ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

BACKGROUND: The genus Paracoccidioides consists of thermodymorphic fungi responsible for Paracoccidioidomycosis (PCM), a systemic mycosis that has been registered to affect ~10 million people in Latin America. Biogeographical data subdivided the genus Paracoccidioides in five divergent subgroups, which have been recently classified as different species. Genomic sequencing of five Paracoccidioides isolates, representing each of these subgroups/species provided an important framework for the development of post-genomic studies with these fungi. However, functional annotations of these genomes have not been submitted to manual curation and, as a result, ~60-90% of the Paracoccidioides protein-coding genes (depending on isolate/annotation) are currently described as responsible for hypothetical proteins, without any further functional/structural description. PRINCIPAL FINDINGS: The present work reviews the functional assignment of Paracoccidioides genes, reducing the number of hypothetical proteins to ~25-28%. These results were compiled in a relational database called ParaDB, dedicated to the main representatives of Paracoccidioides spp. ParaDB can be accessed through a friendly graphical interface, which offers search tools based on keywords or protein/DNA sequences. All data contained in ParaDB can be partially or completely downloaded through spreadsheet, multi-fasta and GFF3-formatted files, which can be subsequently used in a variety of downstream functional analyses. Moreover, the entire ParaDB environment has been configured in a Docker service, which has been submitted to the GitHub repository, ensuring long-term data availability to researchers. This service can be downloaded and used to perform fully functional local installations of the database in alternative computing ecosystems, allowing users to conduct their data mining and analyses in a personal and stable working environment. CONCLUSIONS: These new annotations greatly reduce the number of genes identified solely as hypothetical proteins and are integrated into a dedicated database, providing resources to assist researchers in this field to conduct post-genomic studies with this group of human pathogenic fungi.

Functional and Evolutionary Characterization of a UDP-Xylose Synthase Gene from the Plant Pathogen Xylella fastidiosa, Involved in the Synthesis of Bacterial Lipopolysaccharide.

Xylella fastidiosa is a plant-infecting bacillus, responsible for many important crop diseases, such as Pierce's disease of vineyards, citrus variegated chlorosis, and coffee leaf scorch (CLS), among others. Recent genomic comparisons involving two CLS-related strains, belonging to X. fastidiosa subsp. pauca, revealed that one of them carries a frameshift mutation that inactivates a gene encoding an oxidoreductase of the short-chain dehydrogenase/reductase (SDR) superfamily, which may play important roles in determining structural variations in bacterial glycans and glycoconjugates. However, the exact nature of this SDR has been a matter of controversy, as different annotations of X. fastidiosa genomes have implicated it in distinct reactions. To confirm the nature of this mutated SDR, a comparative analysis was initially performed, suggesting that it belongs to a subgroup of SDR decarboxylases, representing a UDP-xylose synthase (Uxs). Functional assays, using a recombinant derivative of this enzyme, confirmed its nature as XfUxs, and carbohydrate composition analyses, performed with lipopolysaccharide (LPS) molecules obtained from different strains, indicate that inactivation of the X. fastidiosa uxs gene affects the LPS structure among CLS-related X. fastidiosa strains. Finally, a comparative sequence analysis suggests that this mutation is likely to result in a morphological and evolutionary hallmark that differentiates two subgroups of CLS-related strains, which may influence interactions between these bacteria and their plant and/or insect hosts.

Thioridazine inhibits gene expression control of the cell wall signaling pathway (CWI) in the human pathogenic fungus Paracoccidioides brasiliensis.

Paracoccidioides brasiliensis is a thermodimorphic fungus associated with paracoccidioidomycosis (PCM), the most common systemic mycosis in Latin America. PCM treatment involves a long-term chemotherapeutic approach and relapses occur at an alarming frequency. Moreover, the emergence of strains with increased drug-resistance phenotypes puts constant pressure on the necessity to develop new alternatives to treat systemic mycoses. In this work, we show that the phenothiazine (PTZ) derivative thioridazine (TR) inhibits in vitro growth of P. brasiliensis yeasts at micromolar concentrations. We employed microarray hybridization to examine how TR affects gene expression in this fungus, identifying ~1800 genes that were modulated in response to this drug. Dataset evaluation showed that TR inhibits the expression of genes that control the onset of the cell wall integrity (CWI) response, hampering production of all major structural polysaccharides of the fungal cell wall (chitin, α-glucan and ß-glucan). Although TR and other PTZs have been shown to display antimicrobial activity by various mechanisms, inhibition of CWI signaling has not yet been reported for these drugs. Thus, TR may provide a novel approach to treat fungal infections by targeting cell wall biogenesis.