Biology subjects

Silva Pereira, C.

Publications and source records attributed to Silva Pereira, C..

6 recordsLinked to original sources

bioRxiv2026

FAMeDB: A curated Database for the analysis of Fungal Aromatic Compound Metabolism

Aromatic compounds represent the second most abundant class of organic molecules after carbohydrates, and their microbial metabolism is of broad relevance across multiple research disciplines. Metabolic pathways involving aromatic compounds span from highly conserved anabolic routes to more variable catabolic processes. Numerous peripheral catabolic pathways converge on a small number of central intermediates that undergo aromatic ring-opening in the central pathways. Over the past decades, alongside numerous peripheral pathway genes, most of the catabolic genes constituting the central metabolic pathways have finally been characterized in fungi. Here we present FAMeDB, a manually curated database of proteins involved in fungal aromatic compound metabolism, together with associated bioinformatic tools. The database currently includes 349 proteins, primarily enzymes, but also includes transcription factors and transporters. Entries span 65 species and 45 genera of fungi. Most entries are from Ascomycota (81%), with a significant number from Aspergilli (46%). Application of FAMeDB and its tools enables the quick and accurate representation of aromatic metabolism across different fungal proteomes. This resource is designed to provide a useful and accessible platform for researchers worldwide, even those without specialized expertise in fungal aromatic catabolism, facilitating omics analysis and genomic comparisons. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/700319v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@6285f1org.highwire.dtl.DTLVardef@47aa08org.highwire.dtl.DTLVardef@ebfd9eorg.highwire.dtl.DTLVardef@157c7ef_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Bringing up-to-date the toolkit for the catabolism of aromatic compounds in fungi: the unexpected 1,2,3,5-tetrahydroxybenzene central pathway

Saprophytic fungi are able to catabolize many plant-derived aromatics, including, for example, gallate. The catabolism of gallate in fungi is assumed to depend on the five main central pathways, i.e., of the central intermediates catechol, protocatechuate, hydroxyquinol, homogentisate, and gentisate, but a definitive demonstration is lacking. To shed light on this process, we analyzed the transcriptional reprograming of the growth of Aspergillus terreus on gallate compared with acetate as the control condition. Surprisingly, the results revealed that the five main central pathways did not exhibit significant positive regulation. Instead, an in-depth analysis identified four highly expressed and upregulated genes that are part of a conserved gene cluster found in numerous species of fungi, though not in Aspergilli. The cluster comprises a monooxygenase gene and a fumarylacetoacetate hydrolase-like gene, which are recognized as key components of catabolic pathways responsible for aromatic compound degradation. The other two genes encode proteins with no reported enzymatic activities. Through functional analyses of gene deletion mutants, the conserved short protein with no known domains could be linked to the conversion of the novel metabolite 5-hydroxydienelatone, whereas the DUF3500 gene likely encodes a ring-cleavage enzyme for 1,2,3,5-tetrahydroxybenzene. These significant findings establish the existence of a new 1,2,3,5-tetrahydroxybenzene central pathway for the catabolism of gallate and related compounds (e.g., 2,4,6-trihydroxybenzoate) in numerous fungi where this catabolic gene cluster was observed. IMPORTANCEThe lignin found in various economically significant plants, such as major grains like rice, wheat, and maize, comprises a substantial portion of syringyl units (up to 60%). As a result, the future utilization of residues from these plants in biorefineries will yield significant quantities of syringyl derivatives. However, our understanding of how fungi degrade these syringyl derivatives is to date scarce and mostly relies on unproven assumptions. Our study, demonstrates the existence of a new 1,2,3,5-tetrahydroxybenzene central intermediate for the catabolism of gallate in numerous fungi. This finding expands the toolkit of central pathways, proving that the generalized assumption that gallate catabolism depends on the previously known five main central pathways was incorrect. This research reveals a novel crucial central pathway of great ecological and biotechnological importance, not only for fungi but also potentially for bacteria.

microbiology↗

bioRxiv2023

Cutin-Derived Oligomers Act as Damage-Associated Molecular Patterns in Arabidopsis thaliana

The cuticle constitutes the outermost defensive barrier of most land plants. It comprises a polymeric matrix - cutin, surrounded by soluble waxes. Moreover, the cuticle constitutes the first line of defense against pathogen invasion, while also protecting the plant from many abiotic stresses. Aliphatic monomers in cutin have been suggested to act as immune elicitors in plants. This study analyses the potential of tomato cutin oligomers to act as damage-associated molecular patterns (DAMPs) able to induce a rapid immune response in the model plant Arabidopsis. Cutin oligomeric mixtures led to Ca2+ influx and MAPK activation in Arabidopsis. Comparable responses were measured for cutin, which was also able to induce a reactive oxygen species (ROS) burst. Furthermore, treatment of Arabidopsis with cutin oligomers resulted in a unique transcriptional reprogramming profile, having many archetypal features of pattern-triggered immunity (PTI). Targeted spectroscopic and spectrometric analyses of the cutin oligomers suggest that the elicitors compounds consist mostly of two up to three 10,16-dihydroxyhexadecanoic acid monomers linked together through ester bonds. This study demonstrates that cutin breakdown products can act as DAMPs; a novel class of elicitors deserving further characterization.

plant biology↗

bioRxiv2021

Screening of chemical libraries for new antifungal drugs against Aspergillus fumigatus reveals the potential mechanism of action of miltefosine

