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Mancarella A, Procopio FA, Achsel T, De Crignis E, Foley BT, Corradin G, Bagni C, Pantaleo G, Graziosi C. Detection of antisense protein (ASP) RNA transcripts in individuals infected with human immunodeficiency virus type 1 (HIV-1). J Gen Virol 2019; 100:863-876. [PMID: 30896385 DOI: 10.1099/jgv.0.001244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The detection of antisense RNA is hampered by reverse transcription (RT) non-specific priming, due to the ability of RNA secondary structures to prime RT in the absence of specific primers. The detection of antisense RNA by conventional RT-PCR does not allow assessment of the polarity of the initial RNA template, causing the amplification of non-specific cDNAs. In this study we have developed a modified protocol for the detection of human immunodeficiency virus type 1 (HIV-1) antisense protein (ASP) RNA. Using this approach, we have identified ASP transcripts in CD4+ T cells isolated from five HIV-infected individuals, either untreated or under suppressive therapy. We show that ASP RNA can be detected in stimulated CD4+ T cells from both groups of patients, but not in unstimulated cells. We also show that in untreated patients, the patterns of expression of ASP and env are very similar, with the levels of ASP RNA being markedly lower than those of env. Treatment of cells from one viraemic patient with α-amanitin greatly reduces the rate of ASP RNA synthesis, suggesting that it is associated with RNA polymerase II, the central enzyme in the transcription of protein-coding genes. Our data represent the first nucleotide sequences obtained in patients for ASP, demonstrating that its transcription indeed occurs in those HIV-1 lineages in which the ASP open reading frame is present.
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Affiliation(s)
- Antonio Mancarella
- 1Division of Immunology and Allergy, Lausanne University Hospital, Switzerland
| | | | - Tilmann Achsel
- 2Department of Fundamental Neuroscience, University of Lausanne, Switzerland
| | - Elisa De Crignis
- 3Department of Biochemistry, Erasmus Medical Center, Rotterdam, The Netherlands.,†Present address: Clinical Trial Office, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Brian T Foley
- 4Theoretical Biology and Biophysics Group, Los Alamos National Laboratories, Los Alamos, New Mexico, USA
| | | | - Claudia Bagni
- 2Department of Fundamental Neuroscience, University of Lausanne, Switzerland
| | - Giuseppe Pantaleo
- 1Division of Immunology and Allergy, Lausanne University Hospital, Switzerland
| | - Cecilia Graziosi
- 1Division of Immunology and Allergy, Lausanne University Hospital, Switzerland
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2
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Li Y, Yang D, Wang JY, Yao Y, Zhang WZ, Wang LJ, Cheng DC, Yang FK, Zhang FM, Zhuang M, Ling H. Critical amino acids within the human immunodeficiency virus type 1 envelope glycoprotein V4 N- and C-terminals contribute to virus entry. PLoS One 2014; 9:e86083. [PMID: 24465884 PMCID: PMC3897638 DOI: 10.1371/journal.pone.0086083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 12/09/2013] [Indexed: 11/22/2022] Open
Abstract
The importance of the fourth variable (V4) region of the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein (Env) in virus infection has not been well clarified, though the polymorphism of this region has been found to be associated with disease progression to acquired immunodeficiency syndrome (AIDS). In the present work, we focused on the correlation between HIV-1 gp120 V4 region polymorphism and the function of the region on virus entry, and the possible mechanisms for how the V4 region contributes to virus infectivity. Therefore, we analyzed the differences in V4 sequences along with coreceptor usage preference from CCR5 to CXCR4 and examined the importance of the amino acids within the V4 region for CCR5- and CXCR4-tropic virus entry. In addition, we determined the influence of the V4 amino acids on Env expression and gp160 processing intracellularly, as well as the amount of Env on the pseudovirus surface. The results indicated that V4 tended to have a shorter length, fewer potential N-linked glycosylation sites (PNGS), greater evolutionary distance, and a lower negative net charge when HIV-1 isolates switched from a coreceptor usage preference for CCR5 to CXCR4. The N- and C-terminals of the HIV-1 V4 region are highly conserved and critical to maintain virus entry ability, but only the mutation at position 417 in the context of ADA (a R5-tropic HIV-1 strain) resulted in the ability to utilize CXCR4. In addition, 390L, 391F, 414I, and 416L are critical to maintain gp160 processing and maturation. It is likely that the hydrophobic properties and the electrostatic surface potential of gp120, rather than the conformational structure, greatly contribute to this V4 functionality. The findings provide information to aid in the understanding of the functions of V4 in HIV-1 entry and offer a potential target to aid in the development of entry inhibitors.
