Antimicrobial Peptides in Plants: Classes, Databases, and Importance

Uncategorized
  1. Fatema Matkawala1,2
  2. Anand Nighojkar2,
  3. Anil Kumar1*

Authors Affiliation(s)

  • 1School of Biotechnology, Devi Ahilya University, Khandwa Road, Indore 452001, INDIA
  • 2Maharaja Ranjit Singh College of Professional Sciences, Khandwa Road, Indore 452001, INDIA

Can J Biotech, Volume 3, Issue 2, Pages 158-168, DOI: https://doi.org/10.24870/cjb.2019-000130

Received: Jul 12, 2019; Revised: Aug 19, 2019; Accepted: Aug 26, 2019

Abstract

Plant antimicrobial peptides (AMPs) are diverse molecules crucial in host defense mechanisms. These natural compounds display broad-spectrum antimicrobial activities and also play a significant role as immune modulators and anti-infective agents. They are classified into different families like defensins, thionins, cyclotides, snakins, and several others, based on the variation in their structure, the composition of amino acids, number of disulfide bonds, and mechanism of action. The ascending number of drug- resistant plant and animal pathogens has pushed researchers to search for novel peptides, which can be utilized as alternatives to chemical antibiotics. In addition, the exhaustive genomic and proteomic data available on the cyberspace encourage the development of peptide libraries used for the prediction of unexplored peptides, thus saving time and cost for wet-lab experimentation. Understanding the insights of the structure and function of plant AMPs would offer excellent opportunities to expand their use as therapeutics in pharmaceutical and agricultural industries. This study reviewed the basis of plant AMPs, provided information on recent advancements in omic tools, and updated newly added peptides in the databases. The potential application of these peptides in human healthcare and agribusiness was also discussed.

