Restriction of an Extinct Retrovirus by the Human TRIM5α Antiviral Protein

The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys

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Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1

Keele, B. F., Heuverswyn, F. V., Li, Y., Bailes, E., Takehisa, J., Santiago, M. L., Bibollet‐Ruche, F., Chen, Y., Wain, L. V., Liégeois, F., et al. (2006) · Science · doi:10.1126/science.1126531 · Cited by 955 · see citing works

Specific recognition and accelerated uncoating of retroviral capsids by the TRIM5α restriction factor

Stremlau, M. H., Perron, M. J., Lee, M. N., Li, Y., Song, B., Javanbakht, H., Diaz‐Griffero, F., Anderson, D. J., Sundquist, W. I., & Sodroski, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509996103 · Cited by 736 · see citing works

Positive selection of primate <i>TRIM5</i> α identifies a critical species-specific retroviral restriction domain

Sawyer, S. L., Wu, L. I., Emerman, M., & Malik, H. S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409853102 · Cited by 688 · see citing works

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G

Sawyer, S. L., Emerman, M., & Malik, H. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020275 · Cited by 485 · see citing works

A Single Amino Acid Change in the SPRY Domain of Human Trim5α Leads to HIV-1 Restriction

Yap, M. W., Nisole, S., & Stoye, J. P. (2005) · Current Biology · doi:10.1016/j.cub.2004.12.042 · Cited by 408 · see citing works

SIV infection in wild gorillas

Heuverswyn, F. V., Li, Y., Neel, C., Bailes, E., Keele, B. F., Liu, W., Loul, S., Butel, C., Liégeois, F., Bienvenue, Y., et al. (2006) · Nature · doi:10.1038/444164a · Cited by 408 · see citing works

Species-Specific Variation in the B30.2(SPRY) Domain of TRIM5α Determines the Potency of Human Immunodeficiency Virus Restriction

Stremlau, M. H., Perron, M. J., Welikala, S., & Sodroski, J. (2005) · Journal of Virology · doi:10.1128/jvi.79.5.3139-3145.2005 · Cited by 372 · see citing works

Retrovirus resistance factors Ref1 and Lv1 are species-specific variants of TRIM5α

Hatziioannou, T., Pérez-Caballero, D., Yang, A., Cowan, S., & Bieniasz, P. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402361101 · Cited by 371 · see citing works

Reconstitution of an Infectious Human Endogenous Retrovirus

Lee, Y. N., & Bieniasz, P. D. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030010 · Cited by 311 · see citing works

Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements

Dewannieux, M., Harper, F., Richaud, A., Letzelter, C., Ribet, D., Pierron, G., & Heidmann, T. (2006) · Genome Research · doi:10.1101/gr.5565706 · Cited by 309 · see citing works

TRIM5α mediates the postentry block to N-tropic murine leukemia viruses in human cells

Perron, M. J., Stremlau, M. H., Song, B., Ulm, W., Mulligan, R. C., & Sodroski, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403364101 · Cited by 290 · see citing works

Proteasome inhibitors uncouple rhesus TRIM5α restriction of HIV-1 reverse transcription and infection

Wu, X., Anderson, J. L., Campbell, E. M., Joseph, A. M., & Hope, T. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510483103 · Cited by 265 · see citing works

Retrovirus Restriction by TRIM5α Variants from Old World and New World Primates

Song, B., Javanbakht, H., Perron, M. J., Park, D. H., Stremlau, M. H., & Sodroski, J. (2005) · Journal of Virology · doi:10.1128/jvi.79.7.3930-3937.2005 · Cited by 216 · see citing works

Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5α

Newman, R. M., Hall, L. R., Connole, M., Chen, G., Sato, S., Yuste, E., Diehl, W. E., Hunter, E., Kaur, A., Miller, G. M., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605838103 · Cited by 153 · see citing works

Removal of Arginine 332 Allows Human TRIM5α To Bind Human Immunodeficiency Virus Capsids and To Restrict Infection

Li, Y., Xing, L., Stremlau, M. H., Lee, M. N., & Sodroski, J. (2006) · Journal of Virology · doi:10.1128/jvi.00270-06 · Cited by 137 · see citing works

Effects of human TRIM5α polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection

Javanbakht, H., An, P., Gold, B., Petersen, D. C., Ó’hUigín, C., Nelson, G. W., O’Brien, S. J., Kirk, G. D., Detels, R., Buchbinder, S., et al. (2006) · Virology · doi:10.1016/j.virol.2006.06.031 · Cited by 128 · see citing works

