Systematic structure-based search for Ochratoxin-degrading enzymes in Proteomes from Filamentous fungi

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Background: ochratoxins are mycotoxins produced by filamentous fungi with important implications in the food manufacturing industry due to their toxicity. Decontamination by specific ochratoxin-degrading enzymes has become an interesting alternative for the treatment of contaminated food commodities. Methods: using a structure-based approach based on homology modeling, blind molecular docking of substrates and characterization of low-frequency protein motions, we performed a proteome mining in filamentous fungi to characterize new enzymes with potential ochratoxinase activity. Results: the proteome mining results demonstrated the ubiquitous presence of fungal binuclear zinc-dependent amido-hydrolases with a high degree of structural homology to the already characterized ochratoxinase from Aspergillus niger. Ochratoxinase-like enzymes from ochratoxin-producing fungi showed more favorable substrate-binding pockets to accommodate ochratoxins A and B. Conclusions: filamentous fungi are an interesting and rich source of hydrolases potentially capable of degrading ochratoxins, and could be used for the detoxification of diverse food commodities.This work is supported by the Portuguese Foundation for Science and Technology (FCT) under the framework of the research grant PTDC-MED-GEN-29389-2017.info:eu-repo/semantics/publishedVersio

Structural insights into carboxylic polyester-degrading enzymes and their functional depolymerizing neighbors

Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Esters are organic compounds widely represented in cellular structures and metabolism, originated by the condensation of organic acids and alcohols. Esterification reactions are also used by chemical industries for the production of synthetic plastic polymers. Polyester plastics are an increasing source of environmental pollution due to their intrinsic stability and limited recycling efforts. Bioremediation of polyesters based on the use of specific microbial enzymes is an interesting alternative to the current methods for the valorization of used plastics. Microbial esterases are promising catalysts for the biodegradation of polyesters that can be engineered to improve their biochemical properties. In this work, we analyzed the structure-activity relationships in microbial esterases, with special focus on the recently described plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. Our analysis, based on structure-alignment, molecular docking, coevolution of amino acids and surface electrostatics determined the specific characteristics of some polyester hydrolases that could be related with their efficiency in the degradation of aromatic polyesters, such as phthalates.This work is supported by the Portuguese Foundation for Science and Technology (FCT) under the framework of the research grant PTDC-MED-GEN-29389-2017.info:eu-repo/semantics/publishedVersio

Transcriptomic Analysis of Acetaminophen Biodegradation by Penicillium chrysogenum var. halophenolicum and Insights into Energy and Stress Response Pathways

Publisher Copyright: © 2023 by the authors. This research received no external funding(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a recalcitrant compound due to the growth of the global population, the ease of availability, and the inefficient wastewater treatment applied. (2) Methods: In this study, we used a transcriptomic approach to obtain functional and metabolic insights about the metabolization of APAP by a phenol-degrading fungal strain, Penicillium chrysogenum var. halophenolicum. (3) Results: We determined that the transcriptomic profile exhibited by the fungal strain during APAP degradation was very dynamic, being characterized by an abundance of dysregulated transcripts which were proportional to the drug metabolization. Using a systems biology approach, we also inferred the protein functional interaction networks that could be related to APAP degradation. We proposed the involvement of intracellular and extracellular enzymes, such as amidases, cytochrome P450, laccases, and extradiol-dioxygenases, among others. (4) Conclusions: Our data suggested that the fungus could metabolize APAP via a complex metabolic pathway, generating nontoxic metabolites, which demonstrated its potential in the bioremediation of this drug.publishersversionpublishe

Role of microRNAs in the regulation of cardiovascular diseases : focus on remodelling