References

  1. Jhong, J.H., Chi, Y.H., Li, W.C., Lin, T.H., Huang, K.Y. and Lee, T.Y. (2019) dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. Nucleic Acids Res 47: D285–D297. Crossref
  2. Conlon, J.M., Mechkarska, M., Radosavljevic, G., Attoub, S., King, J.D., Lukic, M.L. and McClean, S. (2014) A family of antimicrobial and immunomodulatory peptides related to the frenatins from skin secretions of the Orinoco lime frog Sphaenorhynchus lacteus (Hylidae). Peptides 56: 132–140. Crossref
  3. Roudi, R., Syn, N.L. and Roudbary, M. (2017) Antimicrobial peptides as biologic and immunotherapeutic agents against cancer: a comprehensive overview. Front Immunol 8: 1320. Crossref
  4. Fjell, C.D., Hiss, J.A., Hancock, R.E. and Schneider, G. (2011) Designing antimicrobial peptides: form follows function. Nat Rev Drug Discov 11: 37–51. Crossref
  5. Biswaro, L.S., da Costa Sousa, M.G., Rezende, T.M.B., Dias, S.C. and Franco, O.L. (2018) Antimicrobial peptides and nanotechnology, recent advances and challenges. Front Microbiol 9: 855. Crossref
  6. Lopez-Abarrategui, C., Alba, A., Silva, O.N., Reyes- Acosta, O., Vasconcelos, I.M., Oliveira, J.T., Migliolo, L., Costa, M.P., Costa, C.R., Silva, M.R., Garay, H.E., Dias, S.C., Franco, O.L. and Otero-Gonzalez, A.J. (2012) Functional characterization of a synthetic hydrophilic antifungal peptide derived from the marine snail Cenchritis muricatus. Biochimie 94: 968–974. Crossref
  7. Bamdad, F., Sun, X., Guan, L.L. and Chen, L. (2015) Preparation and characterization of antimicrobial cationized peptides from barley (Hordeum vulgare L.) proteins. LWT – Food Sci Technol 63: 29–36. Crossref
  8. Salas, C.E., Badillo-Corona, J.A., Ramírez-Sotelo, G. and Oliver-Salvador, C. (2015) Biologically active and antimicrobial peptides from plants. Biomed Res Int 2015: 102129. Crossref
  9. Wang, P., Hu, L., Liu, G., Jiang, N., Chen, X., Xu, J., Zheng, W., Li, L., Tan, M., Chen, Z., Song, H., Cai, Y.D. and Chou, K.C. (2011) Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS ONE 6: e18476. Crossref
  10. Nawrot, R., Barylski, J., Nowicki, G., Broniarczyk, J., Buchwald, W. and Gozdzicka-Jozefiak, A. (2014) Plant antimicrobial peptides. Folia Microbiol (Praha) 59: 181– 196. Crossref
  11. Pelegrini, P.B., Del Sarto, R.P., Silva, O.N., Franco, O.L. and Grossi-de-Sa, M.F. (2011) Antibacterial peptides from plants: What they are and how they probably work. Biochem Res Int 2011: 250349. Crossref
  12. Seyedjavadi, S.S., Khani, S., Zare-Zardini, H., Halabian, R., Goudarzi, M., Khatami, S., Imani Fooladi, A.A., Amani, J. and Razzaghi-Abyaneh, M. (2019) Isolation, functional characterization, and biological properties of MCh-AMP1, a novel antifungal peptide from Matricaria chamomilla L. Chem Biol Drug Des 93: 949–959. Crossref
  13. Kerenga, B.K., McKenna, J.A., Harvey, P.J., Quimbar, P., Garcia-Ceron, D., Lay, F.T., Phan, T.K., Veneer, P.K., Vasa, S., Parisi, K., Shafee, T.M.A., van der Weerden, N.L., Hulett, M.D., Craik, D.J., Anderson, M.A. and Bleackley, M.R. (2019) Salt tolerant antifungal and antibacterial activities of the corn defensin ZmD32. Front Microbiol 10: 795. Crossref
  14. Farkas, A., Maroti, G., Kereszt, A. and Kondorosi, E. (2017) Comparative analysis of the bacterial membrane disruption effect of two natural plant antimicrobial peptides. Front Microbiol 8: 51. Crossref
  15. Zhao, S., Han, J., Bie, X., Lu, Z., Zhang, C. and Lv, F. (2016) Purification and characterization of plantaricin JLA-9: A novel bacteriocin against Bacillus spp. produced by Lactobacillus plantarum JLA-9 from Suan- Tsai, a traditional chinese fermented cabbage. J Agric Food Chem 64: 2754–2764. Crossref
  16. Vriens, K., Peigneur, S., De Coninck, B., Tytgat, J., Cammue, B.P. and Thevissen, K. (2016) The antifungal plant defensin AtPDF2.3 from Arabidopsis thaliana blocks potassium channels. Sci Rep 6: 32121. Crossref
