1
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Rodrigo AG, Shpaer EG, Delwart EL, Iversen AK, Gallo MV, Brojatsch J, Hirsch MS, Walker BD, Mullins JI. Coalescent estimates of HIV-1 generation time in vivo. Proc Natl Acad Sci U S A 1999; 96:2187-91. [PMID: 10051616 PMCID: PMC26758 DOI: 10.1073/pnas.96.5.2187] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/1998] [Indexed: 11/18/2022] Open
Abstract
The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here, we describe a new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time. The method is applied to sequences obtained from a long-term nonprogressing individual at five sampling occasions. The estimate of viral generation time using the coalescent method is 1.2 days per generation and is close to that obtained by mathematical modeling (1.8 days per generation), thus strengthening confidence in estimates of a short viral generation time. Apart from the estimation of relevant parameters relating to viral dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.
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Affiliation(s)
- A G Rodrigo
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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2
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Shpaer EG. GeneAssist. Smith-Waterman and other database similarity searches and identification of motifs. Methods Mol Biol 1997; 70:173-87. [PMID: 9089612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- E G Shpaer
- Applied Biosystems Division, Perkin Elmer, Foster City, CA, USA
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3
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Shpaer EG, Robinson M, Yee D, Candlin JD, Mines R, Hunkapiller T. Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA. Genomics 1996; 38:179-91. [PMID: 8954800 DOI: 10.1006/geno.1996.0614] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To predict the functions of a possible protein product of any new or uncharacterized DNA sequence, it is important first to detect all significant similarities between the encoded amino acid sequence and any accumulated protein sequence data. We have implemented a set of queries and database sequences and proceeded to test and compare various similarity search methods and their parameterizations. We demonstrate here that the Smith-Waterman (S-W) dynamic programming method and the optimized version of FASTA are significantly better able to distinguish true similarities from statistical noise than is the popular database search tool BLAST. Also, a simple "log-length normalization" of S-W scores based on the query and target sequence lengths greatly increased the selectivity of the S-W searches, exceeding the default normalization method of FASTA. An implementation of the modified S-W algorithm in hardware (the Fast Data Finder) is able to match the accuracy of software versions while greatly speeding up its execution. We present here the selectivity and sensitivity data from these tests as well as results for various scoring matrices. We present data that will help users to choose threshold score values for evaluation of database search results. We also illustrate the impact of using simple-sequence masking tools such as SEG or XNU.
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Affiliation(s)
- E G Shpaer
- Perkin-Elmer, Applied Biosystems Division, Foster City, California 94404, USA
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4
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Iversen AK, Shpaer EG, Rodrigo AG, Hirsch MS, Walker BD, Sheppard HW, Merigan TC, Mullins JI. Persistence of attenuated rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual. J Virol 1995; 69:5743-53. [PMID: 7637019 PMCID: PMC189435 DOI: 10.1128/jvi.69.9.5743-5753.1995] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
With the goal of examining the functional diversity of human immunodeficiency virus type 1 (HIV-1) env genes within the peripheral blood mononuclear cells of an asymptomatic individual, we substituted four complete env genes into the replication-competent NL4-3 provirus. Despite encoding full-length open reading frames for gp120 and gp41 and the second coding exon of tat and rev, each chimera was replication defective. Site-directed mutagenesis of codon 78 in the Rev activation domain (from a hitherto unique Ile to the subtype B consensus Leu) partially restored infectivity for two of three chimeras tested. Similarly, mutagenesis of rev codon 78 of NL4-3 from Leu to Ile partially attenuated this virus. Ile-78 was found in all 13 clones examined from samples taken from this asymptomatic subject 4.5 years after infection, including 9 from peripheral blood mononuclear cells and 4 from a virus isolate, as well as 4 additional clones each from peripheral blood mononuclear cells sampled 37 and 51 months later. We next examined conservation of the Rev activation domain within and among long-term survivors (LTS) and patients with AIDS, as well as T-cell-line-adapted strains of HIV-1. Putative attenuating mutations were found in a minority of sequences from all five LTS and two of four patients with AIDS. Of the 11 T-cell-line-adapted viruses examined, none had these changes. Among and within LTS virus population had marginally higher levels of diversity in Rev than in Env; patients with AIDS had similar levels of diversity in the two reading frames; and T-cell-line-adapted viruses had higher levels of diversity in Env. These results are consistent with the hypothesis that asymptomatic individuals harbor attenuated variants of HIV-1 which correlate with and contribute to their lack of disease progression.