Retroviral Restriction Factor TRIM5α Is a Trimer

Mische, C. C., Javanbakht, H., Song, B., Diaz‐Griffero, F., Stremlau, M. H., Strack, B., Si, Z., & Sodroski, J. (2005) · Journal of Virology · doi:10.1128/jvi.79.22.14446-14450.2005 · Cited by 124 · see citing works

High-Frequency Persistence of an Impaired Allele of the Retroviral Defense Gene TRIM5α in Humans

Sawyer, S. L., Wu, L. I., Akey, J. M., Emerman, M., & Malik, H. S. (2006) · Current Biology · doi:10.1016/j.cub.2005.11.045 · Cited by 109 · see citing works

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans

Yohn, C. T., Jiang, Z., McGrath, S. D., Hayden, K. E., Khaitovich, P., Johnson, M. E., Eichler, M. Y., McPherson, J. D., Zhao, S., Pääbo, S., et al. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030110 · Cited by 104 · see citing works

Adaptive evolution of primate TRIM5α, a gene restricting HIV-1 infection

Liu, H., Wang, Y., Liao, C., Kuang, Y., Zheng, Y., & Su, B. (2005) · Gene · doi:10.1016/j.gene.2005.06.045 · Cited by 39 · see citing works

Cooperative Effect of Gag Proteins p12 and Capsid during Early Events of Murine Leukemia Virus Replication

Lee, S.-K., Nagashima, K., & Hu, W.-S. (2005) · Journal of Virology · doi:10.1128/jvi.79.7.4159-4169.2005 · Cited by 19 · see citing works

Endogenous viruses: insights into viral evolution and impact on host biology

Feschotte, C., & Gilbert, C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3199 · Cited by 885 · see citing works

Rules of engagement: molecular insights from host–virus arms races

Daugherty, M. D., & Malik, H. S. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155522 · Cited by 515 · see citing works

Effects of Retroviruses on Host Genome Function

Jern, P., & Coffin, J. M. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091501 · Cited by 499 · see citing works

Origins and evolutionary consequences of ancient endogenous retroviruses

Johnson, W. E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0189-2 · Cited by 402 · see citing works

High-resolution comparative analysis of great ape genomes

Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science · doi:10.1126/science.aar6343 · Cited by 350 · see citing works

Evolutionary insights into host–pathogen interactions from mammalian sequence data

Sironi, M., Cagliani, R., Forni, D., & Clerici, M. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3905 · Cited by 302 · see citing works

Protein kinase R reveals an evolutionary model for defeating viral mimicry

Elde, N. C., Child, S. J., Geballe, A. P., & Malik, H. S. (2009) · Nature · doi:10.1038/nature07529 · Cited by 260 · see citing works

Dynamic control of endogenous retroviruses during development

Rowe, H. M., & Trono, D. (2011) · Virology · doi:10.1016/j.virol.2010.12.007 · Cited by 278 · see citing works

The Developmental Control of Transposable Elements and the Evolution of Higher Species

Friedli, M., & Trono, D. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100814-125514 · Cited by 258 · see citing works

Intracellular Nucleic Acid Detection in Autoimmunity

Crowl, J. T., Gray, E. E., Pestal, K., Volkman, H. E., & Stetson, D. B. (2017) · Annual Review of Immunology · doi:10.1146/annurev-immunol-051116-052331 · Cited by 217 · see citing works

The evolutionary conundrum of pathogen mimicry

Elde, N. C., & Malik, H. S. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2222 · Cited by 214 · see citing works

Analyzing protein structure and function using ancestral gene reconstruction

Harms, M. J., & Thornton, J. W. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.03.005 · Cited by 214 · see citing works

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

Gifford, R. J., Katzourakis, A., Tristem, M., Pybus, O. G., Winters, M. A., & Shafer, R. W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807873105 · Cited by 206 · see citing works

Tripartite motif‐containing 22 inhibits the activity of hepatitis B virus core promoter, which is dependent on nuclear‐located RING domain†

Gao, B., Duan, Z., Xu, W., & Xiong, S. (2009) · Hepatology · doi:10.1002/hep.23011 · Cited by 207 · see citing works

The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

LaRue, R. S., Jönsson, S., Silverstein, K. A. T., Lajoie, M., Bertrand, D., El-Mabrouk, N., Hötzel, I., Andrésdóttir, V., Smith, T. P. L., & Harris, R. S. (2008) · BMC Molecular Biology · doi:10.1186/1471-2199-9-104 · Cited by 189 · see citing works

Paleovirology—Modern Consequences of Ancient Viruses

Emerman, M., & Malik, H. S. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000301 · Cited by 184 · see citing works

Discordant Evolution of the Adjacent Antiretroviral Genes TRIM22 and TRIM5 in Mammals