MicroRNAs (miRNAs) are a large class of noncoding RNAs that regulate the expression of protein-coding genes at the post-transcriptional level . They are recognized as regulators of biological processes underlying cardiovascular disorders including hypertrophy, ischemic heart disease, valvular disease and arrhythmias. Particularly, circulating miRNAs are promising biomarkers of cardiovascular pathology (1). MiRNAs are small, noncoding, RNA molecules with approximately 22 nucleotides in length, which act as post-transcriptional regulators of gene expression. Individual miRNAs have been demonstrated to negatively regulate the expression of multiple gene transcripts by the cleavage or suppression of translation of a target mRNA. Conversely, the expression of individual genes can be regulated by multiple miRNAs. Since their experimental description in 1993 (2), a large number of miRNAs known by their gene-regulatory roles in different biological processes, have been catalogued. In fact, miRNAs are known to regulate approximately one third of all coding gene transcripts in mammals, showing their importance as key process modulators (3). Regarding cardiovascular diseases, miRNAs have been identified as key regulators of complex biological processes linked to several conditions as presented above, including left ventricular remodelling, atherosclerosis and myocardial infarction, heart failure, hypertension and arrhythmias (1). miRNAs are expressed in the cardiovascular system, but their role in cardiovascular diseases has not yet been entirely clarified. Moreover, since the discovery that miRNAs are present in the circulation, they have been investigated as novel biomarker as presented bellow. Only 3% of the human genome codes for proteins. Nevertheless, while noncoding RNAs will not act for coding into proteins they modulate all genomic functions. These noncoding RNAs include short miRNAs with approximately 22 nucleotides) and longer, with >200 nucleotides, long noncoding RNAs (lncRNAs) with important biological functions (4) since they are now clearly recognised to play key roles in gene regulation and may simultaneously represent diagnostic and prognostic biomarkers in cardiovascular diseases. (5,6) there are in excess of 2000 human miRNAs (catalogued in mirBase (http://www.mirbase.org) (7). Of note, the key feature of the mechanism of action of miRNAs is that a single miRNA can regulate the expression of several genes, depending on the specificity of the target sequence. On the other side, individual genes can be regulated by different miRNAs particularly if they involve complementary sequences for more than one miRNA. These factors lead to a highly complex regulatory mechanism, often difficult to understand. (8,9). In the healthy adult heart, data from a large sequencing project and other sequential studies, has identified a number of miRNAs that are highly expressed in healthy cardiac tissue and thus expected to play a key role in both normal cardiac function and disease. (10,11) These include miR-1, miR-16, miR-27b, miR-30d, miR-126, miR-133, miR-143, miR-208 and the let-7 family. However, many others have been identified and are now under study. The concept of miRNA-based therapeutics has been emerging and under development, with synthetic antagonists of miRNAs (antagomiRs or antimirs) and very promising in animal models but awaiting new advances in phase II human trials, still in its infancy (12,13). miRNAs clearly intervene in physiological and pathological processes in the cardiovascular diseases. We will review miRNA biology and its role on LV remodeling in myocardial infarction, heart failure, hypertension and aortic stenosis as additionally a note will be provided on the potential of miRNAs for therapeutics.info:eu-repo/semantics/publishedVersio

Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases

© 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.Marina C. Costa was supported by a post-doctoral fellowship from Fundação para a Ciência e Tecnologia, Portugal (Ref. SFRH/BPD/65131/2009).info:eu-repo/semantics/publishedVersio

RNA Regulatory Networks 2.0

© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).The central role of RNA molecules in cell biology has been an expanding subject of study since the proposal of the "RNA world" hypothesis 60 years ago [...].info:eu-repo/semantics/publishedVersio

Non-random genome editing and natural cellular engineering in cognition-based evolution

Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alterna-tive approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a ‘harnessing of stochasticity’. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.publishersversionpublishe

Circular RNA-centered regulatory networks in the physiopathology of cardiovascular diseases

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Non-coding regulatory RNAs are generated as a core output of the eukaryotic genomes, being essential players in cell biology. At the organism level, they are key functional actors in those tissues and organs with limited proliferation capabilities such as the heart. The role of regulatory networks mediated by non-coding RNAs in the pathophysiology of cardiovascular conditions is starting to be unveiled. However, a deeper knowledge of the functional interactions among the diverse non-coding RNA families and their phenotypic consequences is required. This review presents the current knowledge about the functional crosstalk between circRNAs and other biomolecules in the framework of the cardiovascular diseases.This work is supported by COST (European Cooperation in Science and Technology) Action EU-CardioRNA CA17129 and Portuguese Foundation for Science and Technology (FCT) under the framework of the research grant PTDC-MED-GEN-29389-2017.info:eu-repo/semantics/publishedVersio

DNA damage induced by hydroquinone can be prevented by fungal detoxification

© 2014 The Authors. Published by Elsevier Ireland Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).Hydroquinone is a benzene metabolite with a wide range of industrial applications, which has potential for widespread human exposure; however, the toxicity of hydroquinone on human cells remains unclear. The aims of this study are to investigate the cytotoxicity and genotoxicity of hydroquinone in human primary fibroblasts and human colon cancer cells (HCT116). Low doses of hydroquinone (227-454 μM) reduce the viability of fibroblasts and HCT116 cells, determined by resazurin conversion, and induce genotoxic damage (DNA strand breaks), as assessed by alkaline comet assays. Bioremediation may provide an excellent alternative to promote the degradation of hydroquinone, however few microorganisms are known that efficiently degrade it. Here we also investigate the capacity of a halotolerant fungus, Penicillium chrysogenum var. halophenolicum, to remove hydroquinone toxicity under hypersaline condition. The fungus is able to tolerate high concentrations of hydroquinone and can reverse these noxious effects via degradation of hydroquinone to completion, even when the initial concentration of this compound is as high as 7265 μM. Our findings reveal that P. chrysogenum var. halophenolicum efficiently degrade hydroquinone under hypersaline conditions, placing this fungus among the best candidates for the detoxification of habitats contaminated with this aromatic compound.This work was partially supported by a Gulbenkian Foundation research grant (#96526/2009) awarded to JF, and PD received support from Fundação para a Ciência e Tecnologia/FCT-Portugal (SFRH/BD/45502/2008).info:eu-repo/semantics/publishedVersio