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MESH Headings
- Acquired Immunodeficiency Syndrome/mortality
- Acquired Immunodeficiency Syndrome/virology
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Line
- Cells, Cultured
- Chimera
- Chlorocebus aethiops
- DNA Primers
- DNA, Viral/metabolism
- Exons
- Gene Expression Regulation, Viral
- Gene Products, rev/biosynthesis
- Gene Products, rev/genetics
- Genes, rev
- Genome, Viral
- HIV Envelope Protein gp41/biosynthesis
- HIV Envelope Protein gp41/genetics
- HIV Seronegativity/immunology
- HIV Seropositivity/virology
- HIV-1/genetics
- HIV-1/isolation & purification
- Homosexuality, Male
- Humans
- Interleukin-2/pharmacology
- Kidney
- Lymphocytes/immunology
- Lymphocytes/virology
- Macrophages/immunology
- Macrophages/virology
- Male
- Molecular Sequence Data
- Monocytes/immunology
- Monocytes/virology
- Mutagenesis, Site-Directed
- Oligodeoxyribonucleotides
- Polymerase Chain Reaction
- Proviruses/genetics
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/pharmacology
- Restriction Mapping
- Sequence Homology, Amino Acid
- Transfection
- beta-Galactosidase/biosynthesis
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- A K Iversen
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305-5402, USA
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5
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Shpaer EG, Delwart EL, Kuiken CL, Goudsmit J, Bachmann MH, Mullins JI. Conserved V3 loop sequences and transmission of human immunodeficiency virus type 1. AIDS Res Hum Retroviruses 1994; 10:1679-84. [PMID: 7888227 DOI: 10.1089/aid.1994.10.1679] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The third variable region (V3) of the surface glycoprotein (gp120) of envelope sequence subtype B, type 1 human immunodeficiency virus (HIV-1B), is highly variable among T cell line-adapted viruses and syncytium-inducing HIV-1-B isolates. Here we analyze the V3 region sequences from 93 individuals close to the time of seroconversion and show that the cysteine-bridged V3 loop, which also encompasses a major neutralizing determinant, is highly conserved, whereas sequences immediately surrounding the loop are similarly divergent in all HIV-1-B strains. Viruses with this conserved V3 loop have been reported to be more resistant to antibody-mediated neutralization than T cell-adapted viruses with divergent V3 sequences. We hypothesize, therefore, that on transmission from a donor to a recipient, virions inherently more resistant to neutralization by donor antibodies have a greater chance of initiating infection than those more sensitive to neutralization. This might explain the conservation of V3 early in infection and has implications for the design of HIV vaccines.
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Affiliation(s)
- E G Shpaer
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305-5402
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6
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Bachmann MH, Delwart EL, Shpaer EG, Lingenfelter P, Singal R, Mullins JI. Rapid genetic characterization of HIV type 1 strains from four World Health Organization-sponsored vaccine evaluation sites using a heteroduplex mobility assay. WHO Network for HIV Isolation and Characterization. AIDS Res Hum Retroviruses 1994; 10:1345-53. [PMID: 7888187 DOI: 10.1089/aid.1994.10.1345] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To assist in the preparation for the testing of vaccines against human immunodeficiency virus (HIV) we, as part of the World Health Organization Network for HIV Isolation and Characterization (WHO-NHIC), evaluated the genotypic variation of HIV-1 in cohorts from Brazil, Rwanda, Thailand, and Uganda. Here we report the results from a pilot study of 65 HIV-1-infected individuals. In all cases in which viral envelope gene fragments could be amplified by polymerase chain reaction, subtypes could be assigned using a heteroduplex mobility assay (HMA)1 by comparison with HIV-1 strains representing six HIV-1 envelope subtypes. All subtype classifications matched those found by envelope gene sequencing. Phylogenetic relationships were further clarified by heteroduplex formation between samples within each subtype. A relatively homogeneous subtype E virus population predominated over subtype B viruses in the sample set from Thailand. Viruses from the other countries were also limited to one or two subtypes but were more divergent within each subtype. All samples from Rwanda (13/13) and some from Uganda (3/16) were of subtype A; all Brazilian samples were of subtype B, except for one belonging to subtype C; most samples from Uganda (13/16) clustered with the subtype D. Analysis by HMA is therefore applicable for screening of HIV-1 genotypes in countries under consideration for large-scale vaccine trials. It should be generally useful when samples containing at least one variable genetic locus need to be rapidly classified by genotype and/or analyzed for epidemiological clustering.
