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Origin and Functional Diversification of an Amphibian Defense Peptide Arsenal


The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones.

Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.


Vyšlo v časopise: Origin and Functional Diversification of an Amphibian Defense Peptide Arsenal. PLoS Genet 9(8): e32767. doi:10.1371/journal.pgen.1003662
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003662

Souhrn

The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones.

Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.


Zdroje

1. BevinsCL, ZasloffM (1990) Peptides from frog skin. Annu Rev Biochem 59: 395–414.

2. BasirYJ, KnoopFC, DulkaJ, ConlonJM (2000) Multiple antimicrobial peptides and peptides related to bradykinin and neuromedin N isolated from skin secretions of the pickerel frog, Rana palustris. Biochim Biophys Acta 1543: 95–105.

3. LiL, BjoursonAJ, HeJ, CaiG, RaoP, et al. (2003) Bradykinins and their cDNA from piebald odorous frog, Odorrana schmackeri, skin. Peptides 24: 863–872.

4. HoffmannW, RichterK, KreilG (1983) A novel peptide designated PYLa and its precursor as predicted from cloned mRNA of Xenopus laevis skin. EMBO J 2: 711–714.

5. GibsonBW, PoulterL, WilliamsDH, MaggioJE (1986) Novel peptide fragments originating from PGLa and the caerulein and xenopsin precursors from Xenopus laevis. J Biol Chem 261: 5341–5349.

6. GiovanniniMG, PoulterL, GibsonBW, WilliamsDH (1987) Biosynthesis and degradation of peptides derived from Xenopus laevis prohormones. Biochem J 243: 113–120.

7. ZasloffM (1987) Magainins, a class of antimicrobial peptides from Xenopus skin: Isolation, characterization of two active forms, and partial cDNA sequence of a precursor. Proc Natl Acad Sci USA 84: 5449–5453.

8. TerryAS, PoulterL, WilliamsDH, NutkinsJC, GiovanniniMG, et al. (1988) The cDNA sequence coding for Prepro-PGS (Prepro-magainins) and aspects of the processing of this prepro-polypeptide. J Biol Chem 263: 5745–5751.

9. DudaTF, VanhoyeD, NicolasP (2002) Roles of diversifying selection and coordinated evolution in the evolution of amphibian antimicrobial peptides. Mol Biol Evol 19: 858–864.

10. VanhoyeD, BrustonF, NicolasP, AmicheM (2003) Antimicrobial peptides from hylid and ranin frogs originated from a 150-million-year-old ancestral precursor with a conserved signal peptide but a hypermutable antimicrobial domain. Eur J Biochem 270: 2068–2081.

11. LiJ, XuX, XuC, ZhouW, ZhangK, et al. (2007) Anti-infection peptidomics of amphibian skin. Mol Cell Prot 6: 882–894.

12. KönigE, Bininda-EmondsOR (2011) Evidence for convergent evolution in the antimicrobial peptide system in anuran amphibians. Peptides 32: 20–25.

13. AliMF, SotoA, KnoopFC, ConlonJM (2001) Antimicrobial peptides isolated from skin secretions of the diploid frog, Xenopus tropicalis (Pipidae). Biochim Biophys Acta 1550: 81–89.

14. ConlonJM, Al-GhaferiN, AhmedE, MeetaniMA, LeprinceJ, et al. (2010) Orthologs of magainin, PGLa, procaerulein-derived, and proxenopsin-derived peptides from skin secretions of the octoploid frog Xenopus amieti (Pipidae). Peptides 31: 989–994.

15. ConlonJM, MechkarskaM, AhmedE, LeprinceJ, VaudryH, et al. (2011) Purification and properties of antimicrobial peptides from skin secretions of the Eritrea clawed frog Xenopus clivii (Pipidae). Comp Biochem Physiol C Toxicol Pharmacol 153: 350–354.

16. ConlonJM, MechkarskaM, PrajeepM, SonnevendA, CoquetL, et al. (2012) Host-defense peptides in skin secretions of the tetraploid frog Silurana epitropicalis with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). Peptides 37: 113–119.

17. ConlonJM, MechkarskaM, KingJD (2012) Host-defense peptides in skin secretions of African clawed frogs (Xenopodinae, Pipidae). Gen Comp Endocrinol 176: 513–518.

18. KingJD, MechkarskaM, CoquetL, LeprinceJ, JouenneT, et al. (2012) Host-defense peptides from skin secretions of the tetraploid frogs Xenopus petersii and Xenopus pygmaeus, and the octoploid frog Xenopus lenduensis (Pipidae). Peptides 33: 35–43.

