Access the full text.
Sign up today, get DeepDyve free for 14 days.
(2002)
Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif proteinNature, 418
D. Richman, T. Wrin, S. Little, C. Petropoulos (2003)
Rapid evolution of the neutralizing antibody response to HIV type 1 infectionProceedings of the National Academy of Sciences of the United States of America, 100
Sudhir Kumar, G. Stecher, Michael Li, Christina Knyaz, K. Tamura (2018)
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.Molecular biology and evolution, 35 6
Peter Meintjes, A. Rodrigo (2005)
Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type 1Journal of bioinformatics and computational biology, 3 1
Jian-hua Zhou, Jie Zhang, Dong-jie Sun, Q. Ma, Hao-tai Chen, Li-na Ma, Yao-zhong Ding, Yong-sheng Liu (2013)
The Distribution of Synonymous Codon Choice in the Translation Initiation Region of Dengue VirusPLoS ONE, 8
(Foley BT (2000) An overview of the molecular phylogeny of lentiviruses. HIV sequence compendium. pp 35–43)
Foley BT (2000) An overview of the molecular phylogeny of lentiviruses. HIV sequence compendium. pp 35–43Foley BT (2000) An overview of the molecular phylogeny of lentiviruses. HIV sequence compendium. pp 35–43, Foley BT (2000) An overview of the molecular phylogeny of lentiviruses. HIV sequence compendium. pp 35–43
J. Hemelaar (2012)
The origin and diversity of the HIV-1 pandemic.Trends in molecular medicine, 18 3
D. Hoyer, Eric Zorrilla, Pietro Cottone, Sarah Parylak, Micaela Morelli, N. Simola, James Lane, Michael Morgan, M. Christie, Cecilia Hillard, A. Budney, Ryan Vandrey, Trevor Robbins, P. Nencini, M. Milella, Naheed Mirza, V. Harvey, T. Dickenson, Seiya Miyamoto, O. Almeida, N. Sousa, S. Yu, Anthony Absalom, D. Menon, Pedro Delgado, Cyril Höschl, Tara White, R. Depue, C. Baltes, T. Mueggler, Markus Rudin, Peter Flor, I. Neumann, C. Erickson, D. Posey, Kelly Blankenship, Kimberly Stigler, C. McDougle, Etienne Sibille, Nicole Edgar, Malcolm Lader, Theodora Duka, E. Childs, B. Hahn, Jaanus Harro, P. Newhouse, H. Wilkins, Y. Alici, William Breitbart, Eric Nestler, A. Isles, Lawrence Wilkinson, Subhash Pandey, S. Siris, P. Willner, M. Billiard, Björn Lemmer, Jean-Michel Scherrmann, Lawrence Price, Tomek Banasikowski, R. Beninger, John Harvey, Brian Leonard, K. Wolff, A. Padhi, N. Fineberg, Warren Meck, Catalin Buhushi, Lance McMahon, Y. Chudasama, Michael Kuhar, J. Uys, Peter Kalivas, Mohammed Shoaib, Daniel Bertrand, H. Rollema, R. Hurst, Michael Bloch, J. Leckman, B. Sahakian, S. Morein-Zamir, Anne Jackson, Ben Harrison, Christos Pantelis, I. Hindmarch, Alyson Bond, Jaime Monti, D. Christensen, Warren Bickel, M. Bubar, Kathryn Cunningham, Christine Franco, M. Potenza, M. López-Ibor, J. López-Ibor, Joseph Friedman, Alex Hofer, Tomek Banasikowski, R. Beninger, M. Palmatier, Rick Bevins, Thomas Tzschentke, David Roberts, S. Anagnostaras, J. Sage, Stephanie Carmack, Steve Kohut, Anthony Riley, Ronald Mucha, Jos Prickaerts, O. Stiedl, Sven Ögren, Karim Nader, Oliver Hardt, P. Migues, A. Christopoulos, Gregory Stewart, P. Sexton, Y. Shaham, S. Nair, S. Heil, S. Sigmon, Stephen Higgins, S. Heil, S. Sigmon, Marc Branch, M. Cain, M. Bardo, R. Balster, Sharon Walsh, R. Rijk, Ronald Kloet, C. Bourke, Michael Owens, C. Viollet, J. Epelbaum, Karl Mann, Falk Kiefer, Michael Owens, C. Bourke, H. McAllister-Williams, A. Marneros, Rodrigo Andrade, I. Izquierdo, Liar Bevilaqua, M. Cammarota, Christoph Hiemke, M. Colado, Richard Green (2020)
