Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Zhang, Zhao ^a,b,c   Liu, Jun ^a   Li, Meng ^a   Yang, Hui ^b   Zhang, Chiyu ^a,c  

^a JIANGSU UNIVERSITY   (China)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c INSTITUTE PASTEUR OF SHANGHAI   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AQUATIC ENVIRONMENT; ARTICLE; BODY SIZE; CALLITRICHINAE; CONTROLLED STUDY; EVOLUTIONARY ADAPTATION; GENE DUPLICATION; GENE FUNCTION; GENE LOCATION; GENE LOCUS; GENE NUMBER; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC SELECTION; IMMUNE RESPONSE GENE; INTERFERON INDUCED TRANSMEMBRANE 10 GENE; INTERFERON INDUCED TRANSMEMBRANE 5 GENE; INTERFERON INDUCED TRANSMEMBRANE GENE; MOLECULAR EVOLUTION; OSSIFICATION; PHYLOGENY; PRIMATE; PSEUDOGENE; RODENT; SPECIES DIFFERENCE; TERRESTRIAL SPECIES; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, DIFFERENTIATION; BASE SEQUENCE; BAYES THEOREM; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENE DUPLICATION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SELECTION, GENETIC; SPECIES SPECIFICITY; SYNTENY; VERTEBRATES;

ANURA; MARMOSETS; PRIMATES; RODENTIA; VERTEBRATA;

EID: 84869225095     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049265     Document Type: Article

References (71)

