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

BMC Genomics

Research

Gloria Regina Franco¹  Patrícia Pereira Fontes²  Marcos Jorge deMagalhães-Jr²  Elói Quintas Gonçalves daSilva²  Maria Cristina Baracat-Pereira²  Meire de Oliveira Barbosa²  Patrícia Dias Games²  Hebréia Oliveira Almeida-Souza²  Alessandra Faria-Campos³  Sérgio Vale Aguiar Campos³  Paulo Roberto Gomes Pereira⁴  Maura Vianna Prates⁵ 

[1] Department of Biochemistry and Immunology-ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, MG, Brazil;Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil;Department of Computer Science-ICEX, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901, Belo Horizonte, MG, Brazil;Department of Plant Science, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil;Embrapa Genetic Resources & Biotechnology, Brazilian Agricultural Research Corporation, 70770-900, Brasília, DF, Brazil;

关键词: Hevein-like;    Antimicrobial peptide;    Bell pepper;    Plant defense;    Peptidomics;    Computational tools;    Bioinformatics;    Biotechnology;   

DOI  :  10.1186/s12864-016-3332-8

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2016