Chromatin ImmunoprecipitationDefinitions
D. Drummond, Claus Wilke (2008)
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence EvolutionCell, 134
L. Deml, Alexandra Bojak, Stephanie Steck, M. Graf, J. Wild, R. Schirmbeck, H. Wolf, R. Wagner (2001)
Multiple Effects of Codon Usage Optimization on Expression and Immunogenicity of DNA Candidate Vaccines Encoding the Human Immunodeficiency Virus Type 1 Gag ProteinJournal of Virology, 75
Mattia Ficarelli, Irati Antzin-Anduetza, Rupert Hugh-White, A. Firth, Helin Sertkaya, H. Wilson, S. Neil, R. Schulz, Chad Swanson (2019)
CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent MechanismsJournal of Virology, 94
J. Vartanian, M. Henry, S. Wain-Hobson (2002)
Sustained G-->A hypermutation during reverse transcription of an entire human immunodeficiency virus type 1 strain Vau group O genome.The Journal of general virology, 83 Pt 4
S. Shabalina, A. Ogurtsov, N. Spiridonov (2006)
A periodic pattern of mRNA secondary structure created by the genetic codeNucleic Acids Research, 34
A. Kuyl, B. Berkhout (2012)
The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virusRetrovirology, 9
Emily Wong, D. Smith, R. Rabadán, M. Peiris, L. Poon (2010)
Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza VirusBMC Evolutionary Biology, 10
P. Puigbò, I. Bravo, S. García-Vallvé (2008)
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)BMC Bioinformatics, 9
H. Kishino, M. Hasegawa (1989)
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoideaJournal of Molecular Evolution, 29
D. Robertson, J. Anderson, J. Bradac, J. Carr, B. Foley, R. Funkhouser, F. Gao, B. Hahn, M. Kalish, C. Kuiken, G. Learn, T. Leitner, F. McCutchan, S. Osmanov, M. Peeters, D. Pieniążek, M. Salminen, P. Sharp, Steven Wolinsky, B. Korber (2000)
HIV-1 Nomenclature ProposalScience, 288
R. Fry, M. Sayaman, Dickinson, J Pringle, M. Abercrombie, P. Medawar, G. Salt, M. Swann, V. Wigglesworth, M Mayer, K. Vogtmann, B. Bausenwein, R. Wolf, M. Heisenberg, S. Swartz, K. Breuer, Grzegorz Kudla, A. Murray, D. Tollervey, J. Plotkin
References and Notes Supporting Online Material Coding-sequence Determinants of Gene Expression in Escherichia Coli
B. Visseaux, F. Damond, S. Matheron, D. Descamps, C. Charpentier (2016)
Hiv-2 molecular epidemiology.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 46
B. Foley (2001)
An overview of the molecular phylogeny of lentiviruses
K. Motomura, Jianbo Chen, Wei-Shau Hu (2007)
Genetic Recombination between Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2, Two Distinct Human LentivirusesJournal of Virology, 82
P. Sharp, W. Li (1987)
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.Nucleic acids research, 15 3
P. Sharp, G. Shaw, B. Hahn (2005)
Simian Immunodeficiency Virus Infection of ChimpanzeesJournal of Virology, 79
Q. Yu, Darlene Chen, Renate König, R. Mariani, D. Unutmaz, N. Landau (2004)
APOBEC3B and APOBEC3C Are Potent Inhibitors of Simian Immunodeficiency Virus Replication*Journal of Biological Chemistry, 279
Insung Ahn, H. Son (2006)
Epidemiological comparisons of codon usage patterns among HIV-1 isolates from Asia, Europe, Africa and the AmericasExperimental & Molecular Medicine, 38
C. Apetrei, A. Kaur, N. Lerche, Michael Metzger, I. Pandrea, J. Hardcastle, Shelley Falkenstein, R. Bohm, J. Koehler, V. Traina-Dorge, T. Williams, S. Staprans, Gail Plauché, R. Veazey, H. McClure, A. Lackner, B. Gormus, D. Robertson, P. Marx (2005)
