Volume 33 Issue 1
Jan.  2012
Turn off MathJax
Article Contents
LI Ming-Li, TIAN Wei-Wei, GAO Yue-Dong, GUO Yan, HUANG Jing-Fei, ZHANG Hua-Tang. Genome-wide prediction of interferon family members of tree shrew and their molecular characteristics analysis. Zoological Research, 2012, 33(1): 67-74. doi: 10.3724/SP.J.1141.2012.01067
Citation: LI Ming-Li, TIAN Wei-Wei, GAO Yue-Dong, GUO Yan, HUANG Jing-Fei, ZHANG Hua-Tang. Genome-wide prediction of interferon family members of tree shrew and their molecular characteristics analysis. Zoological Research, 2012, 33(1): 67-74. doi: 10.3724/SP.J.1141.2012.01067

Genome-wide prediction of interferon family members of tree shrew and their molecular characteristics analysis

doi: 10.3724/SP.J.1141.2012.01067
  • Received Date: 2011-10-24
  • Rev Recd Date: 2012-01-10
  • Publish Date: 2012-02-22
  • Interferons (IFNs) represent proteins with antiviral activities that are secreted from cells in response to a variety of stimuli. In addition to antiviral, antibacterial and anti-parasitic host-defense functions they are now also recognized as crucial regulators of cell proliferation, differentiation, survival and death as well as activators of specialized cell functions particularly in the immune system and play important roles in infectious and inflammatory diseases, autoimmunity and cancer. Tree shrews (Tupaia belangeri) were found to be susceptible to several human viruses and therefore are widely regarded as good models for analyzing mechanism of human diseases. In this report, we have forecasted the interferon family members of tree shrew from its genome mainly using the methods like Blast (whole genome shotgun sequence) and gene prediction. Our data show that tree shrew interferon system includes: type I IFN: α (five subtypes), β, ω, κ, ε, δ; type II IFN: γ; type III IFN: λ1, λ2/3. Furthermore, the predicted structures of α and λ have similar character with those of other mammals. However, there are some differences in cysteine position and N-glycosylation numbers between human and Tree shrew IFNs. These results provide fundamental basis for further molecular cloning and function analysis of tree shrew IFNs in future.
  • loading
  • [1]
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool
    [J]. J Mol Biol, 215(3): 403-410.
    [3]
    Ank N, West H, Bartholdy C, Eriksson K, Thomsen AR, Paludan SR. 2006. Lambda interferon (IFN-λ), a type III IFN, is induced by viruses and IFNs and displays potent antiviral activity against select virus infections in vivo
    [J]. J Virol, 80(9): 4501-4509.
    [5]
    Brand S, Beigel F, Olszak T, Zitzmann K, Eichhorst ST, Otte JM, Diebold J, Diepolder H, Adler B, Auernhammer CJ, Goke B, Dambacher J. 2005. IL-28A and IL-29 mediate antiproliferative and antiviral signals in intestinal epithelial cells and murine CMV infection increases colonic IL-28A expression
    [J]. Am J Physiol Gastrointest Liver Physiol, 289(5):G960-G968.
    [7]
    Burge CB, Karlin S. 1998. Finding the genes in genomic DNA
    [J]. Curr Opin Struc Biol, 8(3): 346-354.
    [9]
    Cao J, Yang EB, Su JJ, Li Y, Chow P. 2003. The tree shrews: adjuncts and alternatives to primates as models for biomedical research
    [J]. J Med Primatology, 32(3): 123-130.
    [11]
    Conklin D. 2004. Recognition of the helical cytokine fold
    [J]. J Comput Biol, 11(6): 1189-1200.
    [13]
    Dellgren C, Gad HH, Hamming OJ, Melchjorsen J, Hartmann R. 2009. Human interferon-λ3 is a potent member of the type III interferon family
    [J]. Genes Immun, 10(2): 125-131.
    [15]
    Fox BA, Sheppard PO, O'Hara PJ. 2009. The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family
    [J]. PLoS One, 4(3): e4933.
    [17]
    Isaacs A, Lindenmann J. 1987. Virus interference. I. The interferon
    [J]. J Interferon Res, 7(5): 429-438.
    [19]
    Karpala AJ, Morris KR, Broadway MM, McWaters PGD, O'Neil TE, Goossens KE, Lowenthal JW, Bean AGD. 2008. Molecular cloning, expression, and characterization of chicken IFN -λ
    [J]. J Interferon Cytokine Res, 28(6): 341-350.
    [21]
    Karpusas M, Nolte M, Benton CB, Meier W, Lipscomb WN, Goelz S. 1997. The crystal structure of human interferon β at 2.2-? resolution
    [J]. Proc Natl Acad Sci USA, 94(22): 11813-11818.
    [23]
    Kotenko SV, Gallagher G, Baurin VV, Lewis-Antes A, Shen ML, Shah NK, Langer JA, Sheikh F, Dickensheets H, Donnelly RP. 2003. IFN-λs mediate antiviral protection through a distinct class II cytokine receptor complex
    [J]. Nat Immunol, 4(1): 69-77.