19. MechkarskaM, AhmedE, CoquetL, LeprinceJ, JouenneT, et al. (2010) Antimicrobial peptides with therapeutic potential from skin secretions of the Marsabit clawed frog Xenopus borealis (Pipidae). Comp Biochem Physiol C Toxicol Pharmacol 152: 467–472.

20. MechkarskaM, EmanA, CoquetL, JérômeL, JouenneT, et al. (2011) Genome duplications within the Xenopodinae do not increase the multiplicity of antimicrobial peptides in Silurana paratropicalis and Xenopus andrei skin secretions. Comp Biochem Physiol Part D Genomics Proteomics 6: 206–212.

21. MechkarskaM, AhmedE, CoquetL, LeprinceJ, JouenneT, et al. (2011) Peptidomic analysis of skin secretions demonstrates that the allopatric populations of Xenopus muelleri (Pipidae) are not conspecific. Peptides 32: 1502–1508.

22. MechkarskaM, MeetaniM, MichalakP, VaksmanZ, TakadaK, et al. (2012) Hybridization between the African clawed frogs Xenopus laevis and Xenopus muelleri (Pipidae) increases the multiplicity of antimicrobial peptides in skin secretions of female offspring. Comp Biochem Physiol Part D Genomics Proteomics 7: 285–291.

23. ZahidOK, MechkarskaM, OjoOO, Abdel-WahabYH, FlattPR, et al. (2011) Caerulein-and xenopsin-related peptides with insulin-releasing activities from skin secretions of the clawed frogs, Xenopus borealis and Xenopus amieti (Pipidae). Gen Comp Endocrinol 172: 314–320.

24. AnastasiA, BertacciniG, CeiJM, de CaroG, ErspamerV, et al. (1970) Presence of caerulein in extracts of the skin of Leptodactylus pentadactylus labyrinthicus and of Xenopus laevis. Br J Pharmacol 38: 221–228.

25. PoulterL, TerryAS, WilliamsDH, GiovanniniMG, MooreCH, et al. (1988) Levitide, a neurohormone-like peptide from the skin of Xenopus laevis. J Biol Chem 263: 3279–3283.

26. ArakiK, TachibanaS, UchiyamaM, NakajimaT, YasuharaT (1973) Isolation and structure of a new active peptide “Xenopsin” on the smooth muscle, especially on a strip of fundus from a rat stomach, from the skin of Xenopus laevis. Chem Pharm Bull 23: 2801–2804.

27. MooreKS, BevinsCL, BrasseurMM, TomassiniN, TurnerK, et al. (1991) Antimicrobial peptides in the stomach of Xenopus laevis. J Biol Chem 266: 19851–19857.

28. KuchlerK, KreilG, SuresI (1989) The genes for the frog skin peptides GLa, xenopsin, levitide and caerulein contain a homologous export exon encoding a signal peptide sequence and part of an amphiphilic peptide. Eur J Biochem 179: 281–285.

29. RichterK, AschauerH, KreilG (1985) Biosynthesis of peptides in the skin of Xenopus laevis: isolation of novel peptides predicted from the sequence of cloned cDNAs. Peptides 6: 17–21.

30. RoelantsK, FryBG, NormanJA, ClynenE, SchoofsL, et al. (2010) Identical skin toxins by convergent molecular adaptation in frogs. Curr Biol 20: 125–130.

31. PetersenTN, BrunakS, von HeijneG, NielsenH (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785–786.

32. BuchanDW, WardSM, LobleyAE, NugentTC, BrysonK, et al. (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Res 38: W563–568.

33. ZasloffM (2002) Antimicrobial peptides of multicellular organisms. Nature 415: 389–395.

34. BrogdenKA (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 3: 238–250.

35. KönigE, ZhouM, WangL, ChenT, Bininda-EmondsOR, et al. (2012) Antimicrobial peptides and alytesin are co-secreted from the venom of the Midwife toad, Alytes maurus (Alytidae, Anura): Implications for the evolution of frog skin defensive secretions. Toxicon 60: 967–981.

36. MorA, HaniK, NicolasP (1994) The vertebrate peptide antibiotics dermaseptins have overlapping structural features but target specific microorganisms. J Biol Chem 269: 31635–31641.

37. WesterhoffHV, ZasloffM, RosnerJL, HendlerRW, De WaalA, et al. (1995) Functional synergism of the magainins PGLa and magainin-2 in Escherichia coli, tumor cells and liposomes. Eur J Biochem 228: 257–264.

38. MatsuzakiK, MitaniY, AkadaKY, MursaeO, YoneyamaS, et al. (1998) Mechanism of synergism between antimicrobial peptides magainin 2 and PGLa. Biochemistry 37: 15144–15153.

39. RourkeIJ, RehfeldJF, MøllerM, JohnsenAH (1997) Characterization of the cholecystokinin and gastrin genes from the bullfrog, Rana catesbeiana: evolutionary conservation of primary and secondary sites of gene expression. Endocrinology 138: 1719–1727.