Molecular Epidemiology of Simian Immunodeficiency Virus SIVsm in U.S. Primate Centers Unravels the Origin of SIVmac and SIVstmJournal of Virology, 79
F. Gao, E. Bailes, D. Robertson, Yalu Chen, C. Rodenburg, S. Michael, L. Cummins, L. Arthur, M. Peeters, G. Shaw, P. Sharp, B. Hahn (1999)
Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytesNature, 397
F. Hemert, B. Berkhout (1995)
The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availabilityJournal of Molecular Evolution, 41
Grzegorz Kudla, Andrew Murray, David Tollervey, J. Plotkin (2009)
Coding-Sequence Determinants of Gene Expression in Escherichia coliScience, 324
P. Puigbò, I. Bravo, S. García-Vallvé (2008)
CAIcal: A combined set of tools to assess codon usage adaptationBiology Direct, 3
M. Freire-Picos, M. González-Siso, E. Rodríguez-Belmonte, A. Rodríguez-Torres, E. Ramil, M. Cerdán (1994)
Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes.Gene, 139 1
M. Rey-Cuillé, J. Berthier, M. Bomsel-Demontoy, Yves Chaduc, L. Montagnier, A. Hovanessian, L. Chakrabarti (1998)
Simian Immunodeficiency Virus Replicates to High Levels in Sooty Mangabeys without Inducing DiseaseJournal of Virology, 72
B. Desimmie, Krista Delviks-Frankenberrry, Ryan Burdick, Dongfei Qi, Taisuke Izumi, V. Pathak (2014)
Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all.Journal of molecular biology, 426 6
J. Thompson, D. Higgins, T. Gibson (1994)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic acids research, 22 22
N. Sueoka (1988)
Directional mutation pressure and neutral molecular evolution.Proceedings of the National Academy of Sciences of the United States of America, 85 8
Yue Jiang, F. Dèng, Huálín Wáng, Zhìhóng Hú (2008)
An extensive analysis on the global codon usage pattern of baculovirusesArchives of Virology, 153
F. Wright (1990)
The 'effective number of codons' used in a gene.Gene, 87 1
P. Sharp, E. Bailes, D. Robertson, F. Gao, B. Hahn (1999)
Origins and evolution of AIDS viruses.The Biological bulletin, 196 3
James Smith, R. Amara, D. Campbell, Yan Xu, Milloni Patel, Sunita Sharma, S. Butera, D. Ellenberger, Hong Yi, L. Chennareddi, J. Herndon, L. Wyatt, D. Montefiori, B. Moss, H. McClure, H. Robinson (2004)
DNA/MVA vaccine for HIV type 1: effects of codon-optimization and the expression of aggregates or virus-like particles on the immunogenicity of the DNA prime.AIDS research and human retroviruses, 20 12
K. Vidyavijayan, S. Hassan, Lucia Precilla, Manickam Ashokkumar, Padmapriyadharshini Chandrasekeran, S. Swaminathan, L. Hanna (2016)
Biased Nucleotide Composition and Differential Codon Usage Pattern in HIV-1 and HIV-2.AIDS research and human retroviruses, 33 3
F. Gao, Yingying Li, J. Decker, F. Peyerl, F. Bibollet-Ruche, C. Rodenburg, Yalu Chen, D. Shaw, S. Allen, R. Musonda, G. Shaw, A. Zajac, N. Letvin, B. Hahn (2003)
Codon usage optimization of HIV type 1 subtype C gag, pol, env, and nef genes: in vitro expression and immune responses in DNA-vaccinated mice.AIDS research and human retroviruses, 19 9
A. Pandit, S. Sinha (2011)
Differential Trends in the Codon Usage Patterns in HIV-1 GenesPLoS ONE, 6
P. Sharp, Beatrice Hahn (2010)
The evolution of HIV-1 and the origin of AIDSPhilosophical Transactions of the Royal Society B: Biological Sciences, 365
Daniel Goodman, G. Church, Sriram Kosuri (2013)