    [25]
    Lasfar A, Lewis-Antes A, Smirnov SV, Anantha S, Abushahba W, Tian B, Reuhl K, Dickensheets H, Sheikh F, Donnelly RP, Raveche E, Kotenko SV. 2006. Characterization of the mouse IFN-λ ligand-receptor system:IFN-λs exhibit antitumor activity against B16 melanoma
    [J]. Cancer Res, 66(8): 4468-4477.
    [27]
    Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen JY, Xie XH, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. 2011. A high-resolution map of human evolutionary constraint using 29 mammals
    [J]. Nature, 478(7370): 476-482.
    [29]
    Lis H, Sharon N. 1993. Protein glycosylation. Structural and functional aspects
    [J]. Eur J Biochem, 218(1): 1-27.
    [31]
    Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment
    [J]. J Mol Biol, 302(1): 205-217.
    [33]
    Novacek MJ. 1992. Mammalian phylogeny: shaking the tree
    [J]. Nature, 356(6365): 121-125.
    [35]
    ?sterlund P, Veckman V, Sirén J, Klucher KM, Hiscott J, Matikainen S, Julkunen I. 2005. Gene expression and antiviral activity of alpha/beta interferons and interleukin-29 in virus-infected human myeloid dendritic cells
    [J]. J Virol, 79(15): 9608-9617.
    [37]
    Qi ZT, Nie P, Secombes CJ, Zou J. 2010. Intron-containing type I and type III IFN coexist in amphibians: refuting the concept that a retroposition event gave rise to type I IFNs
    [J]. J Immunol, 184(9): 5038-5046.
    [39]
    Rambaldi D, Ciccarelli FD. 2009. FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
    [J]. Bioinformatics, 25(17): 2281-2282
    [41]
    Robertsen B. 2006. The interferon system of teleost fish
    [J]. Fish Shellfish Immunol, 20(2): 172-191.
    [43]
    Samarajiwa SA, Forster S, Auchettl K, Hertzog PJ. 2009. INTERFEROME: the database of interferon regulated genes
    [J]. Nucleic Acids Res, 37(Database issue): D852-D857.
    [45]
    Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human-mouse alignments with BLASTZ
    [J]. Genome Res, 13(1): 103-107.
    [47]
    Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W. 2000. PipMaker-a web server for aligning two genomic DNA sequences
    [J]. Genome Res, 10(4): 577-586.
    [49]
    Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, Whitmore TE, Kuestner R, Garrigues U, Birks C, Roraback J, Ostrander C, Dong D, Shin J, Presnell S, Fox B, Haldeman B, Cooper E, Taft D, Gilbert T, Grant FJ, Tackett M, Krivan W, McKnight G, Clegg C, Foster D, Klucher KM. 2003. IL-28, IL-29 and their class II cytokine receptor IL-28R
    [J]. Nat Immunol, 4(1): 63-68.
    [51]
    Su JJ, Yan QR, Gan YQ, Zhou DN, Huang DR, Huang GH 1987. Study on the HBV infection of adult Tupaia
    [J]. Zhonghua Binglixue Zazhi, (16): 103-105.
    [53]
    Taniguchi T, Fujii-Kuriyama Y, Muramatsu M. 1980a. Molecular cloning of human interferon cDNA
    [J]. Proc Natl Acad Sci USA, 77(7): 4003-4006.
    [55]
    Taniguchi T, Mantei N, Schwarzstein M, Nagata S, Muramatsu M, Weissmann C. 1980b. Human leukocyte and fibroblast interferons are structurally related
    [J]. Nature, 285(5766): 547-549.
    [57]
    Uzé G, Di Marco S, Mouchel-Vielh E, Monneron D, Bandu MT, Horisberger MA, Dorques A, Lutfalla G, Mogensen KE. 1994. domains of interaction between α-interferon and its receptor components
    [J]. J Mol Biol, 243(2): 245-257.
    [59]
    Uzé G, Lutfalla G, Mogensen KE. 1995. α-interferon and β interferon and their receptor and their friends and relations
    [J]. J Interferon Cytokine Res, 15(1): 3-26.
    [61]
    Uzé G, Monneron D. 2007. IL-28 and IL-29: newcomers to the interferon family
    [J]. Biochimie, 89(6-7): 729-734.
    [63]
    Waddell PJ, Kishino H, Ota R. 2001. A phylogenetic foundation for comparative mammalian genomics
    [J]. Genome Inform, 12: 141-154.
    [65]
    Walter E, Keist R, Niederost B, Pult I, Blum HE. 1996. Hepatitis B virus infection of tupaia hepatocytes in vitro and in vivo
    [J]. Hepatology, 24(1): 1-5.
    [67]
    Zdanov A. 2010. Structural analysis of cytokines comprising the IL-10 family
    [J]. Cytokine Growth Factor Rev, 21(5): 325-330.
    [69]
    Zhou P, Cowled C, Todd S, Crameri G, Virtue ER, Marsh GA, Klein R, Shi Z, Wang LF, Baker ML. 2011. Type III IFNs in pteropid bats: differential expression patterns provide evidence for distinct roles in antiviral immunity
    [J]. J Immunol, 186(5): 3138-3147.
    [71]
    Zou J, Tafalla C, Truckle J, Secombes CJ. 2007. Identification of a second group of type I IFNs in fish sheds light on IFN evolution in vertebrates
    [J]. J Immunol, 179(6): 3859-3871.
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (2437) PDF downloads(2001) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return