Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins

Detalhes bibliográficos
Autor(a) principal: Menezes Neto, Armando de
Data de Publicação: 2012
Outros Autores: Alvarenga, Denise Anete Madureira, Rezende, Antônio Mauro de, Resende, Sarah Stela, Ribeiro, Ricardo de Souza, Fontes, Cor Jesus Fernandes, Carvalho, Luzia Helena de, Brito, Cristiana Ferreira Alves de
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/7760
Resumo: Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, Brazil
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spelling Menezes Neto, Armando deAlvarenga, Denise Anete MadureiraRezende, Antônio Mauro deResende, Sarah StelaRibeiro, Ricardo de SouzaFontes, Cor Jesus FernandesCarvalho, Luzia Helena deBrito, Cristiana Ferreira Alves de2014-06-03T18:12:47Z2014-06-03T18:12:47Z2012MENEZES NETO, Armando de et al. Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins. Malaria Journal. 2012, vol.11, pp. 375https://www.arca.fiocruz.br/handle/icict/776010.1186/1475-2875-11-375engBioMed Central Ltd.Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteinsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Parasitologia Celular e Molecular. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilHospital Universitário Julio Muller. Cuiabá, MT BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, BrazilBackground Signal peptide is one of the most important motifs involved in protein trafficking and it ultimately influences protein function. Considering the expected functional conservation among orthologs it was hypothesized that divergence in signal peptides within orthologous groups is mainly due to N-terminal protein sequence misannotation. Thus, discrepancies in signal peptide prediction of orthologous proteins were used to identify misannotated proteins in five Plasmodium species. Methods Signal peptide (SignalP) and orthology (OrthoMCL) were combined in an innovative strategy to identify orthologous groups showing discrepancies in signal peptide prediction among their protein members (Mixed groups). In a comparative analysis, multiple alignments for each of these groups and gene models were visually inspected in search of misannotated proteins and, whenever possible, alternative gene models were proposed. Thresholds for signal peptide prediction parameters were also modified to reduce their impact as a possible source of discrepancy among orthologs. Validation of new gene models was based on RT-PCR (few examples) or on experimental evidence already published (ApiLoc). Results The rate of misannotated proteins was significantly higher in Mixed groups than in Positive or Negative groups, corroborating the proposed hypothesis. A total of 478 proteins were reannotated and change of signal peptide prediction from negative to positive was the most common. Reannotations triggered the conversion of almost 50% of all Mixed groups, which were further reduced by optimization of signal peptide prediction parameters. Conclusions The methodological novelty proposed here combining orthology and signal peptide prediction proved to be an effective strategy for the identification of proteins showing wrongly N-terminal annotated sequences, and it might have an important impact in the available data for genome-wide searching of potential vaccine and drug targets and proteins involved in host/parasite interactions, as demonstrated for five Plasmodium species.Signal peptideOrthologousGene annotationMalariaPlasmodiuminfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALImproving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins - 1475.pdfImproving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins - 1475.pdfapplication/pdf4467792https://www.arca.fiocruz.br/bitstream/icict/7760/1/Improving%20N-terminal%20protein%20annotation%20of%20Plasmodium%20species%20based%20on%20signal%20peptide%20prediction%20of%20orthologous%20proteins%20-%201475.pdf029de6f52f79e48bf0d6e556e12faf62MD51LICENSElicense.txtlicense.txttext/plain; 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dc.title.pt_BR.fl_str_mv Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
title Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
spellingShingle Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
Menezes Neto, Armando de
Signal peptide
Orthologous
Gene annotation
Malaria
Plasmodium
title_short Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
title_full Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
title_fullStr Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
title_full_unstemmed Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
title_sort Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
author Menezes Neto, Armando de
author_facet Menezes Neto, Armando de
Alvarenga, Denise Anete Madureira
Rezende, Antônio Mauro de
Resende, Sarah Stela
Ribeiro, Ricardo de Souza
Fontes, Cor Jesus Fernandes
Carvalho, Luzia Helena de
Brito, Cristiana Ferreira Alves de
author_role author
author2 Alvarenga, Denise Anete Madureira
Rezende, Antônio Mauro de
Resende, Sarah Stela
Ribeiro, Ricardo de Souza
Fontes, Cor Jesus Fernandes
Carvalho, Luzia Helena de
Brito, Cristiana Ferreira Alves de
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Menezes Neto, Armando de
Alvarenga, Denise Anete Madureira
Rezende, Antônio Mauro de
Resende, Sarah Stela
Ribeiro, Ricardo de Souza
Fontes, Cor Jesus Fernandes
Carvalho, Luzia Helena de
Brito, Cristiana Ferreira Alves de
dc.subject.en.pt_BR.fl_str_mv Signal peptide
Orthologous
Gene annotation
Malaria
Plasmodium
topic Signal peptide
Orthologous
Gene annotation
Malaria
Plasmodium
description Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratorio de Malaria. Belo Horizonte, MG, Brazil
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-06-03T18:12:47Z
dc.date.available.fl_str_mv 2014-06-03T18:12:47Z
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.citation.fl_str_mv MENEZES NETO, Armando de et al. Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins. Malaria Journal. 2012, vol.11, pp. 375
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/7760
dc.identifier.doi.none.fl_str_mv 10.1186/1475-2875-11-375
identifier_str_mv MENEZES NETO, Armando de et al. Improving N-terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins. Malaria Journal. 2012, vol.11, pp. 375
10.1186/1475-2875-11-375
url https://www.arca.fiocruz.br/handle/icict/7760
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central Ltd.
publisher.none.fl_str_mv BioMed Central Ltd.
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/7760/1/Improving%20N-terminal%20protein%20annotation%20of%20Plasmodium%20species%20based%20on%20signal%20peptide%20prediction%20of%20orthologous%20proteins%20-%201475.pdf
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