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Affiliation(s)
- Yan Li
- Department of Microbiology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Dan Yang
- Department of Forensic Medicine, Harbin Medical University, Harbin, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Yuan Yao
- Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin, China
| | - Wei-Zhe Zhang
- Department of Parasitology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Lu-Jing Wang
- Department of Biochemistry, Harbin Medical University, Harbin, China
| | - De-Chun Cheng
- Department of Parasitology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Feng-Kun Yang
- Department of Parasitology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Feng-Min Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
| | - Min Zhuang
- Department of Microbiology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
- * E-mail: (HL); (MZ)
| | - Hong Ling
- Department of Microbiology, Harbin Medical University, Harbin, China
- Department of Parasitology, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Key Laboratory of Etiology of Heilongjiang Province Education Bureau, Harbin, China
- * E-mail: (HL); (MZ)
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Role of human immunodeficiency virus type 1 envelope structure in the induction of broadly neutralizing antibodies. J Virol 2012; 86:13152-63. [PMID: 23015715 DOI: 10.1128/jvi.01110-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Very soon after the discovery of neutralizing antibodies (NAbs) toward human immunodeficiency virus type 1 (HIV-1) infection, it became apparent that characterization of these NAbs would be an important step in finding a cure for or a vaccine to eradicate HIV-1. Since the initial description of broadly cross-clade NAbs naturally produced in HIV-1 patients, numerous studies have described new viral targets for these antibodies. More recently, studies concerning new groups of patients able to control their viremia, such as long-term nonprogressors (LTNPs) or elite controllers, have described the generation of numerous envelope-targeted NAbs. Recent studies have marked a new stage in research on NAbs with the description of antibodies obtained from a worldwide screening of HIV-positive patients. These studies have permitted the discovery of NAb families with great potential for both neutralization and neutralization breadth, such as PG, PGT, CH, and highly active agonistic anti-CD4 binding site antibodies (HAADs), of which VRC01 and its variants are members. These antibodies are able to neutralize more than 80% of circulating strains without any autoreactivity and can be rapidly integrated into clinical trials in order to test their protective potential. In this review, we will focus on new insights into HIV-1 envelope structure and their implications for the generation of potent NAbs.
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Prakash SS, Kalra R, Lodha R, Kabra SK, Luthra K. Diversity of HIV type 1 envelope (V3-V5) sequence in HIV type 1-infected Indian children. AIDS Res Hum Retroviruses 2012; 28:505-9. [PMID: 21902590 DOI: 10.1089/aid.2011.0206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Abstract We assessed the viral envelope (V3-V5 region) sequence diversity from 13 HIV-1-infected Indian children from north India. All of the 13 children were found to be infected with subtype C viruses. One of the viral sequences exhibited usage of the CXCR4 coreceptor predicted by Web PSSM and Geno2pheno tools. This virus also had a longer V3 sequence with 37 amino acids, a GRGQ motif, and a methionine residue before it (AIIMS_307). A unique finding was the complete deletion of the V4 region of another virus (AIIMS_363). High sequence diversity was observed in the envelope of the HIV-1-infected Indian children.
