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Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken

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Abstract

Antimicrobial peptides (AMPs) are essential components of innate immunity in a range of species from Drosophila to humans and are generally thought to act by disrupting the membrane integrity of microbes. In order to discover novel AMPs in the chicken, we have implemented a bioinformatic approach that involves the clustering of more than 420,000 chicken expressed sequence tags (ESTs). Similarity searching of proteins—predicted to be encoded by these EST clusters—for homology to known AMPs has resulted in the in silico identification of full-length sequences for seven novel gallinacins (Gal-4 to Gal-10), a novel cathelicidin and a novel liver-expressed antimicrobial peptide 2 (LEAP-2) in the chicken. Differential gene expression of these novel genes has been demonstrated across a panel of chicken tissues. An evolutionary analysis of the gallinacin family has detected sites—primarily in the mature AMP—that are under positive selection in these molecules. The functional implications of these results are discussed.

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References

  • Agerberth B, Gunne H, Odeberg J, Kogner P, Boman HG, Gudmundsson GH (1995) FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis. Proc Natl Acad Sci USA 92:195–199

    CAS  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    PubMed  Google Scholar 

  • Bals R, Wang X, Zasloff M, Wilson JM (1998) The peptide antibiotic LL-37/hCAP-18 is expressed in epithelia of the human lung where it has broad antimicrobial activity at the airway surface. Proc Natl Acad Sci USA 95:9541–9546

    Article  CAS  PubMed  Google Scholar 

  • Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276–280

    CAS  PubMed  Google Scholar 

  • Cowland JB, Johnsen AH, Borregaard N (1995) hCAP-18, a cathelin/pro-bactenecin-like protein of human neutrophil specific granules. FEBS Lett 368:173–176

    CAS  PubMed  Google Scholar 

  • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763

    Article  CAS  PubMed  Google Scholar 

  • Evans EW, Beach GG, Wunderlich J, Harmon BG (1994) Isolation of antimicrobial peptides from avian heterophils. J Leukoc Biol 56:661–665

    CAS  PubMed  Google Scholar 

  • Evans EW, Beach FG, Moore KM, Jackwood MW, Glisson JR, Harmon BG (1995) Antimicrobial activity of chicken and turkey heterophil peptides CHP1, CHP2, THP1, and THP3. Vet Microbiol 47:295–303

    Article  CAS  PubMed  Google Scholar 

  • Frohm Nilsson M, Sandstedt B, Sorensen O, Weber G, Borregaard N, Stahle-Backdahl M (1999) The human cationic antimicrobial protein (hCAP18), a peptide antibiotic, is widely expressed in human squamous epithelia and colocalizes with interleukin-6. Infect Immun 67:2561–2566

    PubMed  Google Scholar 

  • Gallo RL, Kim KJ, Bernfield M, Kozak CA, Zanetti M, Merluzzi L, Gennaro R (1997) Identification of CRAMP, a cathelin-related antimicrobial peptide expressed in the embryonic and adult mouse. J Biol Chem 272:13088–93

    CAS  PubMed  Google Scholar 

  • Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725–736

    PubMed  Google Scholar 

  • Harmon BG (1998) Avian heterophils in inflammation and disease resistance. Poultry Sci 77:972–977

    CAS  Google Scholar 

  • Harwig SS, Swiderek KM, Kokryakov VN, Tan L, Lee TD, Panyutich EA, Aleshina GM, Shamova OV, Lehrer RI (1994) Gallinacins: cysteine-rich antimicrobial peptides of chicken leukocytes. FEBS Lett 342:281–285

    CAS  PubMed  Google Scholar 

  • Hase K, Eckmann L, Leopard JD, Varki N, Kagnoff MF (2002) Cell differentiation is a key determinant of cathelicidin LL-37/human cationic antimicrobial protein 18 expression by human colon epithelium. Infect Immun 70:953–963

    Article  CAS  PubMed  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings of the international conference on intelligent systems molecular biology, pp 138–148

  • Kagan BL, Selsted ME, Ganz T, Lehrer RI (1990) Antimicrobial defensin peptides form voltage-dependent ion-permeable channels in planar lipid bilayer membranes. Proc Natl Acad Sci USA 87:210–214

    CAS  PubMed  Google Scholar 

  • Krause A, Sillard R, Kleemeier B, Kluver E, Maronde E, Conejo-Garcia JR, Forssmann WG, Schulz-Knappe P, Nehls MC, Wattler F, Wattler S, Adermann K (2003) Isolation and biochemical characterization of LEAP-2, a novel blood peptide expressed in the liver. Protein Sci 12:143–152

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245

    CAS  PubMed  Google Scholar 

  • Larrick JW, Hirata M, Zhong J, Wright SC (1995) Anti-microbial activity of human CAP18 peptides. Immunotechnology 1:65–72

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Zhao C, Heng HH, Ganz T (1997) The human β-defensin-1 and α-defensins are encoded by adjacent genes: two peptide families with differing disulfide topology share a common ancestry. Genomics 43:316–320

    Article  CAS  PubMed  Google Scholar 

  • Lynn DJ, Lloyd AT, O’Farrelly C (2003) In silico identification of components of the Toll-like receptor (TLR) signaling pathway in clustered chicken expressed sequence tags (ESTs). Vet Immunol Immunopathol 93:177–184

    Article  CAS  PubMed  Google Scholar 

  • Malm J, Sorensen O, Persson T, Frohm-Nilsson M, Johansson B, Bjartell A, Lilja H, Stahle-Backdahl M, Borregaard N, Egesten A (2000) The human cationic antimicrobial protein (hCAP-18) is expressed in the epithelium of human epididymis, is present in seminal plasma at high concentrations, and is attached to spermatozoa. Infect Immun 68:4297–4302