Aspergillus fumigatus is an important fungal pathogen and the main etiological agent of aspergillosis, a disease characterized by a noninvasive process that can evolve to a more severe clinical manifestation called invasive pulmonary aspergillosis (IPA) in immunocompromised patients. The antifungal arsenal to threat aspergillosis is very restricted. Azoles are the main therapeutic approach to control IPA, but the emergence of azole-resistant A. fumigatus isolates has significantly increased over the last decades. Therefore, new strategies are necessary to combat aspergillosis and drug repurposing has emerged as an efficient and alternative approach for identifying new antifungal drugs. Here, we used a screening approach to analyze A. fumigatus in vitro susceptibility to 1,127 compounds. A. fumigatus was more susceptible to 10 compounds, including miltefosine, a drug that displayed fungicidal activity against A. fumigatus. By screening an A. fumigatus transcription factor null library, we identified a single mutant, which has the rmiA (resistant to miltefosine) gene deleted, conferring a phenotype of susceptibility to miltefosine. The transcriptional profiling (RNA-seq) of the wild-type and the {Delta}rmiA strains and the Chromatin Immunoprecipitation coupled to next generation sequencing (ChIP-Seq) of a RmiA-tagged strain exposed to miltefosine revealed genes of the sphingolipids pathway that are directly or indirectly regulated by RmiA. Sphingolipids analysis demonstrated that the mutant has overall decreased levels of sphingolipids when growing in the presence of miltefosine. The identification of RmiA represents the first genetic element described and characterized which plays a direct role in miltefosine response in fungi. Author summaryThe filamentous fungus Aspergillus fumigatus causes a group of diseases named aspergillosis and their development occurs after the inhalation of conidia dispersed in the environment. Very few classes of antifungal drugs are available for aspergillosis treatment, e.g., azoles, but the emergence of global resistance to azoles in A. fumigatus clinical isolates has increased over the last decades. Repositioning or repurposing drugs already available on the market is an interesting and faster opportunity for the identification of novel antifungals agents. By using a repurposing strategy, we identified 10 different compounds that impact A. fumigatus survival. One of these compounds, miltefosine, demonstrated fungicidal activity against A. fumigatus. The mechanism of action of miltefosine is unknown and aiming to get more insights about it, we identified a transcription factor RmiA (Resistant to miltefosine) important for miltefosine resistance. Our results suggest that miltefosine plays antifungal activity against A. fumigatus interfering in the sphingolipids biosynthesis.

microbiology↗

bioRxiv2020

Twists and turns of the salicylate catabolism in Aspergillus terreus

In fungi, salicylate catabolism was believed to proceed only through the catechol branch of the 3-oxoadipate pathway, as shown e.g. in Aspergillus nidulans. However, the observation of a transient accumulation of gentisate upon cultivation of Aspergillus terreus in salicylate media questions this concept. To address this we have run a comparative analysis of the transcriptome of these two species after growth in salicylate using acetate as a control condition. The results revealed the high complexity of the salicylate metabolism in A. terreus with the concomitant positive regulation of several pathways for the catabolism of aromatic compounds. This included the unexpected joint action of two pathways: the nicotinate and the 3-hydroxyanthranilate, possibly crucial for the catabolism of aromatics in this fungus. New genes participating in the nicotinate metabolism are here proposed, whereas the 3-hydroxyanthranilate catabolic pathway in fungi is described for the first time. The transcriptome analysis showed also for the two species an intimate relationship between salicylate catabolism and secondary metabolism. This study emphasizes that the central pathways for the catabolism of aromatic hydrocarbons in fungi hold many mysteries yet to be discovered. IMPORTANCEAspergilli are versatile cell factories used in industry for production of organic acids, enzymes and pharmaceutical drugs. To date, organic acids bio-based production relies on food substrates. These processes are currently being challenged to switch to renewable non-food raw materials; a reality that should inspire the use of lignin derived aromatic monomers. In this context, Aspergilli emerge at the forefront of future bio-based approaches due to their industrial relevance and recognized prolific catabolism of aromatic compounds. Notwithstanding considerable advances in the field, there are still important knowledge gaps in the central catabolism of aromatic hydrocarbons in fungi. Here, we disclosed a novel central pathway, defying previous established ideas on the central metabolism of the aromatic amino acid tryptophan in Ascomycota. We also observed that the catabolism of the aromatic salicylate greatly activated the secondary metabolism, furthering the significance of using lignin derived aromatic hydrocarbons as a distinctive biomass source.

genetics↗

bioRxiv2020

Novel ionic liquids-based extraction method that preserves molecular structure from cutin

The biopolyester cutin is ubiquitous in land plants, building the polymeric matrix of the plants outermost defensive barrier - the cuticle. Cutin influences many biological processes in planta however due to its complexity and highly branched nature, the native structure remains partially unresolved. Our aim was to define an original workflow for the purification and systematic characterisation of the molecular structure of cutin. To purify cutin we tested the ionic liquids cholinium hexanoate and 1-butyl-3-methyl-imidazolium acetate. The ensuing polymers are highly esterified, amorphous and have the typical monomeric composition as demonstrated by solid state NMR, complemented by spectroscopic (GC-MS), thermal (DSC) and x-ray scattering (WAXS) analyses. A systematic study by solution-state NMR of cryogenically milled cutins extracted from Micro-Tom tomatoes (the wild type and the gpat6 and cus1 mutants) was undertaken. Their molecular structures, relative distribution of ester aliphatics, free acid end-groups and free hydroxyl groups, differentiating between those derived from primary and secondary esters, were solved. The acquired data demonstrate the existence of free hydroxyl groups in cutin and reveal novel insights on how the mutations impact the esterification arrangement of cutin. Compared to conventional approaches, the usage of ionic liquids for the study of plant polyesters opens new avenues since simple modifications can be applied to recover a biopolymer carrying distinct types/degrees of modifications (e.g. preservation of esters or cuticular polysaccharides), which in combination with the solution NMR methodologies developed here, constitutes now essential tools to fingerprint the multi-functionality and the structure of cutin in planta.

plant biology↗