CSIC - Biological Research Center

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Madrid, Spain
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Rodriguez-Fernandez J.L.,CSIC - Biological Research Center
Current Topics in Medicinal Chemistry | Year: 2013

Rheumatoid Arthritis (RA) is a chronic autoimmune inflammatory disease that affects largely synovial joints. It has been postulated that activated autoreactive CD4 T cells play a key role in triggering and/or maintaining the chronic inflammatory process in RA. Dendritic cells (DCs) are antigen-presenting cells that activate cognate clonal CD4 T cells in the lymph nodes. The activation process involves the formation of a molecular structure at the DC-CD4 T cell contact zone called immunological synapse (IS). In RA, the synovium, a thin layer of tissue below the capsule in the joints, shows a massive infiltration of DCs and CD4 T cells. Subjects bearing HLA-DRB1 alleles of the Major Histocompatibility Complex II gene displaying a motif called RA "shared epitope (SE)", have an enhanced susceptibility to suffer RA. Interestingly, the SE-containing HLA-DRB1 molecules display a pocket with a high affinity for citrullinated antigens, which are found at higher levels in subjects prone to develop RA. Thus, it is possible that the DCs of susceptible individuals may form IS with particular features that may present citrullinated peptides to autorreactive naïve CD4 T clones that, after being activated, contribute to the initiation or development of the disease. Herein I put forward a model of RA initiation based on current information on the immune response and RA. © 2013 Bentham Science Publishers.


Perez-Sala D.,CSIC - Biological Research Center
Chemico-Biological Interactions | Year: 2011

Electrophilic eicosanoids are reactive mediators that arise by non-enzymatic transformations of arachidonic acid or of its products and display varied biological actions. Various electrophilic eicosanoids have shown anti-proliferative and anti-inflammatory effects, which have elicited a great interest in their study as potential therapeutic agents. A key feature of these compounds is their ability to covalently modify proteins, thus altering their structure and function. The modification of several components of the NF-κB pathway contributes to the anti-inflammatory effects of electrophilic eicosanoids, whereas addition to redox-sensitive proteins plays a key role in the antioxidant response. However, electrophilic eicosanoids may also have a dark side, and accumulating evidence points towards their involvement in neurotoxicity and/or neurodegeneration. The ability of some electrophilic eicosanoids to induce protein oligomerization or aggregation through various mechanisms may contribute to these effects. Biochemical and proteomic studies have led to the identification of numerous protein targets for modification by electrophilic eicosanoids, the number of which continues to expand, revealing novel potential functions for these compounds and providing a basis for their pleiotropic effects. The ample number of targets identified, together with the non-enzymatic nature of the modification argue against the potential specificity or regulation of electrophilic eicosanoid action. However, protein modification displays selectivity depending on structural features of the proteins and of the electrophilic compounds as well as on context factors such as cell type and GSH availability. Understanding the factors which control the extent and selectivity of protein modification by electrophilic eicosanoids is therefore essential to elucidate their pathophysiological roles and therapeutic potential in specific settings. © 2010 Elsevier Ireland Ltd. All Rights Reserved.


Boya P.,CSIC - Biological Research Center | Reggiori F.,University Utrecht | Codogno P.,University of Paris Descartes
Nature Cell Biology | Year: 2013

Autophagy maintains cell, tissue and organism homeostasis through degradation. Complex post-translational modulation of the Atg (autophagy-related) proteins adds additional entry points for crosstalk with other cellular processes and helps define cell-type-specific regulations of autophagy. Beyond the simplistic view of a process exclusively dedicated to the turnover of cellular components, recent data have uncovered unexpected functions for autophagy and the autophagy-related genes, such as regulation of metabolism, membrane transport and modulation of host defenses-indicating the novel frontiers lying ahead. © 2013 Macmillan Publishers Limited. All rights reserved.


Asensio J.L.,CSIC - Biological Research Center | Arda A.,Institute Quimica Organica General | Canada F.J.,Institute Quimica Organica General | Jimenez-Barbero J.,Institute Quimica Organica General
Accounts of Chemical Research | Year: 2013

The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition.With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units.In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process.The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy. © 2012 American Chemical Society.


Penalva M.A.,CSIC - Biological Research Center
Molecular Microbiology | Year: 2015

The Spitzenkörper (SPK) is an accumulation of vesicles interleaved with actin microfilaments present at the cytosolic side of the apical plasma membrane (PM) of hyphal tips of many species of filamentous fungi. The physiological role of the SPK has captivated fungal biologists over the years, but only very recently this 'organelle' is starting to be understood in the molecular terminology used for cell biological models. One aspect that has received little attention is the role of cellular membrane asymmetry in the organization of membrane traffic, in particular in the genetic and cell biological model Aspergillus nidulans. The paper by Schultzhaus etal. (2015) in this issue breaks the ice, providing original insight that may foster research in phospholipid composition in the context of intracellular traffic and the organization of the SPK. Notably, it shows that like the stout Neurospora crassaSPK, the much slimmer one of A.nidulans, appears to be formed by different strata, altogether suggesting that the SPK might be a mosaic of exocytic carriers with different functional specializations, and a major sorting hub for intracellular membranes. © 2015 John Wiley & Sons Ltd.


