Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais

Detalhes bibliográficos
Autor(a) principal: Brustolini, Otávio José Bernardes
Data de Publicação: 2008
Tipo de documento: Dissertação
Idioma: por
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: http://locus.ufv.br/handle/123456789/5378
Resumo: In this work we have created an in silico system to address secretion of a desired protein among the genome data of Kluyveromyces lactis. The completed K. lactis genome sequencing has provided a tool to construct such a system. In order to explore a potential K. lactis extracellular secretome, four computational prediction algorithms have been applied: SignalP (presence or absence of an N-terminal signal peptide and clivage site), Phobius (transmembrane topology), big-PI Predictor (GPI modification site) and WolfPsort (subcellular addressing, including extracellular prediction). These algorithms have correctly predicted 95 yeast secreted proteins sought in public databases (NCBI, UNIProt and MIPS). They have also predicted as intracellular the same number (i.e. 95) of random sequences found in K. lactis database. The K. lactis database consists of 5327 sequences (http://cbi.labri.fr/Genolevures). When analyzed by SignalP 3.0, it has pointed out 698 putative proteins with N-terminal signal peptides. In this group, 260 were predicted by Phobius to have no transmembrane domains and 236 were found by the big-PI Predictor to have no GPI modifications site. Finally, the predicted K. lactis secretome was estimated to consist of up to 101 sequences by WolfPSORT which eliminates proteins with subcellular targeting. In order to validate theses analysis, both groups of predicted and annotated extracellular proteins were compared by Hotelling s T2 test. The analysis has shown no differences between the mean values of these two groups. The physiological significance of those potential extracellular proteins was similarly investigated by analyzing the relationship between the S. cerevisiae transcriptional regulators ortologues in K. lactis and the putative promoters (i.e. 1 KB upstream) of those extracellular proteins. It was applied the methodology proposed by Yeastract which search for elements such as binding sites that indicates associations between transcriptional factor and target genes. The physiological condition favoring protein expression in extracellular medium was obtained by searching Gene Ontology (http://www.geneontology.org). It has been shown that most of the transcriptional regulators of K. lactis extracellular proteins are related to stress response, especially presence of drugs into the medium. Also pH stress and limiting nitrogen can induce the extracellular proteins.
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spelling Brustolini, Otávio José Bernardeshttp://lattes.cnpq.br/0928279245502410Fietto, Luciano Gomeshttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4763824H8Cruz, Cosme Damiãohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6Passos, Flávia Maria Lopeshttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781817D3Mantovani, Hilário Cuquettohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4727026Z7Yotoko, Karla Suemy Clementehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4763141P72015-03-26T13:52:01Z2015-03-132015-03-26T13:52:01Z2008-07-31BRUSTOLINI, Otávio José Bernardes. Computational analysis of the interaction between the transcriptional factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. 2008. 48 f. Dissertação (Mestrado em Associações micorrízicas; Bactérias láticas e probióticos; Biologia molecular de fungos de interesse) - Universidade Federal de Viçosa, Viçosa, 2008.http://locus.ufv.br/handle/123456789/5378In this work we have created an in silico system to address secretion of a desired protein among the genome data of Kluyveromyces lactis. The completed K. lactis genome sequencing has provided a tool to construct such a system. In order to explore a potential K. lactis extracellular secretome, four computational prediction algorithms have been applied: SignalP (presence or absence of an N-terminal signal peptide and clivage site), Phobius (transmembrane topology), big-PI Predictor (GPI modification site) and WolfPsort (subcellular addressing, including extracellular prediction). These algorithms have correctly predicted 95 yeast secreted proteins sought in public databases (NCBI, UNIProt and MIPS). They have also predicted as intracellular the same number (i.e. 95) of random sequences found in K. lactis database. The K. lactis database consists of 5327 sequences (http://cbi.labri.fr/Genolevures). When analyzed by SignalP 3.0, it has pointed out 698 putative proteins with N-terminal signal peptides. In this group, 260 were predicted by Phobius to have no transmembrane domains and 236 were found by the big-PI Predictor to have no GPI modifications site. Finally, the predicted K. lactis secretome was estimated to consist of up to 101 sequences by WolfPSORT which eliminates proteins with subcellular targeting. In order to validate theses analysis, both groups of predicted and annotated extracellular proteins were compared by Hotelling s T2 test. The analysis has shown no differences between the mean values of these two groups. The physiological significance of those potential extracellular proteins was similarly investigated by analyzing the relationship between the S. cerevisiae transcriptional regulators ortologues in