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Affiliation(s)
- M H Bachmann
- Department of Cancer Biology, Harvard School of Public Health, Boston, Massachusetts 02115
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7
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Sabino EC, Shpaer EG, Morgado MG, Korber BT, Diaz RS, Bongertz V, Cavalcante S, Galvão-Castro B, Mullins JI, Mayer A. Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J Virol 1994; 68:6340-6. [PMID: 8083973 PMCID: PMC237055 DOI: 10.1128/jvi.68.10.6340-6346.1994] [Citation(s) in RCA: 156] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sequence analysis of a human immunodeficiency virus type 1 env gene PCR amplified from a Brazilian woman's peripheral blood mononuclear cell DNA (sample RJIO1) showed that it was likely to have been derived from a double recombination event between human immunodeficiency virus type 1 subtypes B and F. The major portion of the gp120 coding sequence belonged to the B lineage, but a segment of the C2 to V3 region (approximately 135 nucleotides) clearly associated with sequences of the F lineage. The subtype F-like segment had 15 noncontiguous signature nucleotides in common with Brazilian subtype F sequences that were not found, or were rare, in subtype B sequences. In contrast, this same segment had only 3 signature nucleotides shared with subtype B sequences and not present in the Brazilian subtype F sequences. Phylogenetic analysis, amino acid signature pattern analysis, and the pattern of synonymous mutations all supported the hypothesis of a recombinational origin of the RJIO1 sequence. Related recombinant genes were also detected in peripheral blood mononuclear cell DNA obtained from the woman's recent sexual partner, indicating that the recombination event probably occurred at some previous time in the chain of virus transmission. Divergent viral sequences in the V3 region were found in the male sexual partner, while a relatively homogeneous viral population was detected in the woman, consistent with her recent infection.
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Affiliation(s)
- E C Sabino
- Irwin Memorial Blood Centers, San Francisco, California 94118
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8
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Morgado MG, Sabino EC, Shpaer EG, Bongertz V, Brigido L, Guimaraes MD, Castilho EA, Galvão-Castro B, Mullins JI, Hendry RM. V3 region polymorphisms in HIV-1 from Brazil: prevalence of subtype B strains divergent from North American/European prototype and detection of subtype F. AIDS Res Hum Retroviruses 1994; 10:569-76. [PMID: 7522493 DOI: 10.1089/aid.1994.10.569] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Viral DNA sequences were determined over the V3 region of env from 28 infected individuals living in the high HIV-1 prevalence Brazilian cities of Rio de Janeiro and São Paulo. Twenty-six belonged to envelope sequence subtype B, prevalent in North America and Europe, and one was classified as subtype F, found recently in Brazil and in Romania (one appeared to be a B/F recombinant). Octameric sequences at the tip of the subtype B V3 loops were variable and distinct from those prevalent in North America and Europe. The GPGR motif, prevalent in North American/European strains, was found in only 8 (28.5%) sequences, whereas GWGR was found in 12 (43%) and novel sequences in 8 (28.5%). Brazilian subtype B sequences also diverged from the consensus North American/European strains over the remainder of the V3 loop. These results suggest that Brazilian HIV-1 B strains may have important antigenic differences from prototype subtype B strains currently being evaluated for use in HIV vaccines. These results should be taken into account for future vaccine programs in Brazil.
