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Moreiralm Tese.Pdf UNIVERSIDADE DE SÃO PAULO INSTITUTO DE QUÍMICA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOQUÍMICA LEANDRO MARCIO MOREIRA Análise estrutural e funcional do genoma de Xanthomonas axonopodis pv. citri São Paulo Data do Depósito na SPG: 12/09/2006 LEANDRO MARCIO MOREIRA Análise estrutural e funcional do genoma de Xanthomonas axonopodis pv. citri Tese apresentada ao Instituto de Química da Universidade de São Paulo para obtenção do Título de Doutor em Bioquímica Orientadora: Profa. Dra. Aline Maria da Silva São Paulo 2006 2 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. DIVISÃO DE BIBLIOTECA E DOCUMENTAÇÃO DO CONJUNTO DAS QUÍMICAS Moreira, Leandro Marcio. Análise estrutural e funcional do genoma de Xanthomonas axonopodis pv. citri. / Leandro Marcio Moreira; orientadora Aline Maria da Silva. São Paulo, 2006. 170 f. Tese (Doutorado - Programa de Pós-Graduação em Bioquímica. Área de Concentração: Bioquímica) – Instituto de Química da Universidade de São Paulo. 1.Genômica comparativa. 2.Cancrose. 3.Compostos aromáticos. 4.Fitopatógeno. 5.Microarranjos de DNA. 6.Osmoproteção. 3 Leandro Marcio Moreira Análise estrutural e funcional do genoma de Xanthomonas axonopodis pv. citri Tese apresentada ao Instituto de Química da Universidade de São Paulo para obtenção do Título de Doutor em Bioquímica Aprovado em: 12 de Setembro de 2006 Banca Examinadora Prof. Dr. João Paulo Kitajima Instituição: Alellyx Applied Genomics Especialidade: Bioinformata Prof. Dra. Cláudia Monteiro-Vitorello Instituição: Laboratório Nacional de Computação Científica - LNCC Especialidade: Genômica Prof. Dra. Regina Lúcia Baldini Instituição: Instituto de Química da Universidade de São Paulo Especialidade: Bioquímica e biologia molecular de microorganismos Prof. Dr . Shaker Chuck Farah Instituição: Instituto de Química da Universidade de São Paulo Especialidade: Biquímica de proteínas Prof. Dra. Aline Maria da Silva Instituição: Instituto de Química da Universidade de São Paulo Especialidade: Bioquímica e biologia molecular de microorganismos Suplentes Prof. Dr. Gonçalo A. Guimarães Pereira Instituição: Instituto de biologia - UNICAMP Prof. Dr. Julio Rodrigues Neto Instituição: Instituto Biológico - Campinas Prof. Dr. Ricardo Harakava Instituição: Instituto Biológico - SP 4 A minha esposa, Edmara Rocha dos Santos Moreira, que tanto contribuiu, fora do laboratório, para que este trabalho fosse concluído. Eu amo você . 5 AGRADECIMENTOS Agradeço a minha esposa, Edmara Rocha dos Santos Moreira , pelo apoio incondicional durante os momentos mais difíceis, e não foram poucos, ocorridos durante o período em que me dediquei a este trabalho. Ao meu pai, José Osmar Moreira , e minha falecida mãe, Maria P. C. Moreira , pelo esforço para que um dia eu pudesse chegar nesta etapa da vida. Agradeço à Profa. Dra. Aline Maria da Silva por ter me "adotado" no momento em que eu mais precisava de apoio e sobretudo pela orientação e pela paciência, a qual ela teve de sobra, mesmo que muitas vezes eu a tenha "tirado do sério". Agradeço à Profa. Dra. Ana Cláudia Rasera da Silva, minha orientadora no Mestrado e nos primeiros dois anos do Doutorado por ter me oferecido a oportunidade de trabalhar na área da genômica de fitopatógenos. Aos Profs. Drs. Julio Cézar de Oliveira , Jesus Aparecido Ferro e Luiz Roberto Furlan pelo apoio e sugestões durante o desenvolvimento deste projeto. Agradecimento inestimável ao amigo e professor Dr. João Carlos Setúbal pela orientação informal ao logo deste projeto e pelos ensinamentos em gestão de pessoal. Um agradecimento especial aos amigos Robson Francisco de Souza , Stefano Pashalidis , Jean Marcel , Alex Willian , Marcelo Luiz de Laia , Paulo Zaini, Paulo Paiva, José Roberto, Denise Yamamoto, Adriana Matsukuma, Júlio César Levano, Andréa Fogaça, Patrícia Pessoa, Cássia Docena, Daniela Gonzalez, Alexandre Sanchez, Luciano Digiampietri e tantos outros aqui não nomeados. Aos técnicos e funcionários do Instituto de Química da USP , do Laboratório de Bioinformática do Instituto de Computação da UNICAMP e do Laboratório de Biologia Molecular da UNESP Jaboticabal pela enorme ajuda durante todos estes anos. Ao sabiá (Turdus rufiventris ) que durante todas as manhãs ficava a cantar de fronte ao bloco zero dando forças para que o dia fosse sempre mais animado, e aos sapos ( Bufo spp) e grilos ( Grillus campestris ) que me acompanhavam na saída do Instituto durante as noites chuvosas e abafadas. À Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) pela concessão da bolsa de Doutorado e à Universidade de São Paulo em nome do Instituto de Química pela oportunidade. Finalmente, agradeço a Deus por mais esta conquista. 