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Affiliation(s)
- Somi Sankaran Prakash
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kalra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sushil K. Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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De Crignis E, Guglietta S, Foley BT, Negroni M, Di Narzo AF, Waelti Da Costa V, Cavassini M, Bart PA, Pantaleo G, Graziosi C. Nonrandom distribution of cryptic repeating triplets of purines and pyrimidines (RNY)(n) in gp120 of HIV Type1. AIDS Res Hum Retroviruses 2012; 28:493-504. [PMID: 21902591 DOI: 10.1089/aid.2011.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have analyzed purine (R) and pyrimidine (Y) codon patterns in variable and constant regions of HIV-1 gp120 in seven patients infected with different HIV-1 subtypes and naive to antiretroviral therapy. We have calculated the relative frequency of each in-frame codon RNY, YNR, RNR, and YNY (N=any nucleotide) in variable and constant regions of gp120, in the sequence within indels and at indels' flanking sites. Our data show that hypervariable regions V1, V2, V4, and V5 are characterized by the presence of long stretches of RNY codons constituting the majority of the sequence portion within insertions/deletions. In full-length gp120 and within inserted/deleted fragments the number of AVT (V=A, C, G) codons did not exceed 50% of the total RNY codons. RNY strings in variable regions spanned up to 21 codons and were always in frame. In contrast, RNY strings in constant regions were mostly out of frame and their length was limited to five codons. The frequency of the codon RNY was found to be significantly higher in variable regions (p<0.0001; t-test), within indels, and at indels' flanking sites (p<0.0001; χ(2) test). Analysis of the distribution of RNY strings equal to or longer than five codons in the full genome of HXB2 also shows that these sequences are mostly out of frame, unless they contain a potential N-glycosylation site or an asparagine. These data suggest that cryptic repeats of RNY may play a role in the genesis of multiple base insertions and deletions in hypervariable regions of gp120.
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Affiliation(s)
- Elisa De Crignis
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Silvia Guglietta
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Brian T. Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratories, Los Alamos, New Mexico
| | - Matteo Negroni
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | | | | | - Matthias Cavassini
- Division of Infectious Diseases, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Pierre-Alexandre Bart
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
| | - Cecilia Graziosi
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Department of Medicine, CHUV, Lausanne, Switzerland
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Rao RSP, Bernd W. Do N-glycoproteins have preference for specific sequons? Bioinformation 2010; 5:208-12. [PMID: 21364799 PMCID: PMC3040501 DOI: 10.6026/97320630005208] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 10/13/2010] [Indexed: 12/02/2022] Open
Abstract
Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation, the nature of other amino acids at this position is not clear. Using Markov chain analysis of tri-peptide NXS/T from viral, archaeal and eukaryotic proteins as well as experimentally confirmed N-glycosylated sequons from eukaryotic proteins, we show here that the occurrence of most sequon types differ significantly from the expected probability. Sequon types with F, G, I, S, T and V amino acids are consistently preferred while those with P and charged amino acids are under-represented in all four groups. Further, proteins contained far fewer number of possible sequon types (maximum 20 types for NXS or NXT taken separately) for any given number of sequons, which may be explained based on random sampling. Consistent with the present finding, majority of the over-represented sequons found in two important viral envelope glycoproteins (hemagglutinin of influenza A H3N2 and glycoprotein120 of HIV-1) are indeed preferred sequon types, which may provide a selective advantage. Accordingly, although there seems to be some preference for sequons, this preference may not be unique to N-glycosylation.
