DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular

Detalhes bibliográficos
Autor(a) principal: Andrade, Bruno Silva
Data de Publicação: 2011
Tipo de documento: Tese
Idioma: por
Título da fonte: Biblioteca Digital de Teses e Dissertações da UEFS
Texto Completo: http://tede2.uefs.br:8080/handle/tede/1139
Resumo: In this study we evaluated molecular and evolutionary aspects of DNA (DPO) and RNA (RPO) polymerases encoded by M. perniciosa mitochondrial plasmid. Three-dimensional models of these polymerases were constructed using a Homology Modeling approach, followed by Molecular Dynamics simulations of 3500 picoseconds. With modeled and validated 3D structures, we performed a virtual screening process in order to search for chemical compounds, using KEGG, ZINC and PubChem databases, followed by Molecular Docking (AutoDock Vina) and Molecular Dynamics MM/PBSA. Thus, we selected DPO-Entecavir and RPO-Rifampicin as the most stable complexes. The study of the relative expression of DPO and RPO genes was done by RT-qPCR, using cDNA from different developmental stages of M. perniciosa. In the phase of primordium, a significant increase in the activity of these genes occured, which is probably related to a self-defense process of the fungus against T. cacao. Phylogenetic analyses were performed by using DNA and protein sequences of DPO and RPO from M. perniciosa and other 12 fungal polymerases, as well as viral polymerases sequences. Then, Maximum Likelihood and Bayesian analyses were performed by using only fungal polymerase sequences, and the combination of fungal and viral polymerase sequences. Tree topologies results corroborate the hypothesis of Horizontal Gene Transfer (HGT) between fungal and viral polymerases, and delineate the evolutionary relationship of DPO and RPO M. perniciosa mitochondrial plasmid.
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spelling Góes Neto, Aristóteles54434882520http://lattes.cnpq.br/613413383428943800175568561http://lattes.cnpq.br/6692846454039770Andrade, Bruno Silva2020-05-20T01:27:55Z2011-06-20ANDRADE, Bruno Silva. DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acadêmico em Biotecnologia)- Universidade Estadual de Feira de Santana, Feira de Santana, 2011.http://tede2.uefs.br:8080/handle/tede/1139In this study we evaluated molecular and evolutionary aspects of DNA (DPO) and RNA (RPO) polymerases encoded by M. perniciosa mitochondrial plasmid. Three-dimensional models of these polymerases were constructed using a Homology Modeling approach, followed by Molecular Dynamics simulations of 3500 picoseconds. With modeled and validated 3D structures, we performed a virtual screening process in order to search for chemical compounds, using KEGG, ZINC and PubChem databases, followed by Molecular Docking (AutoDock Vina) and Molecular Dynamics MM/PBSA. Thus, we selected DPO-Entecavir and RPO-Rifampicin as the most stable complexes. The study of the relative expression of DPO and RPO genes was done by RT-qPCR, using cDNA from different developmental stages of M. perniciosa. In the phase of primordium, a significant increase in the activity of these genes occured, which is probably related to a self-defense process of the fungus against T. cacao. Phylogenetic analyses were performed by using DNA and protein sequences of DPO and RPO from M. perniciosa and other 12 fungal polymerases, as well as viral polymerases sequences. Then, Maximum Likelihood and Bayesian analyses were performed by using only fungal polymerase sequences, and the combination of fungal and viral polymerase sequences. Tree topologies results corroborate the hypothesis of Horizontal Gene Transfer (HGT) between fungal and viral polymerases, and delineate the evolutionary relationship of DPO and RPO M. perniciosa mitochondrial plasmid.Neste trabalho foram estudados aspectos moleculares e evolutivos das DNA (DPO) e RNA (RPO) polimerases codificadas pelo plasmídeo mitocondrial de M. perniciosa. Modelos tridimensionais