Sawyer, S. L., Emerman, M., & Malik, H. S. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030197 · Cited by 178 · see citing works

TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

Brennan, G., Kozyrev, Y., & Hu, S.-L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709511105 · Cited by 171 · see citing works

Human uniqueness: genome interactions with environment, behaviour and culture

Varki, A. P., Geschwind, D. H., & Eichler, E. E. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2428 · Cited by 168 · see citing works

Deficiency in ubiquitin ligase TRIM2 causes accumulation of neurofilament light chain and neurodegeneration

Balaštík, M., Ferraguti, F., Pires‐daSilva, A., Lee, T. H., Álvarez-Bolado, G., Lu, K. P., & Gruß, P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802261105 · Cited by 151 · see citing works

Endogenous retroviruses: acquisition, amplification and taming of genome invaders

Dewannieux, M., & Heidmann, T. (2013) · Current Opinion in Virology · doi:10.1016/j.coviro.2013.08.005 · Cited by 138 · see citing works

Paleovirology—ghosts and gifts of viruses past

Patel, M. R., Emerman, M., & Malik, H. S. (2011) · Current Opinion in Virology · doi:10.1016/j.coviro.2011.06.007 · Cited by 138 · see citing works

Two-stepping through time: mammals and viruses

Meyerson, N. R., & Sawyer, S. L. (2011) · Trends in Microbiology · doi:10.1016/j.tim.2011.03.006 · Cited by 133 · see citing works

Activation of the innate immune response by endogenous retroviruses

Hurst, T. P., & Magiorkinis, G. (2014) · Journal of General Virology · doi:10.1099/jgv.0.000017 · Cited by 139 · see citing works

Endogenous Retroviruses in the Genomics Era

Johnson, W. E. (2015) · Annual Review of Virology · doi:10.1146/annurev-virology-100114-054945 · Cited by 126 · see citing works

Human transposable elements in Repbase: genomic footprints from fish to humans

Kojima, K. K. (2018) · Mobile DNA · doi:10.1186/s13100-017-0107-y · Cited by 116 · see citing works

Role of retroviral restriction factors in the interferon-α–mediated suppression of HIV-1 in vivo

Pillai, S. K., Abdel‐Mohsen, M., Guatelli, J., Skasko, M., Monto, A., Fujimoto, K., Yukl, S. A., Greene, W. C., Kovari, H., Rauch, A., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111573109 · Cited by 118 · see citing works

Identification of a Genomic Reservoir for New TRIM Genes in Primate Genomes

Han, K., Lou, D. I., & Sawyer, S. L. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002388 · Cited by 120 · see citing works

Molecular evolution of the antiretroviral TRIM5 gene

Johnson, W. E., & Sawyer, S. L. (2009) · Immunogenetics · doi:10.1007/s00251-009-0358-y · Cited by 114 · see citing works

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

Blanco-Melo, D., Gifford, R. J., & Bieniasz, P. D. (2017) · eLife · doi:10.7554/elife.22519 · Cited by 109 · see citing works

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty

Eick, G. N., Bridgham, J. T., Anderson, D. P., Harms, M. J., & Thornton, J. W. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw223 · Cited by 103 · see citing works

Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions

Greenwood, A. D., Ishida, Y., O’Brien, S. P., Roca, A. L., & Eiden, M. V. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-17 · Cited by 103 · see citing works

Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response

Azevedo, L., Serrano, C., Amorim, A., & Cooper, D. N. (2015) · Human Genomics · doi:10.1186/s40246-015-0043-1 · Cited by 89 · see citing works

Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module

Biris, N., Yang, Y., Taylor, A. B., Tomashevski, A., Guo, M., Hart, P. J., Diaz‐Griffero, F., & Ivanov, D. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203536109 · Cited by 89 · see citing works

Innate Antiviral Immune Signaling, Viral Evasion and Modulation by HIV-1

Rustagi, A., & Gale, M. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.12.003 · Cited by 88 · see citing works

Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis

Young, G. R., Stoye, J. P., & Kassiotis, G. (2013) · BioEssays · doi:10.1002/bies.201300049 · Cited by 78 · see citing works

Activation of the innate immune response by endogenous retroviruses

Hurst, T. P., & Magiorkinis, G. (2015) · Journal of General Virology · doi:10.1099/vir.0.000017 · Cited by 82 · see citing works

TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation

Chiramel, A. I., Meyerson, N. R., McNally, K. L., Broeckel, R. M., Montoya, V. R., Méndez-Solís, O., Robertson, S. J., Sturdevant, G. L., Lubick, K. J., Nair, V., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.040 · Cited by 78 · see citing works

Alignment Modulates Ancestral Sequence Reconstruction Accuracy

Vialle, R. A., Tamuri, A. U., & Goldman, N. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy055 · Cited by 75 · see citing works

Is the high virulence of HIV-1 an unfortunate coincidence of primate lentiviral evolution?

