives and seronegatives in the same local cohort. Whereas the nucleotide at gag p17 position 75 (+426) is A in sequences of seropositives, it is G in sequences of seronegatives (Fig. 1C). Moreover, we were not able to find other conserved mutation positions between these four sequences.
We then explored the biological effect of A426G change by creating full-length HIV-1 molecular clones containing A (G5) or G (G6) at nucleotide position +426, based on the parental molecular clone 92TH022 (9,722 bp). Moreover, we also constructed a revertant mutant (reG5) in which the G substitution (G6) was reversed to an A mutation. We detected HIV-1 DNA and similar levels of viral mRNA expression in the transfected cells with the G5, G6, and reG5 clones (Fig. 2A). However, a profound reduction of HIV-1 virion production in the culture supernatant from cells transfected with G6 was observed (Fig. 2B). This also indicates that no undetected mutation was introduced during the construction of the G6 mutant clone. Furthermore, no significant increase in virus production was observed with G6 even after a prolonged period posttransfection, whereas the level of G5 virus production was comparable with that of the parental clone, 93JP-NH1 (Fig. 2C) (12). The levels of intracellular viral protein production as assayed by Western blotting and their stabilities were almost similar in clones G5, G6, and 93JP-NH1 (Fig. 2D), suggesting that the effect of a single synonymous nucleotide substitution at position +426 is not at the level of viral protein synthesis. These experiments were carried out independently in two different laboratories, and essentially the same results were obtained. These findings suggest that the major effect of the A426G nucleotide change might be at the step between viral protein synthesis and virus budding.
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FIG. 2. Viral mRNA expression, viral protein synthesis, and virion production of G5 and G6 HIV-1 clones. (A) Detection of HIV-1 DNA and viral mRNA in cells transfected with the G5, G6 and reG5 clones. HIV-1 DNA and mRNA were detected by DNA PCR and reverse transcription-PCR (RT-PCR) with specific primers previously described (15). G3PDH (glyceraldehyde 3-phosphate dehydrogenase) was amplified as an internal control for RT-PCR. (B) Amounts of HIV-1 p24 antigen in the culture supernatants of cells transfected with replication-competent HIV-1 clones G5, G6, and 93JP-NH1 (12). At 24 h posttransfection, culture supernatants were subjected to the HIV-1 p24 antigen ELISA. The experiments were performed in triplicates, and the means ± standard deviations are indicated. The statistical significance was evaluated by a Student's t test. (C) Time course of HIV-1 virion production in the culture supernatants of transfected cells. Amounts of HIV-1 p24 antigen in the culture supernatants of cells transfected with replication-competent HIV-1 clones G5 (circle), G6 (square), and 93JP-NH1 (triangle) were measured 1, 2 and 3 days posttransfection. The experiments were performed in triplicates, and the means ± standard deviations are indicated. (D) Western blot detection of viral proteins produced in cells 48 h after transfection with replication-competent HIV-1 clones. Lane 1, negative control (vector plasmid); lane 2, G5; lane 3, G6; lane 4, 93JP-NH1 (positive control). The positions of viral Pr55Gag and p24 are indicated on the right. The positions of protein markers are indicated on the left.
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FIG. 3. Transmission electron microscopic examinations of cells transfected with G5 (A) and G6 (B). Note that mature and immature virions were observed in the cell surface of G5-transfected cells, whereas few viral particles were observed in G6-transfected cells. Higher magnifications of the boxes areas are shown as insets. Thick and thin scale bars indicate 0.5 µm and 0.2 µm, respectively.
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FIG. 4. Comparison of viral p24 (Gag) proteins and virion-associated viral RNA among G5, G6, and 93JP-NH1 clones. (A) Amounts of HIV-1 p24 (Gag) proteins in cells transfected with G5, G6, and 93JP-NH1 viruses. At 24 h posttransfection, whole-cell extracts were prepared and subjected to HIV-1 p24 antigen ELISA. (B) Amounts of virion-associated HIV-1 p24 in the supernatants of cells transfected with G5, G6, and 93JP-NH1 viruses. At 24 h posttransfection, cell culture supernatants were collected, and HIV-1 p24 antigen levels were determined. (C) Amounts of HIV-1 viral RNA in the supernatants of cells transfected with G5, G6, and 93JP-NH1 viruses. At 48 h posttransfection, culture supernatants were collected, and the viral RNA copy numbers were determined by an Amplicor HIV-1 Monitor (version 1.5). In these experiments, 293 cells were transfected with replication-competent full-length HIV-1 clones, G5, G6, or 93JP-NH1 (positive control), and the cells or culture supernatants were collected at indicated time points. All measurements were performed in triplicates, and the means ± standard deviations are indicated.
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Findings from electron microscopic examination (Fig. 3) suggested that the G6 virus production was blocked at a step from virion assembly through virus budding in spite of the presence of thick, patchy densities in the cytoplasmic membrane that are indicative of the tethering of viral proteins. Thus, the reduced virion production may be due to diminished protein accumulation to the lipid raft formed at the inner face of the host cell plasma membrane.
HIV-1 virion assembly is initiated by the plasma membrane translocation of Pr55Gag and Pr160Gag-Pol (6). Formation of virus-like particles by Pr55Gag is a self-assembly process with critical Gag-Gag interactions between multiple domains along Gag precursor, and the assembly of virus-like particles does not necessarily require the participation of viral genomic RNA (1). The interaction between Pr55Gag and viral genomic RNA, as well as dimerization of viral genomic RNA, is considered crucial for HIV-1 morphogenesis (17). However, in spite of our repeated trials, an RNA-protein interaction between the HIV-1 packaging sequence spanning +223/+506 containing A426 (G5) or G426 (G6) and HIV-1 nucleocapsid did not show any difference between G5 and G6 sequences, at least in vitro (data not shown). It is possible that a subtle mutation like A426G may not cause a robust loss in the affinity to the nucleocapsid in the absence of a milieu of cellular and viral proteins. Roldan et al. (18) reported that the viral RNA segment spanning the region +400 to +500, containing A426, is involved in the binding to Pr55Gag and acts as a major packaging sequence, which may explain our finding that the nucleotide A426 in the gag p17 gene is crucial for the virion production.
Collectively, although the nucleotide substitution of A to G at position +426 of the gag p17 gene appears to contribute to reduced levels of virus production, further studies are crucial to understand the underlying mechanism. These studies should not only decipher a novel regulatory mechanism of viral production but might also indicate a possible target for novel HIV-1 therapy.
This work was supported by grants-in-aid from the Ministry of Health, Labor and Welfare, Japan; Ministry of Education, Culture, Sports, Science and Technology, Japan; the Sasakawa Memorial Health Foundation; the Japanese Foundation for AIDS Prevention; and the Japan Health Sciences Foundation.
Published ahead of print on 22 November 2006. ![]()
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