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Insilico Studies on Antimicrobial Peptides (AMPs) from Earthworm

  • Shyamasree GhoshEmail author
Article
First Online:

Abstract

The immune system of earthworm is very robust despite being in a primitive invertebrate organism. The immune system confers protection against pollutants and pathogens (Ghosh in Environ Sci Pollut Res 25:6196, 2018) and the cells and molecules in the earthworm coelomic fluid are reported (Bilej et al. In: Madame Curie bioscience database [Internet]. Landes Bioscience, Austin, TX, 2000–2013) to play antibacterial, antitumoral and anti trypanosomal role and contain immune molecule including coelom cytolytic factor (CCF), lyesenin and antimicrobial peptides (AMPs). Due to their diverse and advanced roles, they find importance for study both from the point of view of basic sciences and applied biological sciences. Although the immune molecules are reported from different species of earthworm, the physiochemical proteins of AMPs are yet to be studied. Therefore, we performed an insilico study of the different AMPs reported from different species of earthworm from the NCBI. We report for the first time, diversity amongst the AMPs of different species of earthworms, despite functional similarities.

Keywords

AMP Earthworm E. andrei I tasser L. terrestris P. guillelmi (Michaelsen) PP-1 
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Notes

Acknowledgements

The author acknowledges the national institute of Science Education and Research (NISER) Bhubaneswar for the study.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.