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Affiliation(s)
- M G Morgado
- Department of Immunology, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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9
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Sodora DL, Shpaer EG, Kitchell BE, Dow SW, Hoover EA, Mullins JI. Identification of three feline immunodeficiency virus (FIV) env gene subtypes and comparison of the FIV and human immunodeficiency virus type 1 evolutionary patterns. J Virol 1994; 68:2230-8. [PMID: 8139008 PMCID: PMC236699 DOI: 10.1128/jvi.68.4.2230-2238.1994] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats. As such, FIV appears to be a feline analog of human immunodeficiency virus (HIV). A hallmark of HIV infection is the large degree of viral genetic diversity that can develop within an infected individual and the even greater and continually increasing level of diversity among virus isolates from different individuals. Our goal in this study was to determine patterns of FIV genetic diversity by focusing on a 684-nucleotide region encompassing variable regions V3, V4, and V5 of the FIV env gene in order to establish parallels and distinctions between FIV and HIV type 1 (HIV-1). Our data demonstrate that, like HIV-1, FIV can be separated into distinct envelope sequence subtypes (three are described here). Similar to that found for HIV-1, the pairwise sequence divergence within an FIV subtype ranged from 2.5 to 15.0%, whereas that between subtypes ranged from 17.8 to 26.2%. However, the high number of synonymous nucleotide changes among FIV V3 to V5 env sequences may also include a significant number of back mutations and suggests that the evolutionary distances among FIV subtypes are underestimated. Although only a few subtype B viruses were available for examination, the pattern of diversity between the FIV A and B subtypes was found to be significantly distinct; subtype B sequences had proportionally fewer mutations that changed amino acids, compared with silent changes, suggesting a more advanced state of adaptation to the host. No similar distinction was evident for HIV-1 subtypes. The diversity of FIV genomes within individual infected cats was found to be as high as 3.7% yet twofold lower than that within HIV-1-infected people over a comparable region of the env gene. Despite these differences, significant parallels between patterns of FIV evolution and HIV-1 evolution exist, indicating that a wide array of potentially divergent virus challenges need to be considered in FIV vaccine and pathogenesis studies.
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Affiliation(s)
- D L Sodora
- Department of Microbiology and Immunology, Stanford University School of Medicine, California
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10
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Delwart EL, Shpaer EG, Louwagie J, McCutchan FE, Grez M, Rübsamen-Waigmann H, Mullins JI. Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science 1993; 262:1257-61. [PMID: 8235655 DOI: 10.1126/science.8235655] [Citation(s) in RCA: 669] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The genetic diversity of human immunodeficiency virus (HIV) is a major concern thought to impact on immunologic escape and eventual vaccine efficacy. Here, simple and rapid methods are described for the detection and estimation of genetic divergence between HIV strains on the basis of the observation that DNA heteroduplexes formed between related sequences have a reduced mobility in polyacrylamide gels proportional to their degree of divergence. Reliable phylogenetic subtypes were assigned for HIV-1 strains from around the world. Relationships between viruses were closest when derived from the same or epidemiologically linked individuals. When derived from epidemiologically unlinked individuals, the relationships between viruses in a given geographic region correlated with the length of time HIV-1 had been detected in the population and the number of strains initiating widespread infection. Heteroduplex mobility analysis thus provides a tool to expedite epidemiological investigations by assisting in the classification of HIV and is readily applicable to the screening and characterization of other infectious agents and cellular genes.
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Affiliation(s)
- E L Delwart
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305-5402
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11
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Abstract
A spectrum of pathogenicity has been observed for primate lentiviruses in their natural hosts. For example, human immunodeficiency virus type 1 (HIV-1) is a potent etiologic agent for AIDS in man, whereas there is no evidence to date which indicates that simian immunodeficiency virus from African green monkeys (SIVAGM) causes immunodeficiency in AGM. We measured the relative rates of amino acid change, as the ratio of the number of nonsynonymous to synonymous (silent) nucleotide substitutions, for six primate lentiviruses evolving in their respective hosts. These rates for the external envelope glycoprotein (gp120) and gag coding sequences are 2-3 times higher for pathogenic HIV-1 and SIVmac (macaque) than for minimally pathogenic SIVAGM and SIVsmm (sooty mangabey), and intermediate for HIV-2. We speculate that the increased rates of nonsynonymous changes in gp120 and gag coding sequences are due to viral escape from immune surveillance and are indicative of higher immunogenicity of these proteins in their hosts. Based on these results and available experimental data, we conclude that there is a positive correlation between lentiviral pathogenicity and immunogenicity of the Env and Gag proteins in a given host. This hypothesis is consistent with recent data suggesting that immune system activation or autoimmunity induced by viral antigens may be important in the pathogenesis of AIDS.
