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URI permanente para esta colecciónhttps://hdl.handle.net/10953/111

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A Comparative Analysis of Mitogenomes in Species of the Tapinoma nigerrimum Complex and Other Species of the Genus Tapinoma (Formicidae, Dolichoderinae)
(MDPI, 2024-12-02) Ruiz-Mena, Areli; Mora, Pablo; Rico-Porras, José M.; Kaufmann, Bernard; Seifert, Bernhard; Palomeque, Teresa; Lorite, Pedro
Using next-generation sequencing data, the complete mitogenomes of six species from the genus Tapinoma were assembled. This study explores the mitochondrial genomes of Tapinoma species, among them the five species from the Tapinoma nigerrimum complex, comparing them with each other and with other species from Dolichoderinae subfamily to understand their evolutionary relationships and evolution. Tapinoma mitochondrial genomes contain the typical set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and the A + T-rich control region. A phylogenetic analysis using the protein-coding gene sequences from available Dolichoderinae mitogenomes supports the monophyletic nature of the genus Tapinoma, with the T. nigerrimum complex forming a well-supported clade. Key findings include genetic traits unique to the T. nigerrimum complex, such as a start codon in the atp8 gene and a complete stop codon in cox1, distinguishing them from other Tapinoma species. Additionally, a gene rearrangement involving tRNA-Trp, tRNA-Cys, and tRNA-Tyr was found exclusively in the Tapinoma species, suggesting a potential phylogenetic marker for the genus.
A MicroRNA-Transcription Factor Blueprint for Early Atrial Arrhythmogenic Remodeling
(Wiley, 2015-06-28) Torrado, Mario; Franco, Diego; Lozano-Velasco, Estefanía; Hernández-Torres, Francisco; Calviño, Ramón; Aldama, Guillermo; Centeno, Alberto; Castro-Beiras, Alfonso
Spontaneous self-terminating atrial fibrillation (AF) is one of the most common heart rhythm disorders, yet the regulatory molecular mechanisms underlying this syndrome are rather unclear. MicroRNA (miRNA) transcriptome and expression of candidate transcription factors (TFs) with potential roles in arrhythmogenesis, such as Pitx2, Tbx5, and myocardin (Myocd), were analyzed bymicroarray, qRT-PCR, andWestern blotting in left atrial (LA) samples from pigs with transitory AF established by right atrial tachypacing. Induced ectopic tachyarrhythmia caused rapid and substantial miRNA remodeling associated with a marked downregulation of Pitx2, Tbx5, and Myocd expression in atrial myocardium. The downregulation of Pitx2, Tbx5, and Myocd was inversely correlated with upregulation of the corresponding targeting miRNAs (miR-21, miR-10a/10b, and miR-1, resp.) in the LA of paced animals. Through in vitro transient transfections of HL-1 atrial myocytes, we further showed that upregulation of miR-21 did result in downregulation of Pitx2 in cardiomyocyte background. The results suggest that immediate-early miRNA remodeling coupled with deregulation of TF expression underlies the onset of AF.
A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate
(Taylor and Francis, 2015-06-08) Lozano-Velasco, Estefanía; Vallejo-Pulido, Daniel; Esteban-Ruiz, Francisco José; Doherty, Chris; Hernández-Torres, Francisco; Franco, Diego; Aránega, Amelia Eva
The acquisition of a proliferating-cell status from a quiescent state as well as the shift between proliferation and differentiation are key developmental steps in skeletal-muscle stem cells (satellite cells) to provide proper muscle regeneration. However, how satellite cell proliferation is regulated is not fully understood. Here, we report that the c-isoform of the transcription factor Pitx2 increases cell proliferation in myoblasts by downregulating microRNA 15b (miR-15b), miR-23b, miR-106b, and miR-503. This Pitx2c-microRNA (miRNA) pathway also regulates cell proliferation in early-activated satellite cells, enhancing Myf5 satellite cells and thereby promoting their commitment to a myogenic cell fate. This study reveals unknown functions of several miRNAs in myoblast and satellite cell behavior and thus may have future applications in regenerative medicine.