K. lactis and the putative promoters (i.e. 1 KB upstream) of those extracellular proteins. It was applied the methodology proposed by Yeastract which search for elements such as binding sites that indicates associations between transcriptional factor and target genes. The physiological condition favoring protein expression in extracellular medium was obtained by searching Gene Ontology (http://www.geneontology.org). It has been shown that most of the transcriptional regulators of K. lactis extracellular proteins are related to stress response, especially presence of drugs into the medium. Also pH stress and limiting nitrogen can induce the extracellular proteins.O banco de dados da Kluyveromyces lactis constituído de 5327 seqüências de proteínas (http://cbi.labri.fr/Genolevures) foi submetido a quatro algoritmos de predição para identificar o potencial secretome extracelular. O primeiro,SignalP v3 (http://www.cbs.dtu.dk/services/SignalP-3.0), que identifica a presença de peptideo sinal na porção N-terminal e o sítio de clivagem da peptidase sinalagrupou 698 proteínas.Deste grupo, o Phobius(http://phobius.sbc.su.se), que prevê a topologia de domínios transmembranas a partir das sequencias primárias, indicou 260 sem domínios transmembranas.Outros dois algoritmos, big-PI predictor(http://mendel.imp.ac.at/gpi/gpi_server.html),capaz reconhecer marcas de de ancoras GPI (Glicosilfosfatidilinositol) e WoLF PSORT(http://www.genscript.com/psort/wolf_psort.html)capaz de identificar assinaturas para a localização em compartimentos subcelulares apontaram 236 proteínas sem ancoras GPI e 101 endereçadas ao meio extracelular. Como controle positivo, os mesmos algoritmos foram testados e predisseram corretamente 95 proteínas de leveduras Saccharomycetes encontradas nos bancos de dados públicos (NCBI e UNIProt) e anotadas como extracelulares. Como controle negativo foram preditas como intracelular 95 seqüências aleatórias do banco de dados da K. lactis. O grupo controle positivo e o grupo predito foram comparados pelo teste estatístico T2 de Hotelling. Não foram evidenciadas diferenças significativas entre os valores das médias dos grupos.A condição fisiológicana qual estas proteínas extracelulares são expressas foi analisada relacionando suas seqüências promotoras com os fatores transcricionais ortólogos da Saccharomyces cerevisiae. A metodologia aplicada foi o "Yeastract" (http://www.yeastract.com) que localiza sítios de ligação ao DNA dos fatores transcricionais de S. cerevisiaenas seqüências promotoras dos ORFs das proteínas preditas como extracelulares. A condição fisiológica que favorece a expressão para o meio extracelular foi obtida pela pesquisa dos termos descritos pelo "Gene Ontology"(http://www.geneontology.org). Os fatores transcricionais que mais se relacionam com as seqüências preditas foram aqueles associados com resposta a estresse. Também foi indicado que o estresse ácido e limitação de nitrogênio (aminoácidos) exercem influência na expressão das proteínas extracelulares.Conselho Nacional de Desenvolvimento Científico e Tecnológicoapplication/pdfporUniversidade Federal de ViçosaMestrado em Microbiologia AgrícolaUFVBRAssociações micorrízicas; Bactérias láticas e probióticos; Biologia molecular de fungos de interesseKluyveromyces lactisLeveduras (Fungos)Proteínas microbianasEnzimas microbianasKluyveromyces lactisLeveduras (fungos)Microbianas ProteínasEnzimas microbianasCNPQ::CIENCIAS BIOLOGICAS::MICROBIOLOGIA::BIOLOGIA E FISIOLOGIA DOS MICROORGANISMOSPredição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionaisComputational analysis of the interaction between the transcriptional factors and the predicted secreted proteome of the yeast Kluyveromyces lactisinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALtexto completo.pdfapplication/pdf587076https://locus.ufv.br//bitstream/123456789/5378/1/texto%20completo.pdfd1ad8af5f243dc621caec98155378354MD51TEXTtexto completo.pdf.txttexto completo.pdf.txtExtracted texttext/plain81975https://locus.ufv.br//bitstream/123456789/5378/2/texto%20completo.pdf.txt43af2aa68056e1fec66421e16cd6c633MD52THUMBNAILtexto completo.pdf.jpgtexto completo.pdf.jpgIM Thumbnailimage/jpeg3630https://locus.ufv.br//bitstream/123456789/5378/3/texto%20completo.pdf.jpg6605b80888eb7869795b68228f4447efMD53123456789/53782016-04-10 23:20:24.668oai:locus.ufv.br:123456789/5378Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452016-04-11T02:20:24LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.por.fl_str_mv Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
dc.title.alternative.eng.fl_str_mv Computational analysis of the interaction between the transcriptional factors and the predicted secreted proteome of the yeast Kluyveromyces lactis
title Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
spellingShingle Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
Brustolini, Otávio José Bernardes
Kluyveromyces lactis
Leveduras (Fungos)
Proteínas microbianas
Enzimas microbianas
Kluyveromyces lactis
Leveduras (fungos)
Microbianas Proteínas
Enzimas microbianas
CNPQ::CIENCIAS BIOLOGICAS::MICROBIOLOGIA::BIOLOGIA E FISIOLOGIA DOS MICROORGANISMOS
title_short Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
title_full Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
title_fullStr Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
title_full_unstemmed Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
title_sort Predição in silico de Proteínas Extracelulares de Kluyveromyces lactis e suas relações com fatores transcricionais