  17. Vieira Bard, G.C., Nascimento, V.V., Ribeiro, S.F., Rodrigues, R., Perales, J., Teixeira-Ferreira, A., Carvalho, A.O., Fernandes, K.V. and Gomes, V.M. (2015) Characterization of peptides from Capsicum annuum hybrid seeds with inhibitory activity against α- amylase, serine proteinases and fungi. Protein J 34: 122– 129. Crossref
  18. Rogozhin, E.A., Slezina, M.P., Slavokhotova, A.A., Istomina, E.A., Korostyleva, T.V., Smirnov, A.N., Grishin, E.V., Egorov, T.A. and Odintsova, T.I. (2015) A novel antifungal peptide from leaves of the weed Stellaria media L. Biochimie 116: 125–132. Crossref
  19. Samriti, Biswas, R. and Biswas, K. (2018) Plant antimicrobial peptides: a novel approach against drug resistant microorganisms. Int J Pharm Sci Res 9: 1–15. Crossref
  20. Do, H.M., Lee, S.C., Jung, H.W., Kee, H.S. and Hwang, B.K. (2004) Differential expression and in situ localization of a pepper defensin (CADEF1) gene in response to pathogen infection, abiotic elicitors and environmental stresses in Capsicum annuum. Plant Sci 166: 1297–1305. Crossref
  21. Carvalho Ade, O. and Gomes, V.M. (2009) Plant defensins- prospects for the biological functions and biotechnological properties. Peptides 30: 1007– 1020. Crossref
  22. Lopez-García, B., San Segundo, S. and Coca, M. (2012) ‘Antimicrobial peptides as a promising alternative for plant disease protection’. In Small Wonders: Peptides for Disease Control (Raja Sekaran K, Cary JW, Jaynes J, Montesinos E, Eds). American Chemical Society, Washington DC, USA, 263–294. Crossref
  23. Sher Khan, R, Iqbal, A., Malak, R., Shehryar, K., Attia, S., Ahmed, T., Ali Khan, M., Arif, M. and Mii, M. (2019) Plant defensins: types, mechanism of action and prospects of genetic engineering for enhanced disease resistance in plants. 3 Biotech 9: 192. Crossref
  24. Hammami, R., Ben Hamida, J, Vergoten, G. and Fliss, I. (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 37: D963–D968. Crossref
  25. Candido, E.S., Porto, W.F., Amaro, D.S., Viana, J.C., Dias, S.C. and Franco, O.L. (2011) Structural and functional insights into plant bactericidal peptides. In Science against microbial pathogens: communicating current research and technological advances (Mendez- Vilas A, Ed). Formatex Research Center, 951–960.
  26. Mylne, J.S., Wang, C.K., van der Weerden, N.L. and Craik, D.J. (2010) Cyclotides are a component of the innate defense of Oldenlandia affinis. Biopolymers 94: 635–646. Crossref
  27. De Souza Candido, E., e Silva Cardoso, M.H., Sousa, D.A., Viana, J.C., de Oliveira-Junior, N.G., Miranda, V. and Franco, O.L. (2014) The use of versatile plant antimicrobial peptides in agribusiness and human health. Peptides 55: 65–78. Crossref
  28. Pestana-Calsa, M.C. and Calsa Jr., T. (2011) In silico identification of plant-derived antimicrobial peptides. In Systems and Computational Biology – Molecular and Cellular Experimental Systems (Yang NS, Ed).IntechOpen. Crossref
  29. Carvalho Ade, O. and Gomes, V.M. (2007) Role of plant lipid transfer proteins in plant cell physiology-a concise review. Peptides 28: 1144–1153. Crossref
  30. Archer, B.L. (1960) The proteins of Hevea brasiliensis latex. 4. Isolation and characterization of crystalline hevein. Biochem J 75: 236–40. Crossref
  31. Koo, J.C., Lee, S.Y., Chun, H.J., Cheong, Y.H., Choi, J.S., Kawabata, S., Miyagi, M., Tsunasawa, S., Ha, K.S., bae, D.W., Han, C.D., Lee, B.L. and Cho, M.J. (1998) Two hevein homologs isolated from the seed of Pharbitis nil L. exhibit potent antifungal activity. Biochim Biophys Acta 1382: 80–90. Crossref
  32. Broekaert, W.F., Marien, W., Terras, F.R., De Bolle, M.F., Proost, P., Van Damme, J., Dillen, L., Claeya, M., Rees, S.B., Vanderleyden, J. et al. (1992) Antimicrobial peptides from Amaranthus caudatus seeds with sequence homology to the cysteine/glycine-rich domain of chitin- binding proteins. Biochemistry 31: 4308–4314. Crossref