40. HansenTV (2001) Cholecystokinin gene transcription: promoter elements, transcription factors and signaling pathways. Peptides 22: 1201–1211.

41. RourkeIJ, HansenTV, NerlovC, RehfeldJF, NielsenFC (1999) Negative cooperativity between juxtaposed E-box and cAMP/TPA responsive elements in the cholecystokinin gene promoter. FEBS Lett 448: 15–18.

42. BaileyTL, BodenM, BuskeFA, FrithM, GrantCE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208.

43. MatysV, FrickeE, GeffersR, GösslingE, HaubrockM, et al. (2003) TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374–378.

44. FolettaVC, SegalDH, CohenDR (1998) Transcriptional regulation in the immune system: all roads lead to AP-1. J Leukoc Biol 63: 139–152.

45. BrahmacharyM, SchonbachC, YangL, HuangE, TanS, et al. (2006) Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. BMC Bioinformatics 7 Suppl 5: S8.

46. WuGD, LaiEJ, HuangN, WenX (1997) Oct-1 and CCAAT/enhancer-binding protein (C/EBP) bind to overlapping elements within the interleukin-8 promoter. The role of Oct-1 as a transcriptional repressor. J Biol Chem 272: 2396–2403.

47. KwonSY, CarlsonBA, ParkJM, LeeBJ (2000) Structural organization and expression of the gaegurin 4 gene of Rana rugosa. Biochim Biophys Acta 1492: 185–190.

48. MieleR, BjörklundG, BarraD, SimmacoM, EngströmY (2001) Involvement of Rel factors in the expression of antimicrobial peptide genes in amphibia. Eur J Biochem 268: 443–449.

49. RonquistF, HuelsenbeckJP (2003) MrBayes version 3.0: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.

50. SuchardMA, RedelingsBD (2006) BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22: 2047–2048.

51. RoelantsK, GowerDJ, WilkinsonM, LoaderSP, BijuSD, et al. (2007) Global patterns of diversification in the history of modern amphibians. Proc Natl Acad Sci USA 104: 887–892.

52. YangX, LeeWH, ZhangY (2012) Extremely abundant antimicrobial peptides existed in the skins of nine kinds of Chinese odorous frogs. J Proteome Res 11: 306–319.

53. ParkerJM, MikaelianI, HahnN, DiggsHE (2002) Clinical diagnosis and treatment of epidermal chytridiomycosis in African clawed frogs (Xenopus tropicalis). Comp Med 52: 265–268.

54. RamseyJP, ReinertLK, HarperLK, WoodhamsDC, Rollins-SmithLA (2010) Immune defenses against Batrachochytrium dendrobatidis, a fungus linked to global amphibian declines, in the South African clawed frog, Xenopus laevis. Infect Immun 78: 3981–3992.

55. RosenblumEB, PoortenTJ, SettlesM, MurdochGK, RobertJ, et al. (2009) Genome-Wide Transcriptional Response of Silurana (Xenopus) tropicalis to Infection with the Deadly Chytrid Fungus. PLoS ONE 4: e6494.

56. RibasL, LiM-S, DoddingtonBJ, RobertJ, SeidelJA, et al. (2009) Expression Profiling the Temperature-Dependent Amphibian Response to Infection by Batrachochytrium dendrobatidis. PLoS ONE 4: e8408.

57. SrinivasanD, MechkarskaM, Abdel-WahabYH, FlattPR, ConlonJM (2013) Caerulein precursor fragment (CPF) peptides from the skin secretions of Xenopus laevis and Silurana epitropicalis are potent insulin-releasing agents. Biochimie 95: 429–435.

58. NeiM, RooneyAP (2005) Concerted and Birth-and-Death Evolution of Multigene Families. Annu Rev Genet 39: 121–152.

59. LynchVJ (2007) Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes. BMC Evol Biol 7: 2.

60. FryBG, ScheibH, van der WeerdL, YoungB, McNaughtanJ, RamjanSFR, VidalN, PoelmannRE, NormanJA (2008) Evolution of an Arsenal. Structural and functional diversification of the venom system in the advanced snakes (Caenophidia). Mol Cell Proteomics 7: 215–246.

61. KondrashovFA, KooninEV (2001) Origin of alternative splicing by tandem exon duplication. Hum Mol Genet 10: 2661–2669.

62. McCruddenCM, ZhouM, ChenT, O'RourkeM, WalkerB, et al. (2007) The complex array of bradykinin-related peptides (BRPs) in the peptidome of pickerel frog (Rana palustris) skin secretion is the product of transcriptional economy. Peptides 28: 1275–1281.