Age-related changes of the nitric oxide system in the rat brain
(Elsevier BV, 2002) Siles, Eva; Martínez-Lara, Esther; Cañuelo, Ana R.; Sánchez, Ana M.; Hernández, Raquel; López-Ramos, Juan C.; Del Moral, María L.; Esteban, Francisco J.; Blanco, Santos; Pedrosa, Juan A.; Rodrigo, José; Peinado, María A.
Altered Plant and Nodule Development and Protein S-Nitrosylation in Lotus japonicus Mutants Deficient in S-Nitrosoglutathione Reductases
(OXFORD UNIV PRESS, 2020-01) Matamoros, M.A.; Cutrona, M.C.; Wienkoop, S.; Begara-Morales, J.C.; Sandal, N.; Orera, I.; Barroso, J.B.; Stougaard, J.; Becana, M.
Nitric oxide (NO) is a crucial signaling molecule that conveys its bioactivity mainly through protein S-nitrosylation. This is a reversible post-translational modification (PTM) that may affect protein function. S-nitrosoglutathione (GSNO) is a cellular NO reservoir and NO donor in protein S-nitrosyla tion. The enzyme S-nitrosoglutathione reductase (GSNOR) degrades GSNO, thereby regulating indirectly signaling cas cades associated with this PTM. Here, the two GSNORs of the legume Lotus japonicus, LjGSNOR1 and LjGSNOR2, have been functionally characterized. The LjGSNOR1 gene is very active in leaves and roots, whereas LjGSNOR2 is highly expressed in nodules. The enzyme activities are regulated in vitro by redox-based PTMs. Reducing conditions and hydrogen sulfide-mediated cysteine persulfidation induced both activities, whereas cysteine oxidation or glutathionyla tion inhibited them. Ljgsnor1 knockout mutants contained higher levels of S-nitrosothiols. Affinity chromatography and subsequent shotgun proteomics allowed us to identify 19 proteins that are differentially S-nitrosylated in the mutant and the wild-type. These include proteins involved in biotic stress, protein degradation, antioxidant protection and photosynthesis. We propose that, in the mutant plants, deregulated protein S-nitrosylation contributes to develop mental alterations, such as growth inhibition, impaired nodulation and delayed flowering and fruiting. Our results highlight the importance of GSNOR function in leg ume biology.
Are patients with fibromyalgia in a prothrombotic state?
(Sage Publications Inc, 2019) Molina, Francisco J.; Del Moral, María L.; La Rubia, Mercedes; Blanco, Santos; Carmona, Ramón; Rus, Alma
Biological Implications of a Stroke Therapy Based in Neuroglobin Hyaluronate Nanoparticles. Neuroprotective Role and Molecular Bases
(MDPI, 2022) Peinado, María A.; Ovelleiro, David; Del Moral, María L.; Hernández, Raquel; Martínez-Lara, Esther; Siles, Eva; Pedrajas, José R.; García-Martín, María L.; Caro, Carlos; Peralta, Sebastián; Morales, María E.; Ruiz, María A.; Blanco, Santos
Celiac Immunogenic Potential of α-Gliadin Epitope Variants from Triticum and Aegilops Species
(MDPI, 2019-01) Ruiz-Carnicer, Ángela; Comino, Isabel; Segura, Veronica; Ozuna, Carmen V; Moreno, María de Lourdes; López-Casado, Miguel Ángel; Torres, María Isabel; Barro, Francisco; Sousa, Carolina
This study investigates the immunotoxic potential of α-gliadins in wheat species and their implications for celiac disease (CD). Gluten, the primary structural protein complex in wheat, contains α-gliadins, which are rich in T-cell stimulating epitopes (DQ2.5-glia-α1, DQ2.5-glia-α2, and DQ2.5-glia-α3) that trigger immune responses in individuals with CD. The analysis spanned diploid, tetraploid, and hexaploid wheat species, focusing on the abundance and immunostimulatory capacity of canonical epitopes and their variants.The findings reveal that DQ2.5-glia-α1 and DQ2.5-glia-α3 are more prevalent than DQ2.5-glia-α2. Canonical DQ2.5-glia-α1 is notably abundant in genomes of the BBAADD, AA, and DD types, while DQ2.5-glia-α3 epitope variants are highly represented in BBAADD and BBAA wheats, despite a lower presence of the canonical form. Importantly, the introduction of a natural amino acid substitution (Q to H) at any position effectively neutralized the immunotoxicity of the epitopes without compromising wheat's functional properties.This work underscores the potential of targeted amino acid substitutions as a strategy to develop wheat varieties that are safer for individuals with CD while preserving their technological value.
