Biology subjects

Ormazabal, A.

Publications and source records attributed to Ormazabal, A..

4 recordsLinked to original sources

bioRxiv2025

Towards the Rational Design of RsmE Small-RNA Binders: Insights from Molecular Dynamics Simulations

The RsmZ-RsmE interaction is a key element in post-transcriptional regulation in Pseudomonas species. Experimental studies have shown that alternative fragments of RsmZ, despite displaying only subtle sequence and structural differences, exhibit markedly distinct binding affinities for RsmE. To complicate matters further, the affinities measured for isolated fragments differ substantially from those observed when the same segments are embedded in the full-length sRNA molecule. To explore the origin of these discrepancies, we generated computational models of RsmE dimers bound to one or two sRNA stem loops, including several experimentally studied variants, a couple of truncated forms, and a synthetic construct created by linking two native stem loops with an also native single-stranded region. The unbinding of the RNA fragments from these complexes was studied using Umbrella Sampling simulations, which revealed that base pairs located in the stems, as well as the presence of a linker region, shape the interaction landscape between the protein and RNA, thereby modulating binding affinities. Thus, our findings offer a structural and mechanistic basis for interpreting the experimentally observed differences among RsmZ fragments and establish a conceptual foundation for the future computational design of synthetic sRNAs capable of fine-tuning the RsmZ/RsmE regulatory system in a predictable manner.

biophysics↗

bioRxiv2022

Expanding the repertoire of human tandem repeat RNA-binding proteins

Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. Our results showed that the combination of sequence and structural methods finds more tandem repeat proteins than either method alone. We observed differences in the characteristics of regions predicted as repetitive by sequence-based or structure-based computational methods in terms of their sequence composition, their functions and their protein domains.

bioinformatics↗

bioRxiv2021

Defective Slc7a7 transport reduces systemic arginine availability compromising erythropoiesis and iron homeostasis

AbstractLysinuric Protein Intolerance (LPI) is an inborn error of metabolism resulting from SLC7A7 deficiency that causes diminished plasma concentration of cationic amino acids. The clinical picture is highly heterogeneous among patients, who commonly present intolerance to protein intake and more severe complications such as hematological abnormalities and kidney failure. Although current treatments aim to address the metabolic defects of LPI, they have been unsatisfactory when treating the most severe symptoms. Here we show that the absence of Slc7a7 in mice causes iron overload as a result of erythropoiesis failure. Regarding iron metabolism, we demonstrate that reduced plasma erythropoietin triggers a strong iron overload, as erythropoietin administration restores normal iron levels and mitigate hematological alterations. Interestingly, we found that human LPI is associated with hyperferritinemia but not iron overload, a trait that might be influenced by the citrulline treatment. Furthermore, we show that erythropoietin is a key factor in the hematological abnormalities in LPI. Our study reveals a mechanism leading to LPI-induced hematological complications and identifies erythropoietin supplementation as a promising therapeutic strategy for human LPI. Significance StatementThe systemic metabolic environment derived from Slc7a7-ablation in epithelial cells from kidney and intestine causes erythropoiesis failure prompting therefore iron overload. Here, we identify erythropoietin as the main driver of erythropoiesis failure as exogenous erythropoietin administration restores normal erythroblast population. In addition, we have also analyzed human data and found that patients with LPI have abnormal ferritin levels. Finally, as human LPI, citrulline treatment in mice restores normal iron homeostasis, highlighting the relevance of the systemic environment in LPI. Erythropoietin supplementation emerges as a promising therapeutic strategy for human LPI without the inflammatory effect associated with citrulline supplementation.

molecular biology↗

bioRxiv2021

Kynurenine pathway in post-mortem prefrontal cortex and cerebellum in schizophrenia: relationship with monoamines and symptomatology.

Backgroundthe cortico-cerebellar-thalamic-cortical circuit has been implicated in the emergence of psychotic symptoms in schizophrenia (SZ). The kynurenine pathway (KP) has been linked to alterations in glutamatergic and monoaminergic neurotransmission and to SZ symptomatology through the production of the metabolites quinolinic acid (QA) and kynurenic acid (KYNA). Methodsthis work describes alterations in KP in the post-mortem prefrontal cortex (PFC) and cerebellum (CB) of 15 chronic SZ patients and 14 control subjects in PFC and 13 control subjects in CB using immunoblot for protein levels and ELISA for interleukins and QA and KYNA determinations. Monoamine metabolites were analysed by High Performance Liquid Chromatography and SZ symptomatology was assessed by Positive and Negative Syndrome Scale (PANSS). The association of KP with inflammatory mediators, monoamine metabolism and SZ symptomatology was explored. Resultsin the PFC, the presence of the anti-inflammatory cytokine IL-10 together with IDO2 and KATII enzymes decreased in SZ, while TDO and KMO enzymes expression increased. A network interaction analysis showed that in the PFC IL-10 was coupled to the QA branch of the kynurenine pathway (TDO-KMO-QA), whereas IL-10 associated with KMO in CB. KYNA in the CB inversely correlated with negative and general PANSS psychopathology. Although there were no changes in monoamine metabolites content in the PFC in SZ, a network interaction analysis showed associations between dopamine and methoxyhydroxyphenylglycol degradation metabolite. Direct correlations were found between general PANSS psychopathology and the serotonin degradation metabolite, 5-hydroxyindoleacetic acid. Interestingly, KYNA in the CB inversely correlated with 5-hydroxyindoleacetic acid in the PFC. Conclusionsthus, this work found alterations in KP in two brain areas belonging to the cortico-cerebellar-thalamic-cortical circuit associated with SZ symptomatology, with a possible impact across areas in 5-HT degradation.

neuroscience↗