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

Detalhes bibliográficos
Autor(a) principal: Games, Patrícia Dias
Data de Publicação: 2016
Outros Autores: 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
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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spelling 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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