Loading...
36 results
Search Results
Now showing 1 - 10 of 36
- RNA Regulatory Networks 2.0Publication . Enguita, Francisco J.; Leitão, Ana Lúcia; Mattick, John S.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 [...].
- Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicasesPublication . Leitão, Ana; Costa, Marina C.; Enguita, Francisco J.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.
- Disrupting Plasmodium UIS3–host LC3 interaction with a small molecule causes parasite elimination from host cellsPublication . Setua, Sonali; Enguita, Francisco J.; Chora, Ângelo Ferreira; Ranga-prasad, Harish; Lahree, Aparajita; Marques, Sofia; Sundaramurthy, Varadharajan; Mota, Maria M.The malaria parasite Plasmodium obligatorily infects and replicates inside hepatocytes surrounded by a parasitophorous vacuole membrane (PVM), which is decorated by the host-cell derived autophagy protein LC3. We have previously shown that the parasite-derived, PVM-resident protein UIS3 sequesters LC3 to avoid parasite elimination by autophagy from hepatocytes. Here we show that a small molecule capable of disrupting this interaction triggers parasite elimination in a host cell autophagy-dependent manner. Molecular docking analysis of more than 20 million compounds combined with a phenotypic screen identified one molecule, C4 (4-{[4-(4-{5-[3-(trifluoromethyl) phenyl]-1,2,4-oxadiazol-3-yl}benzyl)piperazino]carbonyl}benzonitrile), capable of impairing infection. Using biophysical assays, we established that this impairment is due to the ability of C4 to disrupt UIS3–LC3 interaction, thus inhibiting the parasite’s ability to evade the host autophagy response. C4 impacts infection in autophagy-sufficient cells without harming the normal autophagy pathway of the host cell. This study, by revealing the disruption of a critical host–parasite interaction without affecting the host’s normal function, uncovers an efficient anti-malarial strategy to prevent this deadly disease.
- Role of microRNAs in the regulation of cardiovascular diseases : focus on remodellingPublication . Almeida, Ana G.; Pinto, Fausto J.; Enguita, Francisco J.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.
- Structural and functional properties of the capsid protein of Dengue and related FlavivirusPublication . Faustino, André F.; Silva Martins, Ana; Karguth, Nina; Artilheiro, Vanessa; Enguita, Francisco J.; Ricardo, Joana; Santos, Nuno C.; Martins, Ivo C.Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
- The circulating non-coding RNA landscape for biomarker research : lessons and prospects from cardiovascular diseasesPublication . Stępień, Ewa; Costa, Marina C.; Kurc, Szczepan; Drożdż, Anna; Cortez-Dias, Nuno; Enguita, Francisco J.Pervasive transcription of the human genome is responsible for the production of a myriad of non-coding RNA molecules (ncRNAs) some of them with regulatory functions. The pivotal role of ncRNAs in cardiovascular biology has been unveiled in the last decade, starting from the characterization of the involvement of micro-RNAs in cardiovascular development and function, and followed by the use of circulating ncRNAs as biomarkers of cardiovascular diseases. The human non-coding secretome is composed by several RNA species that circulate in body fluids and could be used as biomarkers for diagnosis and outcome prediction. In cardiovascular diseases, secreted ncRNAs have been described as biomarkers of several conditions including myocardial infarction, cardiac failure, and atrial fibrillation. Among circulating ncRNAs, micro-RNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been proposed as biomarkers in different cardiovascular diseases. In comparison with standard biomarkers, the biochemical nature of ncRNAs offers better stability and flexible storage conditions of the samples, and increased sensitivity and specificity. In this review we describe the current trends and future prospects of the use of the ncRNA secretome components as biomarkers of cardiovascular diseases, including the opening questions related with their secretion mechanisms and regulatory actions.
- Circular RNAs serve as miRNA sponges in breast cancerPublication . Misir, Sema; Hepokur, Ceylan; Aliyazicioglu, Yüksel; Enguita, Francisco J.Circular RNAs are a large group of non-coding RNAs with a closed-loop structure. circRNAs play significant roles in many biological processes as miRNA sponges, regulators for gene transcription, combining with RNA-binding proteins and translation of protein. Nowadays, circRNAs have become a research hotspot in the field of cancer and molecular biology. Accumulating evidences have indicated that circRNAs participate in the initiation and development of various cancers such as breast cancer. Breast cancer is a heterogeneous disease, which is the most common malignancy in women. The incidence and mortality rates of breast cancer indicate that it is the leading cause of cancer-related deaths. The goal of the present review is to introduce biogenesis, function characteristics and types of circRNAs, and also their biological functions on breast cancer, especially as miRNA sponges. Additionally, we discuss their use as a new therapeutic target for the treatment of breast cancer.
