Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

Abstract

The centipede Scolopendra subspinipes mutilans is an environmentally beneficial and medically important arthropod species. Although this species is increasingly applied as a reliable source of new antimicrobial peptides, the transcriptome of this species is a prerequisite for more rational selection of antimicrobial peptides. In this report, we isolated total RNA from the whole body of adult centipedes, S. subspinipes mutilans, that were nonimmunized and immunized against Escherichia coli, and we generated a total of 77,063 pooled contigs and singletons using high-throughput sequencing. To screen putative antimicrobial peptides, in silico analyses of the S. subspinipes mutilans transcriptome were performed based on the physicochemical evidence of length, charge, isoelectric point, and in vitro and in vivo aggregation scores together with the existence of continuous antimicrobial peptide stretches. Moreover, we excluded some transcripts that showed similarity with both previously known antimicrobial peptides and the human proteome, had a proteolytic cleavage site, and had downregulated expression compared with the nonimmunized sample. As a result, we selected 17 transcripts and tested their antimicrobial activity with a radial diffusion assay. Among them, ten synthetic peptides experimentally showed antimicrobial activity against microbes and no toxicity to mouse erythrocytes. Our results provide not only a useful set of antimicrobial peptide candidates and an efficient strategy for novel antimicrobial peptide development but also the transcriptome data of a big centipede as a valuable resource.

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References

  1. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007) UniProtKB/Swiss-Prot. Methods Mol Biol 406:89–112

    CAS  PubMed  Google Scholar 

  2. Brogden KA (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol 3(3):238–250. doi:10.1038/nrmicro1098

    CAS  PubMed  Article  Google Scholar 

  3. Bulet P, Stocklin R (2005) Insect antimicrobial peptides: structures, properties and gene regulation. Protein Pept Lett 12(1):3–11

    CAS  PubMed  Article  Google Scholar 

  4. Bulet P, Stocklin R, Menin L (2004) Anti-microbial peptides: from invertebrates to vertebrates. Immunol Rev 198:169–184

    CAS  PubMed  Article  Google Scholar 

  5. Chen CY (2011) TCM Database@Taiwan: the world’s largest traditional Chinese medicine database for drug screening in silico. PLoS One 6(1):e15939. doi:10.1371/journal.pone.0015939

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  6. Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, Ventura S (2007) AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinforma 8:65. doi:10.1186/1471-2105-8-65

    Article  Google Scholar 

  7. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22(10):1302–1306. doi:10.1038/nbt1012

    CAS  PubMed  Article  Google Scholar 

  8. Fjell CD, Hiss JA, Hancock RE, Schneider G (2012) Designing antimicrobial peptides: form follows function. Nat Rev Drug Discov 11(1):37–51. doi:10.1038/nrd3591

    CAS  Google Scholar 

  9. Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P, Coudert E, Datta RS, de Lima WC, de Oliveira Lima T, Duvaud S, Farriol-Mathis N, Ferro Rojas S, Feuermann M, Gateau A, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Moinat M, Nikolskaya A, Pedruzzi I, Rivoire C, Roechert B, Schneider M, Stanley E, Tognolli M, Sjolander K, Bougueleret L, Chisholm RL, Bairoch A (2009) Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. Database: J Biol Databases Curation 2009:bap016. doi:10.1093/database/bap016

  10. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. doi:10.1038/nbt.1883

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  11. Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (2010) BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol 10:22. doi:10.1186/1471-2180-10-22

    PubMed Central  PubMed  Article  Google Scholar 

  12. Hilpert K, Volkmer-Engert R, Walter T, Hancock RE (2005) High-throughput generation of small antibacterial peptides with improved activity. Nat Biotechnol 23(8):1008–1012. doi:10.1038/nbt1113

    CAS  PubMed  Article  Google Scholar 

  13. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceedings/International Conference on Intelligent Systems for Molecular Biology; ISMB International Conference on Intelligent Systems for Molecular Biology: 138–148

  14. Jenssen H, Hamill P, Hancock RE (2006) Peptide antimicrobial agents. Clin Microbiol Rev 19(3):491–511. doi:10.1128/CMR.00056-05

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  15. Jenuth JP (2000) The NCBI. Publicly available tools and resources on the Web. Methods Mol Biol 132:301–312

