Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsThe 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.

The mitochondrial genome of Endoconidiophora resinifera is intron rich

“…This special arrangement could be termed “tandem intron” or a “side by side” twintron; for consistency we will refer to this arrangement as a tandem intron. The mS917a and mS917b intron-encoded ORFs of the tandem intron are both related to the mS917 clade of LAGLIDADG ORFs previously characterized 10 , 33 . Phylogenetic analysis showed that the components of the tandem intron mS917a and b ORFs are paralogues and other members of this clade can be located in group ID introns located within the rnl , nad5 , nad6 and cox3 genes.…”

“…have been studied with regards to their taxonomy, blue-staining ability, and pathology 9 , but so far only C . cacaofunesta has been examined in more detail with regards to genomic investigations 10 . Previous studies on this group of fungi with regards to mitochondrial DNA focused on the rRNA genes and these displayed a large variety of intron insertions among various Ceratocystis s .…”

“…Additional mitochondrial genomes have recently been sequenced for members of Ceratocystis but so far a detailed annotation is only available for the mitochondrial genome of C . cacaofunesta 10 , 13 – 16 .…”

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)

“…The strain was generously donated by Dr. Tomas Harrington, from the Iowa State University Department of Plant Pathology. The methodology for nucleic acid isolation was previously described by Ambrosio and coworkers, 2013 [ 100 ].…”

“…RNA-seq reads were obtained via in vitro laboratory experiments. RNA isolation, and RNAseq generation protocols were previously described by Ambrosio and coworkers (2013) [ 100 ]. A second set of RNAseq data was generated in a parallel project for which a manuscript is in preparation.…”