1. Chen YX, Welte K, Gebhard DH, Evans RL, (1984) Induction of T cell aggregation by antibody to a 16kd human leukocyte surface antigen. J Immunol 133: 2496-2501.
2. Siegrist F, Ebeling M, Certa U, (2011) The small interferon-induced transmembrane genes and proteins. J Interferon Cytokine Res 31: 183-197.
3. Moffatt P, Gaumond MH, Salois P, Sellin K, Bessette MC, et al. (2008) Bril: a novel bone-specific modulator of mineralization. J Bone Miner Res 23: 1497-1508.
4. Hanagata N, Li ×, (2011) Osteoblast-enriched membrane protein IFITM5 regulates the association of CD9 with an FKBP11-CD81-FPRP complex and stimulates expression of interferon-induced genes. Biochem Biophys Res Commun 409: 378-384.
5. Daniel-Carmi V, Makovitzki-Avraham E, Reuven EM, Goldstein I, Zilkha N, et al. (2009) The human 1-8D gene (IFITM2) is a novel p53 independent pro-apoptotic gene. Int J Cancer 125: 2810-2819.
6. Martensen PM, Justesen J, (2004) Small ISGs coming forward. J Interferon Cytokine Res 24: 1-19.
7. Yount JS, Moltedo B, Yang YY, Charron G, Moran TM, et al. (2010) Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nat Chem Biol 6: 610-614.
8. Weidner JM, Jiang D, Pan XB, Chang J, Block TM, et al. (2010) Interferon-induced cell membrane proteins, IFITM3 and tetherin, inhibit vesicular stomatitis virus infection via distinct mechanisms. J Virol 84: 12646-12657.
9. Adams AP, Aronson JF, Tardif SD, Patterson JL, Brasky KM, et al. (2008) Common marmosets (Callithrix jacchus) as a nonhuman primate model to assess the virulence of eastern equine encephalitis virus strains. J Virol 82: 9035-9042.
10. Li D, Peng Z, Tang H, Wei P, Kong X, et al. (2011) KLF4-mediated negative regulation of IFITM3 expression plays a critical role in colon cancer pathogenesis. Clin Cancer Res 17: 3558-3568.
11. Tanaka SS, Nagamatsu G, Tokitake Y, Kasa M, Tam PP, et al. (2004) Regulation of expression of mouse interferon-induced transmembrane protein like gene-3, Ifitm3 (mil-1, fragilis), in germ cells. Dev Dyn 230: 651-659.
12. Ai HX, Zhang ZZ, Shen YF, Zhang JX, Zhou XM, et al. (2011) Molecular structure, phylogenetic analysis, tissue distribution, and function characterization of interferon-gamma-inducible lysosomal thiol reductase (GILT) gene in sheep (Ovis aries). Vet Immunol Immunopathol 140: 329-334.
13. Huang IC, Bailey CC, Weyer JL, Radoshitzky SR, Becker MM, et al. (2011) Distinct patterns of IFITM-mediated restriction of filoviruses, SARS coronavirus, and influenza A virus. PLoS Pathog 7: e1001258.
14. Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, et al. (2011) A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472: 481-485.
15. Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, et al. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139: 1243-1254.
16. Lu J, Pan Q, Rong L, He W, Liu SL, et al. (2011) The IFITM proteins inhibit HIV-1 infection. J Virol 85: 2126-2137.
17. Jiang D, Weidner JM, Qing M, Pan XB, Guo H, et al. (2010) Identification of five interferon-induced cellular proteins that inhibit west nile virus and dengue virus infections. J Virol 84: 8332-8341.
18. Feeley EM, Sims JS, John SP, Chin CR, Pertel T, et al. (2011) IFITM3 inhibits influenza A virus infection by preventing cytosolic entry. PLoS Pathog 7: e1002337.
19. Hanagata N, Li X, Morita H, Takemura T, Li J, et al. (2011) Characterization of the osteoblast-specific transmembrane protein IFITM5 and analysis of IFITM5-deficient mice. J Bone Miner Metab 29: 279-290.
20. Han JH, Lee S, Park YS, Park JS, Kim KY, et al. (2011) IFITM6 expression is increased in macrophages of tumor-bearing mice. Oncol Rep 25: 531-536.
21. Zhang C, de Silva S, Wang JH, Wu L, (2012) Co-evolution of primate SAMHD1 and lentivirus Vpx leads to the loss of the vpx Gene in HIV-1 ancestor. PLoS ONE 7: e37477.
22. Sawyer SL, Emerman M, Malik HS, (2004) Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol 2: E275.
23. Zhang J, Webb DM, (2004) Rapid evolution of primate antiviral enzyme APOBEC3G. Hum Mol Genet 13: 1785-1791.
24. Huthoff H, Towers GJ, (2008) Restriction of retroviral replication by APOBEC3G/F and TRIM5alpha. Trends Microbiol 16: 612-619.
25. Liu J, Chen K, Wang JH, Zhang C, (2010) Molecular evolution of the primate antiviral restriction factor tetherin. PLoS ONE 5: e11904.
26. Gupta RK, Hue S, Schaller T, Verschoor E, Pillay D, et al. (2009) Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion. PLoS Pathog 5: e1000443.
27. McNatt MW, Zang T, Hatziioannou T, Bartlett M, Fofana IB, et al. (2009) Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants. PLoS Pathog 5: e1000300.
28. Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, et al. (2012) The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe 11: 194-204.
29. Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Munch J, et al. (2012) Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 11: 205-217.
30. Hickford DE, Frankenberg SR, Shaw G, Renfree MB, (2012) Evolution of vertebrate interferon inducible transmembrane proteins. BMC Genomics 13: 155.
31. Sallman Almen M, Bringeland N, Fredriksson R, Schioth HB, (2012) The dispanins: a novel gene family of ancient origin that contains 14 human members. PLoS ONE 7: e31961.
32. Gu X, Vander Velden K, (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18: 500-501.
33. Yang Z, Nielsen R, Goldman N, Pedersen AM, (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
34. Sawyer S, (1989) Statistical tests for detecting gene conversion. Mol Biol Evol 6: 526-538.
35. Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