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Affiliation(s)
- E G Shpaer
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305-5402
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12
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Kusumi K, Conway B, Cunningham S, Berson A, Evans C, Iversen AK, Colvin D, Gallo MV, Coutre S, Shpaer EG. Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. J Virol 1992; 66:875-85. [PMID: 1731112 PMCID: PMC240788 DOI: 10.1128/jvi.66.2.875-885.1992] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nested-primer polymerase chain reaction (PCR) has been applied to the molecular cloning of 4.6-kb half-genome fragments of human immunodeficiency virus type 1 (HIV-1) taken directly from the peripheral blood mononuclear cells (PBMC) of an individual with neurological symptoms of HIV-1 infection. In a similar manner, gp120-coding portions of the envelope gene were cloned after PBMC from the same blood sample were cocultivated with uninfected PBMC for 28 days. The complete 1.6-kb nucleotide sequence of the gp120 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gp120 genes and 3 of 22 (14%) coculture-derived gp120 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gp120-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence of "strain" was found after coculture that was distinct from the diverse viral genotypes detected in vivo and therefore was selectively amplified during in vitro propagation. Multiple distinct third variable (V3) regions encoding the principal neutralizing domain of the envelope protein were detected in PBMC-derived genes, suggesting the presence of immunologic diversity of HIV env genes in vivo not reflected in the cocultured virus sample. The large size of the HIV fragments generated in this study will permit analysis of the diversity of immunologic reactivity, gene function, and pathogenicity of HIV genomes present within infected individuals, including the functional significance of the loss of diversity that occurs upon coculture.
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Affiliation(s)
- K Kusumi
- Department of Cancer Biology, Harvard School of Public Health, Boston, Massachusetts 02115
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13
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Shpaer EG, Mullins JI. Selection against CpG dinucleotides in lentiviral genes: a possible role of methylation in regulation of viral expression. Nucleic Acids Res 1990; 18:5793-7. [PMID: 2170945 PMCID: PMC332316 DOI: 10.1093/nar/18.19.5793] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Extremely low frequencies of CpG dinucleotides are found in the genomes of the lentivirus subfamily of retroviruses, including the human, simian and feline immunodeficiency viruses (HIV1, HIV2, SIV, and FIV, respectively), equine infectious anemia virus (EIAV), and the ovine lentivirus, Visna. The occurrence of CpG dinucleotides is greater in the 2-3 (NCG) than in the 1-2 (CGN) codon-defined frame, as well as in the gag and env genes, compared to the more conserved pol gene. These differences suggest that CpG depletion in lentiviruses occurs as a result of selection against CpG rather than due to mutational bias, the latter is responsible for low CpG frequencies in vertebrate genomes. CpG levels in the onco-retrovirus subfamily are reduced to a lesser extent, principally due to mutational bias. The difference between the retrovirus subfamilies appears to reflect their evolutionary origin, that is, lentiviruses have no known endogenous counterparts whereas most oncoviruses have endogenous cellular counterparts with which they can undergo recombination. Furthermore, we suggest that the number of CpG dinucleotides in a lentiviral genome determines the maximum potential DNA methylation level of the provirus, which in turn affects viral transcription in host cells.
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Affiliation(s)
- E G Shpaer
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305-5402
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14
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Shpaer EG. Amino acid composition is correlated with protein abundance in Escherichia coli: can this be due to optimization of translational efficiency? Protein Seq Data Anal 1989; 2:107-10. [PMID: 2652142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amino acid occurrence frequencies were found for four groups of Escherichia coli proteins with different abundance levels in the cell. These frequencies decrease with increasing protein abundance for amino acids whose codons are translated by tRNAs present at low concentrations (e.g., Cys, Trp, Ser, etc.); the opposite tendency was observed for amino acids translated by abundant tRNAs (Lys, Val, etc.). The efficiency (rate and accuracy) of codon translation is expected to be proportional to the concentration of the cognate tRNA. Therefore, the observed constraints on amino acid composition may be explained as resulting from evolutionary pressure optimizing the translational efficiency of a gene (the same pressure is responsible for the nonrandom choice of synonymous codons).