- Transcriptomic crosstalk between fungal invasive pathogens and their host cells: opportunities and challenges for next-generation sequencing methodsPublication . Enguita, Francisco J.; Costa, Marina C.; Fusco-Almeida, Ana; Mendes-Giannini, Maria; Leitão, AnaFungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific transcriptional program in their host cells. The detailed knowledge of this transcriptional program will allow for a better understanding of the infection process and consequently will help in the future design of more efficient therapeutic strategies. Simultaneous transcriptomic studies of pathogen and host by high-throughput sequencing (dual RNA-seq) is an unbiased protocol to understand the intricate regulatory networks underlying the infectious process. This protocol is starting to be applied to the study of the interactions between fungal pathogens and their hosts. To date, our knowledge of the molecular basis of infection for fungal pathogens is still very limited, and the putative role of regulatory players such as non-coding RNAs or epigenetic factors remains elusive. The wider application of high-throughput transcriptomics in the near future will help to understand the fungal mechanisms for colonization and survival, as well as to characterize the molecular responses of the host cell against a fungal infection.
- Systematic structure-based search for Ochratoxin-degrading enzymes in Proteomes from Filamentous fungiPublication . Leitão, Ana Lúcia; Enguita, Francisco J.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.
- Catalyzing transcriptomics research in cardiovascular disease: The CardioRNA COST Action CA17129Publication . Gomes, Clarissa; Ágg, Bence; Andova, Andrejaana; Arslan, Serdal; Baker, Andrew; Barteková, Monika; Beis, Dimitris; Betsou, Fay; Wettinger, Stephanie; Bugarski, Branko; Condorelli, Gianluigi; Silva, Gustavo; Danilin, Sabrina; Gonzalo-Calvo, David; Buil, Alfonso; Carmo-Fonseca, Maria; Enguita, Francisco J.; Felekkis, Kyriacos; Ferdinandy, Peter; Gyöngyösi, Mariann; Hackl, Matthias; Karaduzovic-Hadziabdic, Kanita; Hellemans, Jan; Heymans, Stephane; Hlavackova, Markéta; Hoydal, Morten; Jankovic, Aleksandra; Jusic, Amela; Kardassis, Dimitris; Kerkelä, Risto; Kuster, Gabriela; Lakkisto, Päivi; Leszek, Przemyslaw; Lustrek, Mitja; Maegdefessel, Lars; Martelli, Fabio; Novella, Susana; O’Brien, Timothy; Papaneophytou, Christos; Pedrazzini, Thierry; Pinet, Florence; Popescu, Octavian; Potočnjak, Ines; Robinson, Emma; Sasson, Shlomo; Scholz, Markus; Simionescu, Maya; Stoll, Monika; Varga, Zoltan; Vinciguerra, Manlio; Xuereb, Angela; Yilmaz, Mehmet; Emanueli, Costanza; Devaux, YvanCardiovascular disease (CVD) remains the leading cause of death worldwide and, despite continuous advances, better diagnostic and prognostic tools, as well as therapy, are needed. The human transcriptome, which is the set of all RNA produced in a cell, is much more complex than previously thought and the lack of dialogue between researchers and industrials and consensus on guidelines to generate data make it harder to compare and reproduce results. This European Cooperation in Science and Technology (COST) Action aims to accelerate the understanding of transcriptomics in CVD and further the translation of experimental data into usable applications to improve personalized medicine in this field by creating an interdisciplinary network. It aims to provide opportunities for collaboration between stakeholders from complementary backgrounds, allowing the functions of different RNAs and their interactions to be more rapidly deciphered in the cardiovascular context for translation into the clinic, thus fostering personalized medicine and meeting a current public health challenge. Thus, this Action will advance studies on cardiovascular transcriptomics, generate innovative projects, and consolidate the leadership of European research groups in the field.COST (European Cooperation in Science and Technology) is a funding organization for research and innovation networks (www.cost.eu).