Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use

Abstract

BackgroundAntimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves (‘Magali R’) are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses.ResultsAqueous extracts from leaves were enriched in peptide by salt fractionation and ultrafiltration. An antimicrobial peptide was isolated by tandem chromatographic procedures. Mass spectrometry, automated peptide sequencing and bioinformatics tools were used alternately for identification and partial characterization of the Hevein-like peptide, named HEV-CANN. The computational tools that assisted to the identification of the peptide included BlastP, PSI-Blast, ClustalOmega, PeptideCutter, and ProtParam; conventional protein databases (DB) as Mascot, Protein-DB, GenBank-DB, RefSeq, Swiss-Prot, and UniProtKB; specific for peptides DB as Amper, APD2, CAMP, LAMPs, and PhytAMP; other tools included in ExPASy for Proteomics; The Bioactive Peptide Databases, and The Pepper Genome Database. The HEV-CANN sequence presented 40 amino acid residues, 4258.8 Da, theoretical pI-value of 8.78, and four disulfide bonds. It was stable, and it has inhibited the growth of phytopathogenic bacteria and a fungus. HEV-CANN presented a chitin-binding domain in their sequence. There was a high identity and a positive alignment of HEV-CANN sequence in various databases, but there was not a complete identity, suggesting that HEV-CANN may be produced by ribosomal synthesis, which is in accordance with its constitutive nature.ConclusionsComputational tools for proteomics and databases are not adjusted for short sequences, which hampered HEV-CANN identification. The adjustment of statistical tests in large databases for proteins is an alternative to promote the significant identification of peptides. The development of specific DB for plant antimicrobial peptides, with information about peptide sequences, functional genomic data, structural motifs and domains of molecules, functional domains, and peptide-biomolecule interactions are valuable and necessary.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3332-8) contains supplementary material, which is available to authorized users.

Bell Peppers (Capsicum annum L.) Losses and Wastes: Source for Food and Pharmaceutical Applications

“…carotovora in a strain- and concentration-dependent response and mentioned that peptide compounds could be used as a biotechnological alternative for biological control of phytopathogens. Similarly, Dias-Games et al [ 52 ] showed that the Hevein-like peptide extracted from bell pepper leaves showed antimicrobial properties against Clavibacter michiganensis spp. michiganensis (Gram-positive) and Ralstonia solanacearum (Gram-negative).…”

“…Additionally, Dias-Games et al [ 52 ] isolated a Hevein-like peptide from the leaves of bell pepper crops. These compounds showed antibacterial and antifungal activities and exhibited great potential for biotechnological use [ 53 ].…”

Investigation of Antimicrobial Peptide Genes Associated with Fungus and Insect Resistance in Maize

“…Although many AMPs are a part of the constitutive defense [ 1 , 2 , 3 , 7 , 10 , 36 ], insecticidal proteins were of significant interest in this study due to the relatively limited literature available. To investigate these oftentimes inducible AMPs, only plant tissue that was directly wounded by insect feeding was collected.…”

Image-based classification of healthy and diseased bell pepper using the transfer learning method

“…They also suggested that peptide discovery be aided by statistical testing in large protein databases. Peptides are very small compounds [6]. The researcher used the YOLO-V5 algorithm to determine the type of plant disease affecting bell pepper plants.…”