Oeste C.L.,CSIC - Biological Research Center
Histochemistry and cell biology | Year: 2013

Autophagic and endo-lysosomal degradative pathways are essential for cell homeostasis. Availability of reliable tools to interrogate these pathways is critical to unveil their involvement in physiology and pathophysiology. Although several probes have been recently developed to monitor autophagic or lysosomal compartments, their specificity has not been validated through co-localization studies with well-known markers. Here, we evaluate the selectivity and interactions between one lysosomal (Lyso-ID) and one autophagosomal (Cyto-ID) probe under conditions modulating autophagy and/or endo-lysosomal function in live cells. The probe for acidic compartments Lyso-ID was fully localized inside vesicles positive for markers of late endosome-lysosomes, including Lamp1-GFP and GFP-CINCCKVL. Induction of autophagy by amino acid deprivation in bovine aortic endothelial cells caused an early and potent increase in the fluorescence of the proposed autophagy dye Cyto-ID. Cyto-ID-positive compartments extensively co-localized with the autophagosomal fluorescent reporter RFP-LC3, although the time and/or threshold for organelle detection was different for each probe. Interestingly, use of Cyto-ID in combination with Lysotracker Red or Lyso-ID allowed the observation of structures labeled with either one or both probes, the extent of co-localization increasing upon treatment with protease inhibitors. Inhibition of the endo-lysosomal pathway with chloroquine or U18666A resulted in the formation of large Cyto-ID and Lyso-ID-positive compartments. These results constitute the first assessment of the selectivity of Cyto-ID and Lyso-ID as probes for the autophagic and lysosomal pathways, respectively. Our observations show that these probes can be used in combination with protein-based markers for monitoring the interactions of both pathways in live cells.


Penalva M.T.,CSIC - Biological Research Center
Current Opinion in Microbiology | Year: 2010

Endocytosis has been the Cinderella of membrane trafficking studies in filamentous fungi until recent work involving genetically tractable models has boosted interest in the field. Endocytic internalization predominates in the hyphal tips, spatially coupled to secretion. Early endosomes (EEs) show characteristic long-distance motility, riding on microtubule motors. The fungal tip contains a region baptised the 'dynein loading zone' where acropetally moving endosomes reaching the tip shift from a kinesin to dynein, reversing the direction of their movement. Multivesicular body biogenesis starts from these motile EEs. Maturation of EEs into late endosomes and vacuoles appears to be essential. The similarities between fungal and mammalian endocytic trafficking suggest that conditional mutant genetic screens would yield valuable information. © 2010 Elsevier Ltd.


Ruiz-Duenas F.J.,CSIC - Biological Research Center
Mycologia | Year: 2013

The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species representing the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequenced B. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)-oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.


Llave C.,CSIC - Biological Research Center
Trends in Plant Science | Year: 2010

Once a virus enters a cell, viral double-stranded RNA (dsRNA) is targeted by the RNA silencing machinery to initiate a cascade of regulatory events directed by viral small interfering RNAs (vsiRNAs). Recent genetic and functional studies along with the high-throughput sequencing of vsiRNAs have shed light on the genetic and structural requirements for virus targeting, the origins and compositions of vsiRNAs and their potential for controlling gene expression. The precise nature of the triggering molecules of virus-induced RNA silencing or the targeting constraints for viral genome recognition and processing represent outstanding questions that will be discussed in this review. The contribution of vsiRNAs to antiviral defense and host genome modifications has profound implications for our understanding of viral pathogenicity and host specificity in plants. © 2010 Elsevier Ltd.


Boya P.,CSIC - Biological Research Center
Antioxidants and Redox Signaling | Year: 2012

Significance: Lysosomes are organelles in which cellular degradation occurs in a controlled manner, separated from other cellular components. As several pathways terminate in the lysosome, lysosomal dysfunction has a profound impact on cell homeostasis, resulting in manifold pathological situations, including infectious diseases, neurodegeneration, and aging. Recent Advances: Lysosomal biology demonstrates that in addition to regulating the final steps of catabolic processes, lysosomes are essential up-stream modulators of autophagy and other essential lysosomal pathways. Future Directions and Critical Issues: Lysosomal membrane permeabilization offers therapeutic potential in the treatment of cancer, though the molecular regulators of this process remain obscure. This review focuses on recent discoveries in lysosomal function and dysfunction, primarily in in vivo situations. Antioxid. Redox Signal. © 2012 Mary Ann Liebert, Inc.

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