dessas polimerases foram construídos, utilizando Modelagem por Homologia, seguida de uma simulação por Dinâmica Molecular de 3500 picossegundos. Com as estruturas 3D das enzimas modeladas e validadas, foi realizado um processo de triagem virtual de compostos químicos, utilizando os bancos de dados KEGG, ZINC e PubChem, seguido do Docking Molecular (Autodock Vina) e Dinâmica Molecular MM/PBSA. Então, foram selecionados complexos mais estáveis DPO-Entecavir e RPO-Rifampicina. O estudo da expressão relativa dos genes codificadores das DNA e RNA polimerases foi feito através de RT-qPCR, utilizando-se cDNA diferentes fases de desenvolvimento do M. perniciosa. Foi na fase de primórdio em que houve um aumento significativo na atividade desses genes, o que provavelmente está relacionado com um processo de defesa do fungo contra o T. cacao. A análise filogenética foi realizada utilizando-se sequências de DNA e proteína das DPO e RPO do plasmídeo de M. perniciosa e de polimerases de outros 12 plasmídeos fúngicos, além de sequências de polimerases virais. Foram realizadas análises de Máxima Verossimilhança e Bayesiana, apenas de sequências fúngicas e da combinação entre fungos e vírus. As topologias das árvores filogenéticas resultantes dessas análises corroboram as hipóteses de Transferência Horizontal de Genes (THG) entre polimerases fúngicas e virais, além de delimitar as relações evolutivas das DPO e RPO do plasmídeo de M. perniciosa.Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2020-05-20T01:27:55Z No. of bitstreams: 1 Tese_BRuno SIlva.pdf: 5843479 bytes, checksum: cfe9c91b0dc94dcbc8fd4f0e3136700f (MD5)Made available in DSpace on 2020-05-20T01:27:55Z (GMT). No. of bitstreams: 1 Tese_BRuno SIlva.pdf: 5843479 bytes, checksum: cfe9c91b0dc94dcbc8fd4f0e3136700f (MD5) Previous issue date: 2011-06-20application/pdfporUniversidade Estadual de Feira de SantanaDoutorado Acadêmico em BiotecnologiaUEFSBrasilDEPARTAMENTO DE CIÊNCIAS BIOLÓGICASMoniliophthora perniciosaMitocôndriaPolimerasesRT-qPCRFilogenia MolecularMitochondriaPolymerasesMolecular PhylogenyCIENCIAS BIOLOGICAS::BIOLOGIA GERALCIENCIAS BIOLOGICASDNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecularinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesis-68152692297897915436006006006005026123383450589282-1634559385931244697-3439178843068202161info:eu-repo/semantics/openAccessreponame:Biblioteca Digital de Teses e Dissertações da UEFSinstname:Universidade Estadual de Feira de Santana (UEFS)instacron:UEFSORIGINALTese_BRuno SIlva.pdfTese_BRuno SIlva.pdfapplication/pdf5843479http://tede2.uefs.br:8080/bitstream/tede/1139/2/Tese_BRuno+SIlva.pdfcfe9c91b0dc94dcbc8fd4f0e3136700fMD52LICENSElicense.txtlicense.txttext/plain; charset=utf-82089http://tede2.uefs.br:8080/bitstream/tede/1139/1/license.txt7b5ba3d2445355f386edab96125d42b7MD51tede/11392020-05-19 22:27:55.674oai:tede2.uefs.br:8080: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Biblioteca Digital de Teses e Dissertaçõeshttp://tede2.uefs.br:8080/PUBhttp://tede2.uefs.br:8080/oai/requestbcuefs@uefs.br|| bcref@uefs.br||bcuefs@uefs.bropendoar:2020-05-20T01:27:55Biblioteca Digital de Teses e Dissertações da UEFS - Universidade Estadual de Feira de Santana (UEFS)false
dc.title.por.fl_str_mv DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
title DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
spellingShingle DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
Andrade, Bruno Silva
Moniliophthora perniciosa
Mitocôndria
Polimerases
RT-qPCR
Filogenia Molecular
Mitochondria
Polymerases
Molecular Phylogeny
CIENCIAS BIOLOGICAS::BIOLOGIA GERAL
CIENCIAS BIOLOGICAS
title_short DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
title_full DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
title_fullStr DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
title_full_unstemmed DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
title_sort DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular
