DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular
Ano de defesa: | 2011 |
---|---|
Autor(a) principal: | |
Orientador(a): | |
Banca de defesa: | |
Tipo de documento: | Tese |
Tipo de acesso: | Acesso aberto |
Idioma: | por |
Instituição de defesa: |
Universidade Estadual de Feira de Santana
|
Programa de Pós-Graduação: |
Doutorado Acad?mico em Biotecnologia
|
Departamento: |
DEPARTAMENTO DE CI?NCIAS BIOL?GICAS
|
País: |
Brasil
|
Palavras-chave em Português: | |
Palavras-chave em Inglês: | |
Área do conhecimento CNPq: | |
Link de acesso: | 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 |
G?es Neto, Arist?teles54434882520http://lattes.cnpq.br/613413383428943800175568561http://lattes.cnpq.br/6692846454039770Andrade, Bruno Silva2020-05-20T01:27:55Z2011-06-20ANDRADE, Bruno Silva. DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acad?mico 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 plasm?deo mitocondrial de M. perniciosa. Modelos tridimensionais dessas polimerases foram constru?dos, utilizando Modelagem por Homologia, seguida de uma simula??o por Din?mica Molecular de 3500 picossegundos. Com as estruturas 3D das enzimas modeladas e validadas, foi realizado um processo de triagem virtual de compostos qu?micos, utilizando os bancos de dados KEGG, ZINC e PubChem, seguido do Docking Molecular (Autodock Vina) e Din?mica Molecular MM/PBSA. Ent?o, foram selecionados complexos mais est?veis DPO-Entecavir e RPO-Rifampicina. O estudo da express?o relativa dos genes codificadores das DNA e RNA polimerases foi feito atrav?s de RT-qPCR, utilizando-se cDNA diferentes fases de desenvolvimento do M. perniciosa. Foi na fase de prim?rdio em que houve um aumento significativo na atividade desses genes, o que provavelmente est? relacionado com um processo de defesa do fungo contra o T. cacao. A an?lise filogen?tica foi realizada utilizando-se sequ?ncias de DNA e prote?na das DPO e RPO do plasm?deo de M. perniciosa e de polimerases de outros 12 plasm?deos f?ngicos, al?m de sequ?ncias de polimerases virais. Foram realizadas an?lises de M?xima Verossimilhan?a e Bayesiana, apenas de sequ?ncias f?ngicas e da combina??o entre fungos e v?rus. As topologias das ?rvores filogen?ticas resultantes dessas an?lises corroboram as hip?teses de Transfer?ncia Horizontal de Genes (THG) entre polimerases f?ngicas e virais, al?m de delimitar as rela??es evolutivas das DPO e RPO do plasm?deo 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 Acad?mico em BiotecnologiaUEFSBrasilDEPARTAMENTO DE CI?NCIAS BIOL?GICASMoniliophthora perniciosaMitoc?ndriaPolimerasesRT-qPCRFilogenia MolecularMitochondriaPolymerasesMolecular PhylogenyCIENCIAS BIOLOGICAS::BIOLOGIA GERALCIENCIAS BIOLOGICASDNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, 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 plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
title |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
spellingShingle |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular Andrade, Bruno Silva Moniliophthora perniciosa Mitoc?ndria Polimerases RT-qPCR Filogenia Molecular Mitochondria Polymerases Molecular Phylogeny CIENCIAS BIOLOGICAS::BIOLOGIA GERAL CIENCIAS BIOLOGICAS |
title_short |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
title_full |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
title_fullStr |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
title_full_unstemmed |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
title_sort |
DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular |
author |
Andrade, Bruno Silva |
author_facet |
Andrade, Bruno Silva |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
G?es Neto, Arist?teles |
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 |
G?es Neto, Arist?teles |
dc.subject.por.fl_str_mv |
Moniliophthora perniciosa Mitoc?ndria Polimerases RT-qPCR Filogenia Molecular |
topic |
Moniliophthora perniciosa Mitoc?ndria 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 |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
ANDRADE, Bruno Silva. DNA e RNA polimerases do plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acad?mico 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 plasm?deo mitocondrial de moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: caracteriza??o, express?o, estudo de inibidores e filogenia molecular. 2011. 96 f. Tese (Doutorado Acad?mico 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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por |
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por |
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600 600 600 600 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Universidade Estadual de Feira de Santana |
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Doutorado Acad?mico em Biotecnologia |
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UEFS |
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DEPARTAMENTO DE CI?NCIAS BIOL?GICAS |
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Universidade Estadual de Feira de Santana |
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