Kirchhoff, F. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2111 · Cited by 77 · see citing works

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzeePreprint

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How Samhd1 changes our view of viral restriction

Laguette, N., & Benkirane, M. (2011) · Trends in Immunology · doi:10.1016/j.it.2011.11.002 · Cited by 75 · see citing works

An expanded clade of rodent Trim5 genes

Tareen, S. U., Sawyer, S. L., Malik, H. S., & Emerman, M. (2009) · Virology · doi:10.1016/j.virol.2008.12.018 · Cited by 73 · see citing works

Generation of Infectious Molecular Clones of Simian Immunodeficiency Virus from Fecal Consensus Sequences of Wild Chimpanzees

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Anti‐retroviral activity of TRIM5α

Nakayama, E. E., & Shioda, T. (2010) · Reviews in Medical Virology · doi:10.1002/rmv.637 · Cited by 71 · see citing works

Evolution of the Retroviral Restriction Gene Fv1: Inhibition of Non-MLV Retroviruses

Yap, M. W., Colbeck, E. J., Ellis, S., & Stoye, J. P. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1003968 · Cited by 65 · see citing works

Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface

Goldstone, D. C., Yap, M. W., Robertson, L. E., Haire, L. F., Taylor, W. R., Katzourakis, A., Stoye, J. P., & Taylor, I. A. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.08.006 · Cited by 64 · see citing works

Sequencing Primate Genomes: What Have We Learned?

Marquès‐Bonet, T., Ryder, O. A., & Eichler, E. E. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164420 · Cited by 63 · see citing works

Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene

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The decline of human endogenous retroviruses: extinction and survival

Magiorkinis, G., Blanco-Melo, D., & Belshaw, R. D. (2015) · Retrovirology · doi:10.1186/s12977-015-0136-x · Cited by 61 · see citing works

Nonhuman Primate Models for HIV/AIDS Vaccine Development

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Evolutionary Trajectories of Primate Genes Involved in HIV Pathogenesis

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Non-human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins

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Human Endogenous Retrovirus K106 (HERV-K106) Was Infectious after the Emergence of Anatomically Modern Humans

Jha, A. R., Nixon, D. F., Rosenberg, M. G., Martin, J. N., Deeks, S. G., Hudson, R. R., Garrison, K. E., & Pillai, S. K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020234 · Cited by 48 · see citing works

OASes and STING: Adaptive Evolution in Concert

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Characterization of a core fragment of the rhesus monkey TRIM5α protein

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Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes

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Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins

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Modeling Infectious Disease in Mice: Co-Adaptation and the Role of Host-Specific IFNγ Responses

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Determinants of cyclophilin A-dependent TRIM5α restriction against HIV-1

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Tripartite Motif (TRIM) 12c, a Mouse Homolog of TRIM5, Is a Ubiquitin Ligase That Stimulates Type I IFN and NF-κB Pathways along with TNFR-Associated Factor 6

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Stabilized Human TRIM5α Protects Human T Cells From HIV-1 Infection

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Impact of Endogenous Intronic Retroviruses on Major Histocompatibility Complex Class II Diversity and Stability

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Collective Dynamics Differentiates Functional Divergence in Protein Evolution

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TRIM5α and Species Tropism of HIV/SIV

Nakayama, E. E., & Shioda, T. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00013 · Cited by 34 · see citing works

Comparison of anti-viral activity of rhesus monkey and cynomolgus monkey TRIM5αs against human immunodeficiency virus type 2 infection

Kono, K., Song, H., Shingai, Y., Shioda, T., & Nakayama, E. E. (2008) · Virology · doi:10.1016/j.virol.2007.12.022 · Cited by 33 · see citing works

On the classification and evolution of endogenous retrovirus: human endogenous retroviruses may not be ‘human’ after all

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Multiple Epigenetic Modifiers Induce Aggressive Viral Extinction in Extraembryonic Endoderm Stem Cells

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Retroviruses of the RDR superinfection interference group: ancient origins and broad host distribution of a promiscuous Env gene

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Antiretroviral Activity of Ancestral TRIM5α

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Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors

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Identification of Postentry Restrictions to Mason-Pfizer Monkey Virus Infection in New World Monkey Cells

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Porcine endogenous retroviruses PERV A and A/C recombinant are insensitive to a range of divergent mammalian TRIM5α proteins including human TRIM5α

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