    CAS  PubMed  Google Scholar 

  • Maxwell AI, Morrison GM, Dorin JR (2003) Rapid sequence divergence in mammalian β-defensins by adaptive evolution. Mol Immunol 40:413–421

    Article  CAS  PubMed  Google Scholar 

  • Murakami M, Ohtake T, Dorschner RA, Gallo RL (2002a) Cathelicidin antimicrobial peptides are expressed in salivary glands and saliva. J Dent Res 81:845–850

    CAS  PubMed  Google Scholar 

  • Murakami M, Ohtake T, Dorschner RA, Schittek B, Garbe C, Gallo RL (2002b) Cathelicidin anti-microbial peptide expression in sweat, an innate defense system for the skin. J Invest Dermatol 119:1090–1095

    Article  CAS  PubMed  Google Scholar 

  • Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936

    CAS  PubMed  Google Scholar 

  • Nizet V, Ohtake T, Lauth X, Trowbridge J, Rudisill J, Dorschner RA, Pestonjamasp V, Piraino J, Huttner K, Gallo RL (2001) Innate antimicrobial peptide protects the skin from invasive bacterial infection. Nature 414:454–457

    CAS  PubMed  Google Scholar 

  • Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple-sequence alignment. J Mol Biol 302:205–217

    CAS  PubMed  Google Scholar 

  • Pennisi E (2003) Human genome. A low number wins the GeneSweep Pool. Science 300:1484

    Article  CAS  Google Scholar 

  • Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  CAS  PubMed  Google Scholar 

  • Ramanathan B, Davis EG, Ross CR, Blecha F (2002) Cathelicidins: microbicidal activity, mechanisms of action, and roles in innate immunity. Microbes Infect 4:361–372

    Article  CAS  PubMed  Google Scholar 

  • Satchell DP, Sheynis T, Shirafuji Y, Kolusheva S, Ouellette AJ, Jelinek R (2003) Interactions of mouse Paneth cell α-defensins and α-defensin precursors with membranes. Prosegment inhibition of peptide association with biomimetic membranes. J Biol Chem 278:13838–13846

    Article  CAS  PubMed  Google Scholar 

  • Scocchi M, Wang S, Zanetti M (1997) Structural organization of the bovine cathelicidin gene family and identification of a novel member. FEBS Lett 417:311–315

    CAS  PubMed  Google Scholar 

  • Shin SY, Kang SW, Lee DG, Eom SH, Song WK, Kim JI (2000) CRAMP analogues having potent antibiotic activity against bacterial, fungal, and tumor cells without hemolytic activity. Biochem Biophys Res Commun 275:904–909

    Article  CAS  PubMed  Google Scholar 

  • Tamamura H, Murakami T, Horiuchi S, Sugihara K, Otaka A, Takada W, Ibuka T, Waki M, Yamamoto N, Fujii N (1995) Synthesis of protegrin-related peptides and their antibacterial and anti-human immunodeficiency virus activity. Chem Pharm Bull (Tokyo) 43:853–858

    Google Scholar 

  • Travis SM, Anderson NN, Forsyth WR, Espiritu C, Conway BD, Greenberg EP, McCray PB Jr, Lehrer RI, Welsh MJ, Tack BF (2000) Bactericidal activity of mammalian cathelicidin-derived peptides. Infect Immun 68:2748–2755

    CAS  PubMed  Google Scholar 

  • Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556

    Google Scholar 

  • Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568–573

    PubMed  Google Scholar 

  • Yang Z, Nielsen R (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46:409–418

    CAS  PubMed  Google Scholar 

  • Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449

    Google Scholar 

  • Zhao C, Nguyen T, Liu L, Sacco RE, Brogden KA, Lehrer RI (2001) Gallinacin-3, an inducible epithelial β-defensin in the chicken. Infect Immun 69:2684–2691

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by the Food Institutional Research Measure grant no. 01/R&D/D/135 from the Irish Department of Agriculture, Food and Rural Development. All experiments described in this manuscript comply with the current laws of the Republic of Ireland. Authors David Lynn and Rowan Higgs contributed equally to this work.

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Authors and Affiliations

  1. Education and Research Centre, St. Vincent’s University Hospital, 4, Dublin, Ireland

    David J. Lynn, Rowan Higgs, Susan Gaines, Tharappel James, Andrew T. Lloyd & Cliona O’Farrelly

  2. Department of Medicine, University College Dublin, 4, Belfield, Dublin, Ireland

    David J. Lynn & Rowan Higgs

  3. Moyne Institute of Preventive Medicine, Trinity College Dublin, 2, Dublin, Ireland

    Tharappel James

  4. Department of Genetics, Trinity College Dublin, 2, Dublin, Ireland

    Andrew T. Lloyd

  5. Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University College Dublin, 4, Belfield, Dublin, Ireland

    Joanna Tierney & Grace Mulcahy

  6. Biology Department, National University of Ireland, Maynooth, Ireland

    Mario A. Fares

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  1. David J. Lynn
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  2. Rowan Higgs
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  3. Susan Gaines
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  8. Grace Mulcahy
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  9. Cliona O’Farrelly
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Correspondence to Cliona O’Farrelly.

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Lynn, D.J., Higgs, R., Gaines, S. et al. Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken. Immunogenetics 56, 170–177 (2004). https://doi.org/10.1007/s00251-004-0675-0

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  • DOI: https://doi.org/10.1007/s00251-004-0675-0

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