author Brustolini, Otávio José Bernardes
author_facet Brustolini, Otávio José Bernardes
author_role author
dc.contributor.authorLattes.por.fl_str_mv http://lattes.cnpq.br/0928279245502410
dc.contributor.author.fl_str_mv Brustolini, Otávio José Bernardes
dc.contributor.advisor-co1.fl_str_mv Fietto, Luciano Gomes
dc.contributor.advisor-co1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4763824H8
dc.contributor.advisor-co2.fl_str_mv Cruz, Cosme Damião
dc.contributor.advisor-co2Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4788274A6
dc.contributor.advisor1.fl_str_mv Passos, Flávia Maria Lopes
dc.contributor.advisor1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4781817D3
dc.contributor.referee1.fl_str_mv Mantovani, Hilário Cuquetto
dc.contributor.referee1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4727026Z7
dc.contributor.referee2.fl_str_mv Yotoko, Karla Suemy Clemente
dc.contributor.referee2Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4763141P7
contributor_str_mv Fietto, Luciano Gomes
Cruz, Cosme Damião
Passos, Flávia Maria Lopes
Mantovani, Hilário Cuquetto
Yotoko, Karla Suemy Clemente
dc.subject.por.fl_str_mv Kluyveromyces lactis
Leveduras (Fungos)
Proteínas microbianas
Enzimas microbianas
topic Kluyveromyces lactis
Leveduras (Fungos)
Proteínas microbianas
Enzimas microbianas
Kluyveromyces lactis
Leveduras (fungos)
Microbianas Proteínas
Enzimas microbianas
CNPQ::CIENCIAS BIOLOGICAS::MICROBIOLOGIA::BIOLOGIA E FISIOLOGIA DOS MICROORGANISMOS
dc.subject.eng.fl_str_mv Kluyveromyces lactis
Leveduras (fungos)
Microbianas Proteínas
Enzimas microbianas
dc.subject.cnpq.fl_str_mv CNPQ::CIENCIAS BIOLOGICAS::MICROBIOLOGIA::BIOLOGIA E FISIOLOGIA DOS MICROORGANISMOS
description In this work we have created an in silico system to address secretion of a desired protein among the genome data of Kluyveromyces lactis. The completed K. lactis genome sequencing has provided a tool to construct such a system. In order to explore a potential K. lactis extracellular secretome, four computational prediction algorithms have been applied: SignalP (presence or absence of an N-terminal signal peptide and clivage site), Phobius (transmembrane topology), big-PI Predictor (GPI modification site) and WolfPsort (subcellular addressing, including extracellular prediction). These algorithms have correctly predicted 95 yeast secreted proteins sought in public databases (NCBI, UNIProt and MIPS). They have also predicted as intracellular the same number (i.e. 95) of random sequences found in K. lactis database. The K. lactis database consists of 5327 sequences (http://cbi.labri.fr/Genolevures). When analyzed by SignalP 3.0, it has pointed out 698 putative proteins with N-terminal signal peptides. In this group, 260 were predicted by Phobius to have no transmembrane domains and 236 were found by the big-PI Predictor to have no GPI modifications site. Finally, the predicted K. lactis secretome was estimated to consist of up to 101 sequences by WolfPSORT which eliminates proteins with subcellular targeting. In order to validate theses analysis, both groups of predicted and annotated extracellular proteins were compared by Hotelling s T2 test. The analysis has shown no differences between the mean values of these two groups. The physiological significance of those potential extracellular proteins was similarly investigated by analyzing the relationship between the S. cerevisiae transcriptional regulators ortologues in K. lactis and the putative promoters (i.e. 1 KB upstream) of those extracellular proteins. It was applied the methodology proposed by Yeastract which search for elements such as binding sites that indicates associations between transcriptional factor and target genes. The physiological condition favoring protein expression in extracellular medium was obtained by searching Gene Ontology (http://www.geneontology.org). It has been shown that most of the transcriptional regulators of K. lactis extracellular proteins are related to stress response, especially presence of drugs into the medium. Also pH stress and limiting nitrogen can induce the extracellular proteins.
publishDate 2008
dc.date.issued.fl_str_mv 2008-07-31
dc.date.accessioned.fl_str_mv 2015-03-26T13:52:01Z
dc.date.available.fl_str_mv 2015-03-13
2015-03-26T13:52:01Z
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dc.identifier.citation.fl_str_mv BRUSTOLINI, Otávio José Bernardes. Computational analysis of the interaction between the transcriptional factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. 2008. 48 f. Dissertação (Mestrado em Associações micorrízicas; Bactérias láticas e probióticos; Biologia molecular de fungos de interesse) - Universidade Federal de Viçosa, Viçosa, 2008.
dc.identifier.uri.fl_str_mv http://locus.ufv.br/handle/123456789/5378
identifier_str_mv BRUSTOLINI, Otávio José Bernardes. Computational analysis of the interaction between the transcriptional factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. 2008. 48 f. Dissertação (Mestrado em Associações micorrízicas; Bactérias láticas e probióticos; Biologia molecular de fungos de interesse) - Universidade Federal de Viçosa, Viçosa, 2008.
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dc.publisher.country.fl_str_mv BR
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publisher.none.fl_str_mv Universidade Federal de Viçosa
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