References

  1. Bilej M, Procházková P, Šilerová M, Josková R (2000–2013) Earthworm immunity. In: Madame Curie bioscience database [Internet]. Landes Bioscience, Austin, TXGoogle Scholar
  2. Blom N, Gammeltoft S, Brunak S (1999) Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 294(5):1351–1362PubMedCrossRefPubMedCentralGoogle Scholar
  3. Blom N, Ponten T, Gupta R, Gammeltoft S, Brunak S (2004) Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4(6):1633–1649 (Review 2004) PubMedCrossRefPubMedCentralGoogle Scholar
  4. Bruno R, Maresca M, Canaan S, Cavalier J-F, Mabrouk K, Boidin-Wichlacz C, Olleik H, Zeppilli D, Brodin P, Massol F, Jollivet D, Jung S, Tasiemski A (2019) Worms’ antimicrobial peptides. Mar Drugs 17:512PubMedCentralCrossRefGoogle Scholar
  5. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 31:3497–3500PubMedPubMedCentralCrossRefGoogle Scholar
  6. Cho JH, Park CB, Yoon YG, Kim SC (1998) Lumbricin I, a novel proline-rich antimicrobial peptide from the earthworm: purification, cDNA cloning and molecular characterization. Biochim Biophys Acta 1408(1):67–76PubMedCrossRefPubMedCentralGoogle Scholar
  7. Conti E, Uy M, Leighton L, Blobel G, Kuriyan J (1998) Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 94:193–204PubMedCrossRefPubMedCentralGoogle Scholar
  8. de Paula VS, Valente AP (2018) A dynamic overview of antimicrobial peptides and their complexes. Molecules 23(8):2040PubMedCentralCrossRefGoogle Scholar
  9. Engelmann P, Cooper EL, Opper B, Németh P (2011) Earthworm innate immune system. In: Karaca A (ed) Biology of earthworms. Soil biology, vol 24. Springer, BerlinGoogle Scholar
  10. Epand R, Vogel H (1999) Diversity of antimicrobial peptides and their mechanisms of action. Biochim Biophys Acta 1462:11–28PubMedCrossRefGoogle Scholar
  11. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, Totowa, pp 571–607CrossRefGoogle Scholar
  12. Ghosh S (2018) Environmental pollutants, pathogens and immune system in earthworms. Environ Sci Pollut Res 25:6196CrossRefGoogle Scholar
  13. Gomes-Neto F, Valente AP, Almeida FCL (2013) Modeling the interaction of dodecylphosphocholine micelles with anticoccidial peptide PW2 guided by NMR data. Molecules 18:10056–10080PubMedPubMedCentralCrossRefGoogle Scholar
  14. Harel A, Forbes DJ Importin (2004) Importin beta: conducting a much larger cellular symphony. Mol Cell 16:319–330PubMedPubMedCentralGoogle Scholar
  15. Higgins DG (1994) CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol Biol 25:307–318PubMedPubMedCentralGoogle Scholar
  16. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244PubMedCrossRefPubMedCentralGoogle Scholar
  17. Higgins DG, Sharp PM (1989) Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci 5:151–153PubMedPubMedCentralGoogle Scholar
  18. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8:189–191PubMedPubMedCentralGoogle Scholar
  19. Higgins DG, Thompson JD, Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266:383–402PubMedCrossRefPubMedCentralGoogle Scholar
  20. Hirigoyenberry F, Lassalle F, Lassegues M (1990) Antibacterial activity of Eisenia fetida andrei coelomic fluid: transcription and translation regulation of lysozyme and proteins evidenced after bacterial infestation. Comp Biochem Physiol B 95(1):71–75PubMedCrossRefPubMedCentralGoogle Scholar
  21. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403–405PubMedCrossRefPubMedCentralGoogle Scholar
  22. Kim DH, Lee IH, Nam ST, Hong J, Zhang P, Hwang JS, Seok H, Choi H, Lee DG, Kim JI, Kim H (2014) Neurotropic and neuroprotective activities of the earthworm peptide Lumbricusin. Biochem Biophys Res Commun 448(3):292–297PubMedCrossRefPubMedCentralGoogle Scholar
  23. Kim DH, Lee IH, Nam ST, Hong J, Zhang P, Lu LF, Hwang JS, Park KC, Kim HJ (2015) Antimicrobial peptide, lumbricusin, ameliorates motor dysfunction and dopaminergic neurodegeneration in a mouse model of Parkinson’s disease. Microbiol Biotechnol 25(10):1640–1647CrossRefGoogle Scholar
  24. Kosugi S, Hasebe M, Entani T, Takayama S, Tomita M, Yanagawa H (2008a) Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. Chem Biol 15:940–949PubMedCrossRefPubMedCentralGoogle Scholar
  25. Kosugi S, Hasebe M, Tomita M, Yanagawa H (2008b) Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic 9:2053–2062PubMedCrossRefPubMedCentralGoogle Scholar
  26. Kosugi S, Hasebe M, Tomita M, Yanagawa H (2009a) Systematic identification of yeast cell cycle-dependent nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci USA 106:10171–10176PubMedCrossRefGoogle Scholar
  27. Kosugi S, Hasebe M, Matsumura N, Takashima H, Miyamoto-Sato E, Tomita M, Yanagawa H (2009b) J Biol Chem 284:478–485PubMedCrossRefPubMedCentralGoogle Scholar
  28. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefPubMedCentralGoogle Scholar
  29. Lee BJ, Cansizoglu AE, Suel KE, Louis TH, Zhang Z, Chook YM (2006) Rules for nuclear localization sequence recognition by karyopherin beta 2. Cell 126:543–558PubMedPubMedCentralCrossRefGoogle Scholar
  30. Li W, Li S, Zhong J, Zhu Z, Liu J, Wang W (2011) A novel antimicrobial peptide from skin secretions of the earthworm, Pheretima guillelmi (Michaelsen). Peptides 32(6):1146–1150PubMedCrossRefPubMedCentralGoogle Scholar
  31. Liu YQ, Sun ZJ, Wang C, Li SJ, Liu YZ (2004) Purification of a novel antibacterial short peptide in earthworm Eisenia foetida. Acta Biochim Biophys Sin (Shanghai) 36(4):297–302CrossRefGoogle Scholar
  32. Mattar EH, Almehdar HA, Yacoub HA, Uversky VN, Redwan EM (2016) Antimicrobial potentials and structural disorder of human and animal defensins. Cytokine Growth Factor Rev 28:95–111PubMedCrossRefPubMedCentralGoogle Scholar
  33. Mo X, Qiao Y, Sun Z, Sun X, Li Y (2012) Molecular toxicity of earthworms induced by cadmium contaminated soil and biomarkers screening. J Environ Sci (China) 24(8):1504–1510CrossRefGoogle Scholar
  34. Ossareh-Nazari B, Gwizdek C, Dargemont C (2001) Protein export from the nucleus. Traffic 2:684–689PubMedCrossRefPubMedCentralGoogle Scholar
  35. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725–738PubMedPubMedCentralCrossRefGoogle Scholar
  36. Seo M, Lee JH, Baek M, Kim MA, Ahn MY, Kim SH, Yun EY, Hwang JS (2017) A novel role for earthworm peptide Lumbricusin as a regulator of neuroinflammation. Biochem Biophys Res Commun 490(3):1004–1010PubMedCrossRefPubMedCentralGoogle Scholar
  37. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedPubMedCentralCrossRefGoogle Scholar
  38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedPubMedCentralCrossRefGoogle Scholar
  39. Travkova OG, Moehwald H, Brezesinski G (2017) The interaction of antimicrobial peptides with membranes. Adv Colloid Interface Sci 247:521–532PubMedCrossRefPubMedCentralGoogle Scholar
  40. Valente AP, Miyamoto C, Almeida FCL (2006) Implications of protein conformational diversity for binding and development of new biological active compounds. Curr Med Chem 13:3697–3703PubMedCrossRefPubMedCentralGoogle Scholar
  41. Wang X, Wang X, Zhang Y, Qu X, Yang S (2003) An antimicrobial peptide of the earthworm Pheretima tschiliensis: cDNA cloning, expression and immunolocalization. Biotechnol Lett 25(16):1317–1323PubMedCrossRefPubMedCentralGoogle Scholar
  42. Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43:W174–W181PubMedPubMedCentralCrossRefGoogle Scholar
  43. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER Suite: protein structure and function prediction. Nat Methods 12:7–8PubMedPubMedCentralCrossRefGoogle Scholar
  44. Zhang LJ, Gallo RL (2016) Antimicrobial peptides. Curr Biol 26:R14–R19PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of Biological SciencesNational Institute of Science Education and Research (NISER)BhubaneswarIndia
  2. 2.Homi Bhabha National InstituteMumbaiIndia

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