Characterization of interaction sites in the Saccharomyces cerevisiae ribosomal stalk components
(Wiley, 2002-10-31) Lalioti, Vasiliki S.; Pérez-Fernández, Jorge; Remacha, Miguel; García Ballesta, Juan Pedro
The interactions among the yeast stalk components(P0, P1⍺, P1ꞵ, P2⍺ and P2ꞵ) and with EF-2 have been explored using immunoprecipitation, affinity chromatography and the two-hybrid system. No stable association was detected between acidic proteins of the same type. In contrast, P1⍺ and P1ꞵ were found to interact with P2ꞵ and P2⍺ respectively. An interaction of P0 with P1 proteins, but not with P2 proteins, was also detected. This interaction is strongly increased with the P0 carboxyl end, which is able to form a pentameric complex with the four acidic proteins. The P1/P2 binding site has been located between residues 212 and 262 using different C-terminal P0 fragments. Immunoprecipitation shows the association of EF-2 with protein P0. However, the interaction is stronger with the P1/P2 proteins than with P0 in the two-hybrid assay. This interaction improves using the 100-amino-acid-long C-end of P0 and is even higher with the last 50 amino acids. The data indicate a specific association of P1⍺ with P2ꞵ and of P1ꞵ with P2⍺ rather than the dimerization of the acidic proteins found in prokaryotes. In addition, they suggest that stalk assembly begins by the interaction of the P1 proteins with P0. Moreover, as functional interactions of the complete P0 were found to increase using protein fragments, the data suggest that some active sites are exposed in the ribosome as a result of conformational changes that take place during stalk assembly and function.
Comparative proteomic study of early hypoxic response in the cerebral cortex of rats submitted to two different hypoxic models
(Wiley - V C H Verlag GmbH, 2017) Ovelleiro, David; Blanco, Santos; Hernández, Raquel; Peinado, María A.
Complex Evolutionary Histor of Mboumar, a Mariner Element Widely Represented in Ant Genomes
(Nature Research, 2020-02) Sanllorente, Olivia; Vela, Jesús; Mora, Pablo; Ruiz-Mena, Areli; Torres, María Isabel; Lorite, Pedro; Palomeque, Teresa
This study examines the mariner-like transposable element Mboumar, previously identified in the ant Messor bouvieri, across 22 ant species from nine subfamilies, including both primitive and derived lineages. The widespread presence of Mboumar-like elements in ant genomes is evident, but the phylogenetic relationships of these elements do not align with the evolutionary history of their ant hosts. Genetic analysis revealed conserved transposable elements with uninterrupted open reading frames in 11 species, encoding transposases closely resembling the active Mboumar-9 transposase. Selection tests indicate purifying selection has shaped the evolution of these elements.