author Andrade, Bruno Silva
author_facet Andrade, Bruno Silva
author_role author
dc.contributor.advisor1.fl_str_mv Góes Neto, Aristóteles
dc.contributor.advisor1ID.fl_str_mv 54434882520
dc.contributor.advisor1Lattes.fl_str_mv http://lattes.cnpq.br/6134133834289438
dc.contributor.authorID.fl_str_mv 00175568561
dc.contributor.authorLattes.fl_str_mv http://lattes.cnpq.br/6692846454039770
dc.contributor.author.fl_str_mv Andrade, Bruno Silva
contributor_str_mv Góes Neto, Aristóteles
dc.subject.por.fl_str_mv Moniliophthora perniciosa
Mitocôndria
Polimerases
RT-qPCR
Filogenia Molecular
topic Moniliophthora perniciosa
Mitocôndria
Polimerases
RT-qPCR
Filogenia Molecular
Mitochondria
Polymerases
Molecular Phylogeny
CIENCIAS BIOLOGICAS::BIOLOGIA GERAL
CIENCIAS BIOLOGICAS
dc.subject.eng.fl_str_mv Mitochondria
Polymerases
Molecular Phylogeny
dc.subject.cnpq.fl_str_mv CIENCIAS BIOLOGICAS::BIOLOGIA GERAL
CIENCIAS BIOLOGICAS
description In this study we evaluated molecular and evolutionary aspects of DNA (DPO) and RNA (RPO) polymerases encoded by M. perniciosa mitochondrial plasmid. Three-dimensional models of these polymerases were constructed using a Homology Modeling approach, followed by Molecular Dynamics simulations of 3500 picoseconds. With modeled and validated 3D structures, we performed a virtual screening process in order to search for chemical compounds, using KEGG, ZINC and PubChem databases, followed by Molecular Docking (AutoDock Vina) and Molecular Dynamics MM/PBSA. Thus, we selected DPO-Entecavir and RPO-Rifampicin as the most stable complexes. The study of the relative expression of DPO and RPO genes was done by RT-qPCR, using cDNA from different developmental stages of M. perniciosa. In the phase of primordium, a significant increase in the activity of these genes occured, which is probably related to a self-defense process of the fungus against T. cacao. Phylogenetic analyses were performed by using DNA and protein sequences of DPO and RPO from M. perniciosa and other 12 fungal polymerases, as well as viral polymerases sequences. Then, Maximum Likelihood and Bayesian analyses were performed by using only fungal polymerase sequences, and the combination of fungal and viral polymerase sequences. Tree topologies results corroborate the hypothesis of Horizontal Gene Transfer (HGT) between fungal and viral polymerases, and delineate the evolutionary relationship of DPO and RPO M. perniciosa mitochondrial plasmid.
publishDate 2011
dc.date.issued.fl_str_mv 2011-06-20
dc.date.accessioned.fl_str_mv 2020-05-20T01:27:55Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/doctoralThesis
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status_str publishedVersion
dc.identifier.citation.fl_str_mv ANDRADE, Bruno Silva. DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acadêmico em Biotecnologia)- Universidade Estadual de Feira de Santana, Feira de Santana, 2011.
dc.identifier.uri.fl_str_mv http://tede2.uefs.br:8080/handle/tede/1139
identifier_str_mv ANDRADE, Bruno Silva. DNA e RNA polimerases do plasmídeo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracterização, expressão, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acadêmico em Biotecnologia)- Universidade Estadual de Feira de Santana, Feira de Santana, 2011.
url http://tede2.uefs.br:8080/handle/tede/1139
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language por
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600
600
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dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.publisher.none.fl_str_mv Universidade Estadual de Feira de Santana
dc.publisher.program.fl_str_mv Doutorado Acadêmico em Biotecnologia
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dc.publisher.country.fl_str_mv Brasil
dc.publisher.department.fl_str_mv DEPARTAMENTO DE CIÊNCIAS BIOLÓGICAS
publisher.none.fl_str_mv Universidade Estadual de Feira de Santana
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