63. Bowie JH, Tyler MJ (2006) Host defense peptides from Australian amphibians: Caerulein and other neuropeptides. In: Kastin AJ, editor. Handbook of biologically active peptides. San Diego: Academic Press. pp. 283–289.

64. CheclerF, LabbéC, GranierC, van RietschotenJ, KitabgiP, VincentJP (1982) [TRP11]-neurotensin and xenopsin discriminate between rat and guinea-pig neurotensin receptors. Life Sci 31: 1145–1150.

65. ClemensA, KatsoulisS, NustedeR, SeebeckJ, SeyfarthK, Morys-WortmannC, FeurleGE, FolschUR, SchmidtWE (1997) Relaxant effect of xenin on rat ileum is mediated by apamin-sensitive neurotensin-type receptors. Am J Physiol 272: G190–G196.

66. FeurleGE (1998) Xenin -– a review. Peptides 19: 609–615.

67. KalafatakisK, TriantafyllouK (2011) Contribution of neurotensin in the immune and neuroendocrine modulation of normal and abnormal enteric function. Regul Pept 170: 7–17.

68. KitabgiP (2006) Differential processing of pro-neurotensin/neuromedin N and relationship to pro-hormone convertases. Peptides 27: 2508–2514.

69. ChowVTK, QuekHH (1997) Alpha coat protein COPA (HEP-COP): presence of an Alu repeat in cDNA and identity of the amino terminus to xenin. Ann Hum Genet 61: 369–373.

70. CasewellNR, WagstaffSC, HarrisonRA, RenjifoC, WüsterW (2011) Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes. Mol Biol Evol 28: 2637–2649.

71. ChangD, DudaTFJr (2012) Extensive and continuous duplication facilitates rapid evolution and diversification of gene families. Mol Biol Evol 29: 2019–2029.

72. WongES, BelovK (2012) Venom evolution through gene duplications. Gene 496: 1–7.

73. Ohno S (1970) Evolution by Gene Duplication. Berlin: Springer.

74. ForceA, LynchM, Bryan PickettF, AmoresA, YanY, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531–1545.

75. HittingerCT, CarrollSB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677–681.

76. SikosekT, ChanHS, Bornberg-BauerE (2012) Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness. Proc Natl Acad Sci USA 109: 14888–14893.

77. BergthorssonU, AnderssonDI, RothJR (2007) Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A 104: 17004–17009.

78. Kozminsky-AtiasA, Bar-ShalomA, MishmarD, ZilberbergN (2008) Assembling an arsenal, the scorpion way. BMC Evol Biol 8: 333.

79. WangL, ChenY, YangM, ZhouM, ChenT, et al. (2010) Peptide DV-28 amide: An inhibitor of bradykinin-induced arterial smooth muscle relaxation encoded by Bombina orientalis skin kininogen-2. Peptides 31: 979–982.

80. MurayamaN, HayashiMA, OhiH, FerreiraLA, HermannVV, et al. (1997) Cloning and sequence analysis of a Bothrops jararaca cDNA encoding a precursor of seven bradykinin-potentiating peptides and a C-type natriuretic peptide. Proc Natl Acad Sci USA 94: 1189–1193.

81. FryBG, RoelantsK, WinterK, HodgsonWC, GriesmanL, et al. (2010) Novel venom proteins produced by differential domain-expression strategies in beaded lizards and gila monsters (genus Heloderma). Mol Biol Evol 27: 395–407.

82. MorA, DelfaourA, NicolasP (1991) Identification of a D-alanine-containing polypeptide precursor for the peptide opioid, dermorphin. J Biol Chem 266: 6264–6270.

83. ChenM, CheQ, WangX, LiJ, YangH, et al. (2010) Cloning and characterization of the first amphibian bradykinin gene. Biochimie 92: 226–231.

84. PerkinsDN, PappinDJ, CreasyDM, CottrellJS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551–3567.

85. Tossi A, Sandri L, Giangaspero A (2002) New consensus hydrophobicity scale extended to non-proteinogenic amino acids. In: Peptides 2002: Proceedings of the twenty-seventh European peptide symposium. Napoli: Edizioni Ziino. pp. 416–417.

86. ProhaskaSJ, FriedC, FlammC, WagnerGP, StadlerPF (2004) Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol Phylogenet Evol 31: 581–604.

87. KatohK, KumaK, TohH, MiyataT (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511–518.

88. Rambaut A, Drummond AJ (2007) Tracer v1.5. Available: http://beast.bio.ed.ac.uk/Tracer. Accessed: 01 February, 2010.

89. Kosakovsky PondSL, FrostSDW, MuseSV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676–679.

90. Kosakovsky PondSL, FrostSDW (2005) Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. Mol Biol Evol 22: 1208–1222.

91. YangZ (2007) PAML4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 24: 1586–1591.

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