Computational Prediction of Candidate Proteins for S-Nitrosylation in Arabidopsis thaliana
(PUBLIC LIBRARY SCIENCE, 2014-10-21) Chaki, Mounira; Kovacs, Izabella; Spannagl, Manuel; Lindermayr, Christian
Nitric oxide (NO) is an important signaling molecule that regulates many physiological processes in plants. One of the most important regulatory mechanisms of NO is S-nitrosylation—the covalent attachment of NO to cysteine residues. Although the involvement of cysteine S-nitrosylation in the regulation of protein functions is well established, its substrate specificity remains unknown. Identification of candidates for S-nitrosylation and their target cysteine residues is fundamental for studying the molecular mechanisms and regulatory roles of S-nitrosylation in plants. Several experimental methods that are based on the biotin switch have been developed to identify target proteins for S-nitrosylation. However, these methods have their limits. Thus, computational methods are attracting considerable attention for the identification of modification sites in proteins. Using GPS-SNO version 1.0, a recently developed S-nitrosylation site-prediction program, a set of 16,610 candidate proteins for S-nitrosylation containing 31,900 S-nitrosylation sites was isolated from the entire Arabidopsis proteome using the medium threshold. In the compartments ‘‘chloroplast,’’ ‘‘CUL4-RING ubiquitin ligase complex,’’ and ‘‘membrane’’ more than 70% of the proteins were identified as candidates for S-nitrosylation. The high number of identified candidates in the proteome reflects the importance of redox signaling in these compartments. An analysis of the functional distribution of the predicted candidates showed that proteins involved in signaling processes exhibited the highest prediction rate. In a set of 46 proteins, where 53 putative S-nitrosylation sites were already experimentally determined, the GPS-SNO program predicted 60 S-nitrosylation sites, but only 11 overlap with the results of the experimental approach. In general, a computer-assisted method for the prediction of targets for S-nitrosylation is a very good tool; however, further development, such as including the three dimensional structure of proteins in such analyses, would improve the identification of S-nitrosylation sites.
Constitutive nitric oxide synthases are responsible for the nitric oxide production in the ischemic aged cerebral cortex
(Elsevier BV, 2005) Martínez-Lara, Esther; Cañuelo, Ana R.; Siles, Eva; Hernández, Raquel; Del Moral, María L.; Blanco, Santos; Pedrosa, Juan A.; Rodrigo, José; Peinado, María A.
Coupling the endophytic microbiome with the host transcriptome in olive roots
(2021) Luque, Francisco
Cre recombinase microinjection for single-cell tracing and localised gene targeting
(COMPANY BIOLOGISTS LTD, 2023-02-15) Sendra, Miquel; Hourcade, Juan de Dios; Temiño, Susana; Sarabia, Antonio José; Ocaña, Oscar H; Domínguez, Jorge N; Torres, Miguel
Las técnicas de análisis de linajes celulares son esenciales para comprender el desarrollo embrionario. Las microinyecciones de colorantes lipofílicos, la transfección viral y la iontoforesis han sido técnicas clave para mapear el origen de las células progenitoras que forman los diferentes órganos en el embrión de ratón post-implantación. Estas técnicas requieren habilidades avanzadas de manipulación, y solo la técnica de iontoforesis, técnica compleja y de eficiencia limitada, ha sido utilizada para el marcaje de células individuales. En este estudio, hemos optimizado una nueva herramienta para llevar a cabo el trazado de linajes celulares y ablación génica localizada, utilizando microinyección de recombinasa Cre permeable a células (TAT-Cre). En primer lugar, hemos “mapeado” el destino de las células progenitoras indiferenciadas hacia las diferentes cámaras del corazón embrionario. Por otro lado, hemos logrado optimizar las condiciones para, ajustando la dosis de TAT-Cre, lo que permite realizar análisis clonales de los progenitores de mesodermo naciente. Finalmente, la microinyección de TAT-Cre en embriones Mycnflox/flox en el tubo cardíaco primitivo reveló que el gen Mycn desempeña un papel autónomo en la proliferación de cardiomiocitos. Esta herramienta ayudará a los investigadores a identificar las células progenitoras y rutas moleculares involucradas en el desarrollo de órganos, contribuyendo a entender el origen de los defectos congénitos.