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Affiliation(s)
- E G Shpaer
- Institute of Organic Synthesis, Latvian SSR Academy of Sciences, Riga, USSR
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15
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Abstract
The constraints on nucleotide sequences of highly and weakly expressed genes from Escherichia coli have been analysed and compared. Differences in synonymous codon spectra in highly and weakly expressed genes lead to different frequencies of nucleotides (in the first and third codon positions) and dinucleotides in the two groups of genes. It has been found that the choice of synonymous codons in highly expressed genes depends on the nucleotides adjacent to the codon. For example, lysine is preferably encoded by the AAA codon if guanosine is 3' to the lysine codon (AAA-G, P less than 10(-9)). And, on the contrary, AAG is used more often than AAA (P less than 0.001) if cytidine is 3' adjacent to lysine. Guanosine occurs more frequently than adenosine 5' to all the lysine codons (AAR, P less than 10(-5), i.e. NNG codons are preferred over the synonymous NNA codons 5' to the positions of lysine in the genes. The context effect was observed in nonsense and missense suppression experiments. Therefore, a hypothesis has been suggested that the efficiency of translation of some codons (for which the constraints on the adjacent nucleotides were found) can be modulated by the codon context. The rules for preferable synonymous codon choice in highly expressed genes depending on the nucleotides surrounding the codon are presented. These rules can be used in the chemical synthesis of genes designed for expression in E. coli.
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16
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Shpaer EG. [Analysis of the primary structure of mRNA from Escherichia coli: occurrence of nucleotides on the 3'-side of the codon]. Mol Biol (Mosk) 1985; 19:791-9. [PMID: 2412106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The occurrence of nucleotides of the 3' side of codons has been determined in highly and weakly expressed genes from Escherichia coli. It was found that the usage of some amino acid codons in highly expressed genes was site specific, depending on the base 3' to the codon. The role of the 3' nucleotide as a modulator of codon translation effectiveness is discussed. The rules of synonymous codon usage in relation to the 3' flanking nucleotide have been established for highly expressed genes. For example, if a triplet next to the lysine codon starts with guanosine, lysine is preferably encoded by AAA and not by AAG (P less than 10(-8), while of cytidine is 3' to the lysine codon, AAG is preferred over AAA (P less than 0.001). These rules are observed in highly and absent in weakly expressed mRNAs and can be used in the chemical synthesis of genes designed for expression in E. coli.
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17
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Shpaer EG. The secondary structure of mRNAs from Escherichia coli: its possible role in increasing the accuracy of translation. Nucleic Acids Res 1985; 13:275-88. [PMID: 3889832 PMCID: PMC340990 DOI: 10.1093/nar/13.1.275] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A secondary structure model was proposed for mRNAs during translation (in a polysome) where the secondary structure is described by a set of small unbranched hairpins. Computer simulation experiments reveal that the number of hairpins is much greater (P less than 10(-6) in highly expressed mRNAs from E. coli as compared with the random sequences coding for the same amino acid sequence, i.e. certain synonymous codons are used in definite mRNA positions to increase the number of hairpins. No constraints on the amino acid sequence, which would affect the secondary structure of mRNAs, were found. The codons UGU, UGC (Cys), GCC (Ala), ACA, ACG (Thr), CCU, CCC (Pro), etc. translated by minor tRNAs were found to occur significantly more frequently in the position 5' to the hairpins than the other codons translated by major tRNAs (P less than 5.10(-6). This correlation leads to the hypothesis that the process of hairpin unfolding can increase the time of translocation from the A to P ribosome site of the codon 5' to the hairpin, thus decreasing the probability of translational error (the latter would likely occur more frequently in the codons translated by minor tRNAs).
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