36. Hanagata N, Takemura T, Monkawa A, Ikoma T, Tanaka J, (2007) Phenotype and gene expression pattern of osteoblast-like cells cultured on polystyrene and hydroxyapatite with pre-adsorbed type-I collagen. J Biomed Mater Res A 83: 362-371.
37. Gu X, Wang Y, Gu J, (2002) Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet 31: 205-209.
38. Sakai H, Koyanagi KO, Imanishi T, Itoh T, Gojobori T, (2007) Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene 389: 196-203.
39. Yao L, Dong H, Zhu H, Nelson D, Liu C, et al. (2011) Identification of the IFITM3 gene as an inhibitor of hepatitis C viral translation in a stable STAT1 cell line. J Viral Hepat 18: e523-529.
40. Andersson M, Ahlberg V, Jensen-Waern M, Fossum C, (2011) Intestinal gene expression in pigs experimentally co-infected with PCV2 and PPV. Vet Immunol Immunopathol 142: 72-80.
41. Piontkivska H, Nei M, (2003) Birth-and-death evolution in primate MHC class I genes: divergence time estimates. Mol Biol Evol 20: 601-609.
42. Nei M, Gu X, Sitnikova T, (1997) Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci U S A 94: 7799-7806.
43. Kyuregyan KK, Poleschuk VF, Zamyatina NA, Isaeva OV, Michailov MI, et al. (2005) Acute GB virus B infection of marmosets is accompanied by mutations in the NS5A protein. Virus Res 114: 154-157.
44. Yue Y, Barry PA, (2008) Rhesus cytomegalovirus a nonhuman primate model for the study of human cytomegalovirus. Adv Virus Res 72: 207-226.
45. Zhang Y, Cui W, Liu L, Wang J, Zhao H, et al. (2011) Pathogenesis study of enterovirus 71 infection in rhesus monkeys. Lab Invest 91: 1337-1350.
46. Zapata JC, Pauza CD, Djavani MM, Rodas JD, Moshkoff D, et al. (2011) Lymphocytic choriomeningitis virus (LCMV) infection of macaques: a model for Lassa fever. Antiviral Res 92: 125-138.
47. Crostarosa F, Aravantinou M, Akpogheneta OJ, Jasny E, Shaw A, et al. (2009) A macaque model to study vaginal HSV-2/immunodeficiency virus co-infection and the impact of HSV-2 on microbicide efficacy. PLoS ONE 4: e8060.
48. Trott KA, Chau JY, Hudgens MG, Fine J, Mfalila CK, et al. (2011) Evidence for an increased risk of transmission of simian immunodeficiency virus and malaria in a rhesus macaque coinfection model. J Virol 85: 11655-11663.
49. Miyoshi-Akiyama T, Ishida I, Fukushi M, Yamaguchi K, Matsuoka Y, et al. (2011) Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model. J Infect Dis 203: 1574-1581.
50. Sun W, Nisalak A, Gettayacamin M, Eckels KH, Putnak JR, et al. (2006) Protection of Rhesus monkeys against dengue virus challenge after tetravalent live attenuated dengue virus vaccination. J Infect Dis 193: 1658-1665.
51. Omatsu T, Moi ML, Hirayama T, Takasaki T, Nakamura S, et al. (2011) Common marmoset (Callithrix jacchus) as a primate model of dengue virus infection: development of high levels of viraemia and demonstration of protective immunity. J Gen Virol 92: 2272-2280.
52. Weatherford T, Chavez D, Brasky KM, Lanford RE, (2009) The marmoset model of GB virus B infections: adaptation to host phenotypic variation. J Virol 83: 5806-5814.
53. Shi LY, Li M, Yuan LJ, Wang Q, Li XM, (2008) A new paramyxovirus, Tianjin strain, isolated from common cotton-eared marmoset: genome characterization and structural protein sequence analysis. Arch Virol 153: 1715-1723.
54. Wong SK, Connole M, Sullivan JS, Choe H, Carville A, et al. (2009) A New World primate deficient in tetherin-mediated restriction of human immunodeficiency virus type 1. J Virol 83: 8771-8780.
55. Kramski M, Matz-Rensing K, Stahl-Hennig C, Kaup FJ, Nitsche A, et al. (2010) A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection. PLoS ONE 5: e10412.
56. Carrion R Jr, Ro Y, Hoosien K, Ticer A, Brasky K, et al. (2011) A small nonhuman primate model for filovirus-induced disease. Virology 420: 117-124.
57. Saika S, Kidokoro M, Ohkawa T, Aoki A, Suzuki K, (2002) Pathogenicity of mumps virus in the marmoset. J Med Virol 66: 115-122.
58. Matz-Rensing K, Stahl-Hennig C, Kramski M, Pauli G, Ellerbrok H, et al. (2012) The pathology of experimental poxvirus infection in common marmosets (Callithrix jacchus): further characterization of a new primate model for orthopoxvirus infections. J Comp Pathol 146: 230-242.
59. Jacob JR, Lin KC, Tennant BC, Mansfield KG, (2004) GB virus B infection of the common marmoset (Callithrix jacchus) and associated liver pathology. J Gen Virol 85: 2525-2533.
60. Carrion R Jr, Brasky K, Mansfield K, Johnson C, Gonzales M, et al. (2007) Lassa virus infection in experimentally infected marmosets: liver pathology and immunophenotypic alterations in target tissues. J Virol 81: 6482-6490.
61. Sreenivasa BP, Singh RP, Mondal B, Dhar P, Bandyopadhyay SK, (2006) Marmoset B95a cells: a sensitive system for cultivation of Peste des petits ruminants (PPR) virus. Vet Res Commun 30: 103-108.
62. Shi P, Zhang J, Yang H, Zhang YP, (2003) Adaptive diversification of bitter taste receptor genes in Mammalian evolution. Mol Biol Evol 20: 805-814.
63. Zhang Z, Harrison PM, Liu Y, Gerstein M, (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13: 2541-2558.
64. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
65. Posada D, (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
66. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
67. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
68. Wilgenbusch JC, Swofford D (2003) Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics Chapter 6: Unit 6 4.
69. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
70. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, et al. (2012) Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8: e1002764.
71. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, et al. (2011) A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol 28: 3033-3043.