6 “O que afeta diretamente uma pessoa, afeta a todos indiretamente.” ”Enfrentaremos a força física com a nossa força moral.” ”Tenho visto demasiado ódio para querer odiar.” ”Eu tentei ser direito e caminhar ao lado do próximo.” ”Não permita que ninguém o faça descer tão baixo a ponto de você sentir ódio.” Martin Luther King “Nunca permita que um problema a ser resolvido se torne mais importante do que uma pessoa a ser amada." Barbara Johnson 7 LISTA DE ABREVIATURAS E SIGLAS ABC Motivo de ligação de ATP, do inglês ATP Binding Cassete Avr Genes de av irulência BLAST Basic Local Alignment Search Tool CDS Sequências Codificadoras, do inglês Coding Sequences COG Cl usters of Orthologous Groups CVC Clorose Variegada dos Citros DF Moléculas difusíveis, do inglês Diffusible Factor DPO Degradação de Poli e Oligossacarídeos DSF Moléculas sinalizadoras, do inglês Diffusible Signal Factor ECA Erwinia carotovora subsp . atroseptica EDPCV Enzimas de Degradação de Parede Celular Vegetal EPS Polissacarídeos extracelulares, do inglês Extracellular Poly saccharides GC % Porcentagem (%) de nucleotídeos G e C GSP Via secretória geral, do inglês General Secretory Pathway HR Resposta de hiperssensibilidade, do inglês Hypersensitive Response Hrp Genes envolvidos com respostas de interação planta-patógeno, do inglês Hypersensitive Response and Pathogenicity IP Ilhas de Patogenicidade ITL Ilhas de Transferência Lateral KEGG Kyoto Encyclopedia of Genes and Genomes Kpb Milhares de pares de bases LPS Lipopolissacarídeos, do inglês Lipo poly saccharides LXX Leifsonia xyli subsp . xyli MCP Methyl-accepting Chemotactic Protein, envolvida com quimiotaxia MFS Principal superfamília de transportadores, do inglês Major Facilitator Superfamily of transporters Mpb Milhões de pares de bases NCBI National Center for Biotechnology Information 8 PAMGO Ontologia de genes de microorganismos associados a plantas, do inglês Plant-Associated Microbe Gene Ontology pb Pares de bases PCR Reação em cadeia da polimerase, do inglês Polymerase Chain Reaction PD Doença de Pierce, do inglês Pierce´s Disease PFAM Protein FAM ily PInDel Regiões prováveis de inserção e deleção, do inglês Putative In sertion and Del etion Regions POY Phytoplasma asteris cepa OY PSP Pseudomonas syringae pv. phaseolicola cepa 1448A PST Pseudomonas syringae pv. t omato cepa DC3000 PTS Sistema de fosfo-transferência, do inglês Phosphotransferase System RM Sistema de Restrição e Modificação de DNA RT-qPCR PCR quantitativo precedido de transcrição reversa SB Síntese de Biotina SPI-7 Ilha de patogenicidade determinada em Salmonella enterica SS-I Sistema Secretório tipo I SS-II Sistema Secretório tipo II SS-III Sistema Secretório tipo III SS-IV Sistema Secretório tipo IV Swiss-Prot Swiss-Prot Protein knowledgebase TIGR The Institute of Genome Research UFC Unidades Formadoras de Colônias UV Radiação ultra violeta XAA-B Xanthomonas axonopodis pv. aurantifolii cepa B XAA-C Xanthomonas axonopodis pv. aurantifolii cepa C XAC/XAC-306 Xanthomonas axonopodis pv. citri cepa 306 XAC-A* Xanthomonas axonopodis pv. citri variante A* XAC-W Xanthomonas axonopodis pv. citri variante W XAM Xanthomonas axonopodis pv. manihots XAP Xanthomonas axonopodis pv. phaseoli XCC Xanthomonas campestris pv. campestris cepa não especificada 9 XCC-8004 Xanthomonas campestris pv. campestris cepa 8004 XCC-ATCC Xanthomonas campestris pv. campestris cepa ATCC 33913 XCC-B100 Xanthomonas campestris pv. campestris cepa B100 XCP Xanthomonas campestris pv. passiflorae Xcs Segundo agrupamento de genes que codificam o SS-II XCV Xanthomonas campestris pv. vesicatoria XFA Xylella fastidiosa XF-Ann-1 Xylella fastidiosa pv. oleander cepa Ann-1 XF-CVC Xylella fastidiosa cepa 9a5c, agente causal da CVC XF-Dixon Xylella fastidiosa pv. almond cepa Dixon XF-PD Xylella fastidiosa cepa temecula, agente causal da PD XM Xanthomonas malvacearum XOO Xanthomonas oryzae pv. oryzae cepa KAC10331 Xps Primeiro agrupamento de genes que codificam o SS-II XT Xanthomonas translucens 10 RESUMO Moreira, L.M. Análise estrutural e funcional do genoma de Xanthomonas axonopodis pv. citri . 2006. 170p. Tese (Doutorado) - Programa de Pós- Graduação em Bioquímica. Instituto de Química. Universidade de São Paulo. O cancro cítrico é uma doença que afeta diversas espécies de Citrus , cujo agente causal é Xanthomonas axonopodis pv citri (XAC). O genoma desta fitobactéria consiste de um cromossomo de ~5 Mpb e dois plasmídeos, que juntos codificam 4313 CDS (seqüências codificadoras), das quais 2710 apresentam similaridade com proteínas conhecidas. Neste trabalho realizamos uma análise comparativa detalhada do genoma de XAC com genomas de três fitopatógenos, Xanthomonas campestris campestris, Xylella fastidiosa 9a5c e Xylella fastidiosa temecula. Com esta análise identificamos genes espécie
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