  33. Nielsen, K.K., Nielsen, J.E., Madrid, S.M. and Mikkelsen, J.D. (1997)£ Characterization of a new antifungal chitin-binding peptide from sugar beet leaves. Plant Physiol 113: 83–91. Crossref
  34. Hall, K., Mozsolits, H. and Aguilar, M.I. (2003) Surface plasmon resonance analysis of antimicrobial peptide-membrane interactions: affinity & mechanism of action. Lett Pept Sci 10: 475–485. Crossref
  35. Kang, S.J., Park, S.J., Mishig-Ochir, T. and Lee, B.J. (2014) Antimicrobial peptides: therapeutic potentials. Expert Rev Anti Infect Ther 12: 1477–1486. Crossref
  36. Cruz, J., Ortiz, C., Guzman, F., Fernandez-Lafuente, R. and Torres, R. (2014) Antimicrobial peptides: promising compounds against pathogenic microorganisms. Curr Med Chem 21: 2299–2321. Crossref
  37. Maestri, E., Marmiroli, M. and Marmiroli, N. (2016) Bioactive peptides in plant-derived foodstuffs. J Proteomics 147: 140–155. Crossref
  38. Wang, G., Li, X. and Wang, Z. (2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res 44: D1087–D1093. Crossref
  39. Pirtskhalava, M., Gabrielian, A., Cruz, P., Griggs, H.L., Squires, R.B., Hurt, D.E., Grigolova, M., Chubinidze, M., Gogoladze, G., Vishnepolsky, B., Alekseyev, V., Rosenthal, A. and Tartakovsky, M. (2016) DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides. Nucleic Acids Res 44: D1104–D1112. Crossref
  40. Waghu, F.H., Gopi, L., Barai, R.S., Ramteke, P., Nizami, B. and Idicula-Thomas, S. (2014) CAMP: collection of sequences and structures of antimicrobial peptides. Nucleic Acids Res 42: D1154–D1158. Crossref
  41. Lee, H.T., Lee, C.C., Yang, J.R., Lai, J.Z.C. and Chang, K.Y. (2015) A large scale structural classification of antimicrobial peptides. BioMed Res Int 2015: 475062. Crossref
  42. Zhao, X., Wu, H., Lu, H., Li, G. and Huang, Q. (2013) LAMP: A database linking antimicrobial peptides. PLoS One 8: e66557. Crossref
  43. Piotto, S.P., Sessa, L., Concilio, S. and Iannelli, P. (2012) YADAMP: yet another database of antimicrobial peptides. Int J Antimicrob Agents 39: 346–351. Crossref
  44. Fjell, C.D., Hancock, R.E. and Cherkasov, A. (2007) AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23: 1148–1155. Crossref
  45. Thomas, S., Karnik, S., Barai, R.S., Jayaraman, V.K. and Idicula-Thomas, S. (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38: D774–D780. Crossref
  46. Hammami, R. and Fliss, I. (2010) Current trends in antimicrobial agent research: chemo- and bioinformatics approaches. Drug Discov Today 15: 540–546. Crossref
  47. Almaghrabi B., Ali, M.A., Zahoor A., Shah, K.H. and Bohlmann., H. (2019) Arabidopsis thionin-like genes are involved in resistance against the beet-cyst nematode (Heterodera schachtii). Plant Physiol Biochem 140: 55– 67. Crossref
  48. Ramada, M.H.S., Brand, G.D., Abrao, F.Y., Oliveira, M., Cardozo Filho, J.L., Galbieri, R., Gramacho, K.P., Prates, M.V. and Bloch Jr., C. (2017) Encrypted antimicrobial peptides from plant proteins. Sci Rep 7: 13263. Crossref
  49. Porto, W.F. and Franco, O.L. (2013) Theoretical structural insights into the snakin/GASA family. Peptides 44: 163–167. Crossref
  50. Melo, F.R., Rigden, D.J., Franco O.L., Mello, L.V., Ary, M.B., Grossi de Sa, M.F. and Bloch Jr., C. (2002) Inhibition of trypsin by cowpea thionin: characterization, molecular modeling, and docking. Proteins 48: 311–319. Crossref
  51. Shelenkov, A.A., Slavokhotova, A.A. and Odintsova, T.I. (2018) Cysmotif searcher pipeline for antimicrobial peptide identification in plant transcriptomes. Biochemistry (Mosc) 83: 1424–1432. Crossref
  52. Wang, M. and Hu, X. (2017) Antimicrobial peptide repertoire of Thitarodes armoricanus, a host species of Ophiocordyceps sinensis, predicted based on de novo transcriptome sequencing and analysis. Infect Genet Evol 54: 238–244. Crossref
