Global Analyses Of Ceratocystis Cacaofunesta Mitochondria: From Genome To Proteome.

The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated omics approaches. The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization. The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.149

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

Abstract Background The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated “omics” approaches. Results The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization. Conclusions The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity

Omics' application for the study of two fungal cocoa diseases

Orientadores: Gonçalo Amarante Guimarães Pereira, Odalys Garcia CabreraTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: O cacaueiro (Theobroma cacao L., Sterculiaceae), planta nativa da região amazônica, é aprincipal espécie dentre as 22 do gênero que é comercialmente explorada para aprodução de sementes, as quais tem grande importância econômica principalmente porser usado na produção de chocolate.Por conta disso, a produção das sementes sempre foiuma grande preocupação para as regiões produtoras, e o fator que causa o maior declínioda produção de cacau é o aparecimento de doenças. No Brasil, o cacaueiro apresentacomo principais doenças causadoras de perdas na produção a vassoura-de-bruxa e o maldo-facão. A vassoura-de-bruxa é causa pelo fungo Moniliophthora perniciosa e tem comosintomas característicos a hiperplasia e hipertrofia das células que dão lugar a tecidosanômalos chamados de vassoura. O mal-do-facão, causado pelo fungo Ceratocystiscacaofunesta, é uma doença assintomática, sendo detectada somente com a morte daplanta. As duas doenças foram estudadas neste trabalho atravez de ferramentas dagenômica na tentativa de identificação de mecanismos de interação patógenohospedeiro.Em Ceratocystis cacaofunesta foi feita uma análise global da mitocôndriaintegrando dados de genômica, transcritômica e proteômica. Foi gerado o primeiroinventário de proteinas mitocondriais de um fitopatógeno, sendo preditas um total de1.124 proteinas, das quais 304 foram identificadas experimentalmente. Dentre asproteinas listadas no inventário, 117 tem função desconhecida e 7 parecem ser específicasdeste fungo.Análises dos dados do genoma de M. perniciosa sugerem que o fungo poderiaestar produzindo giberelina, o que explica muito dos eventos que acontecem durante ainteração M. perniciosa-cacaueiro durante a fase biotrófica do fungo. Este trabalho demonstrou a importância desse hormônio na progressão da doença, assim como aalteração do metabolismo de giberelina na planta durante a interação. Os dados obtidosneste trabalho geraram conhecimento para desenvolvimento de estrátégias de controledas duas doenças, além de direcionar estudos com outros fitopatógenosAbstract: Cacao tree (Theobroma cacao L., Sterculeaceae) is a native plant from Amazon region andthe main species commercially exploited for seed production among the 22 of the genus.This plant has a great economic importance because of its use in the production ofchocolate. Due to this, producing regions always has been concern to seed production,and diseases are the most important factors of decline in cocoa production. In Brazil,cacao witches' broom and ceratocystis wilt are major diseases causing production losses.The witches' broom is caused by the fungus Moniliophthora perniciosa and thecharacteristic hyperplasia and hypertrophy symptoms of cells gives rise to anomaloustissue called broom. Meanwhile, the ceratocystis wilt caused by Ceratocystis cacaofunestais an asymptomatic disease; it is detected only with the death of the plant. Both diseaseswere studied using genomic tools in an attempt to identify mechanisms of host-pathogeninteraction. In Ceratocystis cacaofunesta, a mitochondrial global analysis integrating datafrom genomics, transcriptomics and proteomics was made. This work generated the firstinventory of mitochondrial proteins of a plant pathogenic fungus, in which 1,124 proteinswere predicted and 304 were identified experimentally. Among the proteins listed in theinventory, 117 have unknown function and 7 appear to be specific to this fungus. Dataanalysis of the genome of M. perniciosa suggests that the fungus could be producinggibberellin, it may explain much of the events that happen during the interaction M.perniciosa-cacao in biotrophic phase of the fungus. Therefore, this work showed theimportance of this hormone in disease progression, as well as altered metabolism ofgibberellin in the plant during the interaction. The data obtained in this work generatedknowledge to develop strategies to control these two diseases, and can drive studies withother pathogensDoutoradoGenetica de MicroorganismosDoutor em Genetica e Biologia Molecula