Crosstalk between hydroxytyrosol, a major olive oil phenol, and HIF-1 in MCF-7 breast cancer cells
(Nature Research, 2020) Calahorra, Jesús; Martínez-Lara, Esther; Granadino-Roldán JM, José M.; Martí; Cañuelo, Ana R.; Blanco, Santos; Oliver, Javier; Siles, Eva
Differential chamber-specific expression and regulation of long non-coding RNAs during cardiac development
(Elsevier, 2019-10) García-Padilla, Carlos; Domínguez-Macías, Jorge Nicolás; Aránega, Amelia Eva; Franco, Diego
Cardiovascular development is governed by a complex interplay between inducting signals such as Bmps and Fgfs leading to activation of cardiac specific transcription factors such as Nkx2.5, Mef2c and Srf that orchestrate the initial steps of cardiogenesis. Over the last decade we have witnessed the discovery of novel layers of gene regulation, i.e. post-transcriptional regulation exerted by non-coding RNAs. The function role of small non coding RNAs has been widely demonstrated, e.g. miR-1 knockout display several cardiovascular abnormalities during embryogenesis. More recently long non-coding RNAs have been also reported to modulate gene expression and function in the developing heart, as exemplified by the embryonic lethal phenotypes of Fendrr and Braveheart knock out mice, respectively. In this study, we investigated the differential expression profile during cardiogenesis of previously reported lncRNAs in heart development. Our data revealed that Braveheart, Fendrr, Carmen display a preferential adult expression while Miat, Alien, H19 preferentially display chamber-specific expression at embryonic stages. We also demonstrated that these lncRNAs are differentially regulated by Nkx2.5, Srf and Mef2c, Pitx2 > Wnt > miRNA signaling pathway and angiotensin II and thyroid hormone administration. Importantly isoform-specific expression and distinct nuclear vs cytoplasmic localization of Braveheart, Carmen and Fendrr during chamber morphogenesis is observed, suggesting distinct functional roles of these lncRNAs in atrial and ventricular chambers. Furthermore, we demonstrate by in situ hybridization a dynamic epicardial, myocardial and endocardial expression of H19 during cardiac development. Overall our data support novel roles of these lncRNAs in different temporal and tissue-restricted fashion during cardiogenesis.
Differential modulation of S-nitrosoglutathione reductase and reactive nitrogen species in wild and cultivated tomato genotypes during development and powdery mildew infection.
(ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER, 2020-10) Jahnová, J.; Činčalová, L.; Sedlářová, M.; Jedelská, T.; Sekaninová, J.; Mieslerová, B.; Luhová, L.; Barroso, J.B.; Petřivalský, M.
Nitric oxide plays an important role in the pathogenesis of Pseudoidium neolycopersici, the causative agent of tomato powdery mildew. S-nitrosoglutathione reductase, the key enzyme of S-nitrosothiol homeostasis, was investigated during plant development and following infection in three genotypes of Solanum spp. differing in their resistance to P. neolycopersici. Levels and localization of reactive nitrogen species (RNS) including NO, S nitrosoglutathione (GSNO) and peroxynitrite were studied together with protein nitration and the activity of nitrate reductase (NR). GSNOR expression profiles and enzyme activities were modulated during plant devel opment and important differences among Solanum spp. genotypes were observed, accompanied by modulation of NO, GSNO, peroxynitrite and nitrated proteins levels. GSNOR was down-regulated in infected plants, with exception of resistant S. habrochaites early after inoculation. Modulations of GSNOR activities in response to pathogen infection were found also on the systemic level in leaves above and below the inoculation site. Infection strongly increased NR activity and gene expression in resistant S. habrochaites in contrast to susceptible S. lycopersicum. Obtained data confirm the key role of GSNOR and modulations of RNS during plant development under normal conditions and point to their involvement in molecular mechanisms of tomato responses to bio trophic pathogens on local and systemic levels.