    CAS  PubMed  Google Scholar 

  16. Menousek J, Mishra B, Hanke ML, Heim CE, Kielian T, Wang G (2012) Database screening and in vivo efficacy of antimicrobial peptides against methicillin-resistant Staphylococcus aureus USA300. Int J Antimicrob Agents 39(5):402–406. doi:10.1016/j.ijantimicag.2012.02.003

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  17. Oh C, Deung M, Kang B, Shin M, Lee J (2002) Medicinal animal science. Uisungdang, Seoul

    Google Scholar 

  18. Peng K, Kong Y, Zhai L, Wu X, Jia P, Liu J, Yu H (2010) Two novel antimicrobial peptides from centipede venoms. Toxicon Off J Int Soc Toxicol 55(2–3):274–279. doi:10.1016/j.toxicon.2009.07.040

    CAS  Article  Google Scholar 

  19. 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(5):651–652

    CAS  PubMed  Article  Google Scholar 

  20. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16(6):276–277

    CAS  PubMed  Article  Google Scholar 

  21. Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, Chuon D, Beuerman R, Verma C (2007) Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res 35(Database issue):D265–D268

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  22. Shai Y (2002) Mode of action of membrane active antimicrobial peptides. Biopolymers 66(4):236–248. doi:10.1002/bip.10260

    CAS  PubMed  Article  Google Scholar 

  23. Sieprawska-Lupa M, Mydel P, Krawczyk K, Wojcik K, Puklo M, Lupa B, Suder P, Silberring J, Reed M, Pohl J, Shafer W, McAleese F, Foster T, Travis J, Potempa J (2004) Degradation of human antimicrobial peptide LL-37 by Staphylococcus aureus-derived proteinases. Antimicrob Agents Chemother 48(12):4673–4679. doi:10.1128/AAC.48.12.4673-4679.2004

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  24. Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38(Database issue):D774–D780. doi:10.1093/nar/gkp1021

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  25. Torrent M, Nogues VM, Boix E (2009) A theoretical approach to spot active regions in antimicrobial proteins. BMC Bioinforma 10:373. doi:10.1186/1471-2105-10-373

    Article  Google Scholar 

  26. Torrent M, Andreu D, Nogues VM, Boix E (2011a) Connecting peptide physicochemical and antimicrobial properties by a rational prediction model. PLoS One 6(2):e16968. doi:10.1371/journal.pone.0016968

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  27. Torrent M, Pulido D, de la Torre BG, Garcia-Mayoral MF, Nogues MV, Bruix M, Andreu D, Boix E (2011b) Refining the eosinophil cationic protein antibacterial pharmacophore by rational structure minimization. J Med Chem 54(14):5237–5244. doi:10.1021/jm200701g

    CAS  PubMed  Article  Google Scholar 

  28. Torrent M, Di Tommaso P, Pulido D, Nogues MV, Notredame C, Boix E, Andreu D (2012) AMPA: an automated Web server for prediction of protein antimicrobial regions. Bioinformatics 28(1):130–131. doi:10.1093/bioinformatics/btr604

    CAS  PubMed  Article  Google Scholar 

  29. Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37(Database issue):D933–D937. doi:10.1093/nar/gkn823

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  30. Wenhua R, Shuangquan Z, Daxiang S, Kaiya Z, Guang Y (2006) Induction, purification and characterization of an antibacterial peptide scolopendrin I from the venom of centipede Scolopendra subspinipes mutilans. Indian J Biochem Biophys 43(2):88–93

    CAS  PubMed  Google Scholar 

  31. Yeaman MR, Yount NY (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55(1):27–55. doi:10.1124/pr.55.1.2

    CAS  PubMed  Article  Google Scholar 

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Acknowledgment

This work was supported by a grant from the Next-Generation BioGreen 21 Program (no. PJ008158, PJ008196), Rural Development Administration, Republic of Korea.

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Correspondence to Junhyung Park or Jae Sam Hwang.

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Won Gi Yoo and Joon Ha Lee equally contributed to this paper.

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Yoo, W.G., Lee, J.H., Shin, Y. et al. Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans . Funct Integr Genomics 14, 275–283 (2014). https://doi.org/10.1007/s10142-014-0366-3

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Keywords

  • RNA-seq
  • Physicochemical properties
  • Antimicrobial peptide
  • Scolopendra subspinipes mutilans