  53. Kim, I.W., Markkandan, K., Lee, J.H., Subramaniyam, S., Yoo, S., Park, J. and Hwang, J.S. (2016) Transcriptome profiling and in silico analysis of the antimicrobial peptides of the grasshopper Oxya chinensis sinuosa. J Microbiol Biotechnol 26: 1863–1870. Crossref
  54. Candido Ede, S., Pinto, M.F., Pelegrini, P.B., Lima, T.B., Silva, O.N., Pogue, R., Grossi-de-Sá, M.F. and Franco, O.L. (2011) Plant storage proteins with antimicrobial activity: novel insights into plant defense mechanisms. FASEB J 25: 3290–3305. Crossref
  55. Ghag, S.B., Shekhawat, U.K.S. and Ganapathi T.R. (2014) Transgenic banana plants expressing a Stellaria media defensin gene (Sm-AMP-D1) demonstrate improved resistance to Fusarium oxysporum. Plant Cell Tissue Organ Cult 119: 247–255. Crossref
  56. Lacerda, A.F., Del Sarto, R.P., Silva, M.S., de Vasconcelos, E.A.R., Coelho, R.R., Dos Santos, V.O., Godoy, C.V., Seixas, C.D.S., da Silva, M.C.M. and Grossi-de-Sa, M.F. (2016). The recombinant pea defensin Drr230a is active against impacting soybean and cotton pathogenic fungi from the genera Fusarium, Colletotrichum and Phakopsora. 3 Biotech 6: 59. Crossref
  57. Schaefer, S.C., Gasic, K., Cammue, B., Broekaert, W., van Damme, E.J., Peumans, W.J. and Korban, S.S. (2005) Enhanced resistance to early blight in transgenic tomato lines expressing heterologous plant defense genes. Planta 222: 858–866. Crossref
  58. Koo, J.C., Chun, H.J., Park, H.C., Kim, M.C., Koo, Y.D., Koo, S.C., Ok, H.M., Park, S.J., Lee, S.H., Yun, D.J., Lim, C.O., Bahk, J.D., Lee, S.Y. and Cho, M.J. (2002) Over-expression of a seed specific hevein-like antimicrobial peptide from Pharbitis nil enhances resistance to a fungal pathogen in transgenic tobacco plants. Plant Mol Biol 50: 441–452. Crossref
  59. Gao, A.G, Hakimi, S.M., Mittanck, C.A., Wu, Y., Woerner, B.M., Stark, D.M., Shah, D.M., Liang, J. and Rommens, C.M. (2000) Fungal pathogen protection in potato by expression of a plant defensin peptide. Nat Biotechnol 18: 1307–1310. Crossref
  60. Ali, S., Ganai, B.A., Kamili, A.N., Bhat, A.A., Mir, Z.A., Bhat, J.A., Tyagi, A., Islam, S.T., Mushtaq, M., Yadav, P., Rawat, S. and Grover, A. (2018) Pathogenesis-related proteins and peptides as promising tools for engineering plants with multiple stress tolerance. Microbial Res 212– 213: 29–37. Crossref
  61. Taveira, G.B., Mathias, L.S., da Motta, O.V., Machado, O.L., Rodrigues, R., Carvalho, A.O., Teixeira-Ferreira, A., Perales, J., Vasconcelos, I.M. and Gomes, V.M. (2014) Thionin-like peptides from Capsicum annuum fruits with high activity against human pathogenic bacteria and yeasts. Biopolymers 102: 30–39. Crossref
  62. Da Rocha Pitta, M.G., da Rocha Pitta, M.G. and Galdino, S.L. (2010) Development of novel therapeutic drugs in humans from plant antimicrobial peptides. Curr Protein Pept Sci 11: 236–247. Crossref
  63. Dutta, P. and Das, S. (2016) Mammalian antimicrobial peptides: promising therapeutic targets against infection and chronic inflammation. Curr Top Med Chem 16: 99– 129. Crossref
  64. Kumar, P., Kizhakkedathu, J.N. and Straus, S.K. (2018) Antimicrobial peptides: diversity, mechanism of action and strategies to improve the activity and biocompatibility in vivo. Biomolecules 8: E4. Crossref
  65. Seo, M.D., Won, H.S., Kim, J.H., Mishig-Ochir, T. and Lee, B.J. (2012) Antimicrobial peptides for therapeutic applications: A review. Molecules 17: 12276– 12286. Crossref
  66. Da Cunha, N.B., Cobacho, N.B., Viana, J.F.C., Lima, L.A., Sampaio, K.B.O., Dohms, S.S.M., Ferreira, A.C.R., de la Fuente-Nunez, C., Costa, F.F., Franco, O.L. and Dias, S.C. (2017) The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts. Drug Discov Today 22: 234–248. Crossref