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Affiliation(s)
- R Shyama Prasad Rao
- CH20, 3 cross, 7 main, Saraswathipuram, Mysore 570009, India
- Aarhus University, Department of Genetics and Biotechnology, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Wollenweber Bernd
- Aarhus University, Department of Genetics and Biotechnology, Forsøgsvej 1, Slagelse 4200, Denmark
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Rao RSP, Wollenweber B. Subtle evolutionary changes in the distribution of N-glycosylation sequons in the HIV-1 envelope glycoprotein 120. Int J Biol Sci 2010; 6:407-18. [PMID: 20714439 PMCID: PMC2920574 DOI: 10.7150/ijbs.6.407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/14/2010] [Indexed: 01/09/2023] Open
Abstract
Many viruses are known to undergo rapid evolutionary changes under selective pressures. The HIV-1 envelope glycoprotein 120 (gp120) shows extreme selection for NXS/T sequons, the potential sites of N-glycosylation. Although the average number of sequons in gp120 appears to be relatively stable in the recent past, even slight changes in the distribution of sequons may potentially play crucial roles in protein interaction and viral infection. This study tracked the prevalence and distribution of NXS/T sequons in gp120 over a period of 29 years (from 1981 to 2009). The gp120 showed location specific distribution of sequons with higher density in the outer domain of the molecule. The NXT sequon density decreased in the outer domain (despite the increase in the sequon specific amino acid threonine), but increased in the inner domain. By contrast, the NXS sequon density increased specifically in the outer domain. Related changes were also seen in the distribution probabilities of sequons in two domains. The results indicate that the gp120, chiefly in subtype B, is redistributing NXS/T sequons within the molecule with specific selection for NXS sequons. The subtle evolution of sequons in gp120 may have implications in viral resistance and infection.
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Affiliation(s)
- R Shyama Prasad Rao
- Aarhus University, Department of Genetics and Biotechnology, Slagelse 4200, Denmark.
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Lopez CA, Vazquez M, Hill MD, Del C. Colon M, Porrata-Doria T, Johnston ICD, Lorenzo E. Characterization of HIV-1 RNA forms in the plasma of patients undergoing successful HAART. Arch Virol 2010; 155:895-903. [PMID: 20414690 PMCID: PMC2880236 DOI: 10.1007/s00705-010-0659-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 03/10/2010] [Indexed: 12/20/2022]
Abstract
An assay to characterize plasma human immunodeficiency virus 1 (HIV-1) sequences for patients with low viral loads was developed by combining the selective binding of anti-CD44 MicroBeads with a nested RT-PCR targeting the env C2V4 region. Sequences were obtained from 10 of 20 HIV+ patients who had viral loads below 48 copies/ml. Sequences derived from plasma were compared to those from CD14+ CD16 +monocytes and CD4+ T cells. The plasma sequences were most closely related to those amplified from monocytes, suggesting that during successful antiretroviral therapy, the predominant plasma virus originates from myeloid cells. By characterizing HIV-1 RNA sequences from 8 ml of plasma while avoiding multiple steps, which can lead to contamination and deterioration, this method can help elucidate the viral forms in patients with therapeutically suppressed HIV-1. Understanding the source of residual viremia is crucial in developing approaches for viral eradication.
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Affiliation(s)
- Carlos A. Lopez
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
| | - Manuel Vazquez
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
| | - Martin D. Hill
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
| | - Maria Del C. Colon
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
| | - Tirtsa Porrata-Doria
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
| | - Ian C. D. Johnston
- Miltenyi Biotec GmbH, Friedrich-Ebert-Str. 68, 51429 Bergisch Gladbach, Germany
| | - Eric Lorenzo
- Molecular Virology Laboratory, Department of Physiology and Pharmacology, Ponce School of Medicine, P.O. Box 7004, Ponce, PR 00732 USA
- Present Address: Scientific Review Program, AIDS Research Review Branch, NIAID, Division of Extramural Activities (DEA), 6700B Rockledge Dr., Room 3134, Bethesda, MD 20892-7616 USA
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Rao RSP, Buus OT, Wollenweber B. Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies. Bioinform Biol Insights 2010; 4:9-17. [PMID: 20213012 PMCID: PMC2832299 DOI: 10.4137/bbi.s4337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT) have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accordingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.
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Affiliation(s)
- R Shyama Prasad Rao
- Aarhus University, Department of Genetics and Biotechnology, Forsøgsvej 1, Slagelse 4200, Denmark.
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Long sequence duplications, repeats, and palindromes in HIV-1 gp120: length variation in V4 as the product of misalignment mechanism. Virology 2010; 399:167-175. [PMID: 20106497 DOI: 10.1016/j.virol.2009.12.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/14/2009] [Accepted: 12/19/2009] [Indexed: 11/22/2022]
Abstract
We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p < or = 3.00E-7), and significantly lower in Tat (p < or = 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.
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