Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | http://dx.doi.org/10.1186/s12864-016-3332-8 http://www.locus.ufv.br/handle/123456789/12544 |
Resumo: | Antimicrobial 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. Aqueous 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. Computational 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 |
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Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological useHevein-likeAntimicrobial peptideBell pepperPlant defensePeptidomicsComputational toolsBioinformaticsBiotechnologyAntimicrobial 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. Aqueous 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. Computational 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 necessaryBioMed Central Genomics2017-10-30T17:09:52Z2017-10-30T17:09:52Z2016-12-15info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlepdfapplication/pdf14712164http://dx.doi.org/10.1186/s12864-016-3332-8http://www.locus.ufv.br/handle/123456789/12544eng17(Suppl 12):999, December 2016Games, Patrícia DiasSilva, Elói Quintas Gonçalves daBarbosa, Meire de OliveiraAlmeida-Souza, Hebréia OliveiraFontes, Patrícia PereiraMagalhães-Jr, Marcos Jorge dePereira, Paulo Roberto GomesPrates, Maura ViannaFranco, Gloria ReginaFaria-Campos, AlessandraCampos, Sérgio Vale AguiarBaracat-Pereira, Maria Cristinainfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFV2024-07-12T06:42:34Zoai:locus.ufv.br:123456789/12544Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452024-07-12T06:42:34LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.none.fl_str_mv |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
title |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
spellingShingle |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use Games, Patrícia Dias Hevein-like Antimicrobial peptide Bell pepper Plant defense Peptidomics Computational tools Bioinformatics Biotechnology |
title_short |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
title_full |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
title_fullStr |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
title_full_unstemmed |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
title_sort |
Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use |
author |
Games, Patrícia Dias |
author_facet |
Games, Patrícia Dias Silva, Elói Quintas Gonçalves da Barbosa, Meire de Oliveira Almeida-Souza, Hebréia Oliveira Fontes, Patrícia Pereira Magalhães-Jr, Marcos Jorge de Pereira, Paulo Roberto Gomes Prates, Maura Vianna Franco, Gloria Regina Faria-Campos, Alessandra Campos, Sérgio Vale Aguiar Baracat-Pereira, Maria Cristina |
author_role |
author |
author2 |
Silva, Elói Quintas Gonçalves da Barbosa, Meire de Oliveira Almeida-Souza, Hebréia Oliveira Fontes, Patrícia Pereira Magalhães-Jr, Marcos Jorge de Pereira, Paulo Roberto Gomes Prates, Maura Vianna Franco, Gloria Regina Faria-Campos, Alessandra Campos, Sérgio Vale Aguiar Baracat-Pereira, Maria Cristina |
author2_role |
author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Games, Patrícia Dias Silva, Elói Quintas Gonçalves da Barbosa, Meire de Oliveira Almeida-Souza, Hebréia Oliveira Fontes, Patrícia Pereira Magalhães-Jr, Marcos Jorge de Pereira, Paulo Roberto Gomes Prates, Maura Vianna Franco, Gloria Regina Faria-Campos, Alessandra Campos, Sérgio Vale Aguiar Baracat-Pereira, Maria Cristina |
dc.subject.por.fl_str_mv |
Hevein-like Antimicrobial peptide Bell pepper Plant defense Peptidomics Computational tools Bioinformatics Biotechnology |
topic |
Hevein-like Antimicrobial peptide Bell pepper Plant defense Peptidomics Computational tools Bioinformatics Biotechnology |
description |
Antimicrobial 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. Aqueous 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. Computational 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 |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-12-15 2017-10-30T17:09:52Z 2017-10-30T17:09:52Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
14712164 http://dx.doi.org/10.1186/s12864-016-3332-8 http://www.locus.ufv.br/handle/123456789/12544 |
identifier_str_mv |
14712164 |
url |
http://dx.doi.org/10.1186/s12864-016-3332-8 http://www.locus.ufv.br/handle/123456789/12544 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
17(Suppl 12):999, December 2016 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
pdf application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central Genomics |
publisher.none.fl_str_mv |
BioMed Central Genomics |
dc.source.none.fl_str_mv |
reponame:LOCUS Repositório Institucional da UFV instname:Universidade Federal de Viçosa (UFV) instacron:UFV |
instname_str |
Universidade Federal de Viçosa (UFV) |
instacron_str |
UFV |
institution |
UFV |
reponame_str |
LOCUS Repositório Institucional da UFV |
collection |
LOCUS Repositório Institucional da UFV |
repository.name.fl_str_mv |
LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV) |
repository.mail.fl_str_mv |
fabiojreis@ufv.br |
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1817559861468069888 |