Causes and Effects of N-Terminal Codon Bias in Bacterial GenesScience, 342
Xian Jia, Shuyu Liu, Hao Zheng, Bo Li, Qi-En Qi, Lei Wei, T. Zhao, Jian He, Jingchen Sun (2015)
Non-uniqueness of factors constraint on the codon usage in Bombyx moriBMC Genomics, 16
A. Standen (1957)
Causes and Effects.Science, 125 3253
A. Kofman, M. Graf, Ludwid Deml, H. Wolf, R. Wagner (2003)
Codon usage-mediated inhibition of HIV-1 gag expression in mammalian cells occurs independently of translation.Tsitologiia, 45 1
A. Jordan-Paiz, M. Nevot, Kevin Lamkiewicz, Marie Lataretu, S. Franco, M. Marz, M. Martínez (2020)
HIV-1 Lethality and Loss of Env Protein Expression Induced by Single Synonymous Substitutions in the Virus Genome Intronic-Splicing SilencerJournal of Virology, 94
P. Sharp, Wen-Hsiung Li (1986)
An evolutionary perspective on synonymous codon usage in unicellular organismsJournal of Molecular Evolution, 24
BackgroundPrimate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma.ObjectiveThis study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic characteristics commonly or specifically expressed in HIV1, HIV2, and SIV.MethodsThe gag, pol, and env gene sequences of HIV1, HIV2, and SIV were analyzed to determine their evolutionary relationships, nucleotide compositions, codon usage patterns, neutrality, selection pressure (influence of mutational pressure and natural selection), and viral adaptation to human codon usage.ResultsA strong ‘A’ bias was confirmed in all three structural genes, consistent with previous findings regarding HIV. Notably, the ENC-GC3s plot and neutral evolution analysis showed that all primate lentiviruses were more affected by selection pressure than by mutation caused by the GC composition of the gene, consistent with prior reports regarding HIV1. The overall codon usage bias of pol was highest among the structural genes, while the codon usage bias of env was lowest. The virus groups showing high codon bias in all three genes were HIV1 and SIVcolobus. The codon adaptation index (CAI) and similarity D(A, B) values indicated that although there was a high degree of similarity to human codon usage in all three structural genes of HIV, this similarity was not caused by translation pressure. In addition, compared with HIV1, the codon usage of HIV2 is more similar to the human codon usage, but the overall codon usage bias is lower.ConclusionThe origin viruses of HIV (SIVcpz_gor and SIVsmm) exhibit greater similarity to human codon usage in the gag gene, confirming their robust adaptability to human codon usage. Therefore, HIV1 and HIV2 may have evolved to avoid human codon usage by selection pressure in the gag gene after interspecies transmission from SIV hosts to humans. By overcoming safety and stability issues, information from codon usage analysis will be useful for attenuated HIV1 vaccine development. A recoded HIV1 variant can be used as a vaccine vector or in immunotherapy to induce specific innate immune responses. Further research regarding HIV1 dinucleotide usage and codon pair usage will facilitate new approaches to the treatment of AIDS.
Genes & Genomics – Springer Journals
Published: Jul 1, 2022
Keywords: Human immunodeficiency virus 1; Human immunodeficiency virus 2; Simian immunodeficiency virus; Codon usage pattern; Relative synonymous codon usage; Mutational pressure; Natural selection
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.