Differential molecular response of monodehydroascorbate reductase and glutathione reductase by nitration and S-nitrosylation
(Oxford Academic, 2015-06-25) Begara-Morales, Juan C.; Sánchez-Calvo, Beatriz; Chaki, Mounira; Mata-Pérez, Capilla; Valderrama, Raquel; Padilla, María N.; Jaramillo, Javier; Luque, Francisco; Corpas, Francisco J.; Barroso, Juan B.
The ascorbate–glutathione cycle is a metabolic pathway that detoxifies hydrogen peroxide and involves enzymatic and non-enzymatic antioxidants. Proteomic studies have shown that some enzymes in this cycle such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), and glutathione reductase (GR) are potential targets for post-translational modifications (PMTs) mediated by nitric oxide-derived molecules. Using purified recombinant pea peroxisomal MDAR and cytosolic and chloroplastic GR enzymes produced in Escherichia coli, the effects of peroxynitrite (ONOO–) and S-nitrosoglutathione (GSNO) which are known to mediate protein nitration and S-nitrosylation processes, respectively, were analysed. Although ONOO– and GSNO inhibit peroxisomal MDAR activity, chloroplastic and cytosolic GR were not affected by these molecules. Mass spectrometric analysis of the nitrated MDAR revealed that Tyr213, Try292, and Tyr345 were exclusively nitrated to 3-nitrotyrosine by ONOO–. The location of these residues in the structure of pea peroxisomal MDAR reveals that Tyr345 is found at 3.3 Å of His313 which is involved in the NADP-binding site. Site-directed mutagenesis confirmed Tyr345 as the primary site of nitration responsible for the inhibition of MDAR activity by ONOO–. These results provide new insights into the molecular regulation of MDAR which is deactivated by nitration and S-nitrosylation. However, GR was not affected by ONOO– or GSNO, suggesting the existence of a mechanism to conserve redox status by maintaining the level of reduced GSH. Under a nitro-oxidative stress induced by salinity (150mM NaCl), MDAR expression (mRNA, protein, and enzyme activity levels) was increased, probably to compensate the inhibitory effects of S-nitrosylation and nitration on the enzyme. The present data show the modulation of the antioxidative response of key enzymes in the ascorbate–glutathione cycle by nitric oxide (NO)-PTMs, thus indicating the close involvement of NO and reactive oxygen species metabolism in antioxidant defence against nitro-oxidative stress situations in plants.
Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves
(Oxford Academic, 2014-06) Begara-Morales, Juan C.; Sánchez-Calvo, Beatriz; Luque, Francisco; Leyva-Pérez, María O.; Leterrier, Marina; Corpas, Francisco J.; Barroso, Juan B.
S-Nitrosoglutathione (GSNO) is a nitric oxide-derived molecule that can regulate protein function by a post-translational modification designated S-nitrosylation. GSNO has also been detected in different plant organs under physiological and stress conditions, and it can also modulate gene expression. Thirty-day-old Arabidopsis plants were grown under hydroponic conditions, and exogenous 1 mM GSNO was applied to the root systems for 3 h. Differential gene expression analyses were carried out both in roots and in leaves by RNA sequencing (RNA-seq). A total of 3,263 genes were identified as being modulated by GSNO. Most of the genes identified were associated with the mechanism of protection against stress situations, many of these having previously been identified as target genes of GSNO by array-based methods. However, new genes were identified, such as that for methionine sulfoxide reductase (MSR) in leaves or different miscellaneous RNA (miscRNA) genes in Arabidopsis roots. As a result, 1,945 GSNO-responsive genes expressed differently in leaves and roots were identified, and 114 of these corresponded exclusively to one of these organs. In summary, it is demonstrated that RNA-seq extends our knowledge of GSNO as a signaling molecule which differentially modulates gene expression in roots and leaves under non-stress conditions.

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