Biology subjects

Lagares, A.

Publications and source records attributed to Lagares, A..

7 recordsLinked to original sources

bioRxiv2026

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate-specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

bioinformatics↗

bioRxiv2025

A systems-level insight into PHB-driven metabolic adaptation orchestrated by the PHB-binding transcriptional regulator AniA (PhaR)

Polyhydroxybutyrate (PHB) is a carbon and energy storage polymer, whose accumulation under nutrient imbalances with excess carbon is a widespread phenomenon in bacteria. PhaR is a conserved transcriptional regulator found to be associated to PHB granules in several species. Although its role in modulating PHB storage and metabolism has been extensively studied across the bacterial phylogeny, a comprehensive analysis of the PhaR regulon within the context of its dual role as a metabolic sensor and regulator remains missing. To bridge this gap, we integrated co-expression network analysis with proteome profiling across multiple mutant backgrounds (lack of PhaR (AniA) and/or PHB synthesis) in the free-living state of the PHB-accumulating alphaproteobacterial root nodule symbiont Sinorhizobium meliloti. This analysis was enriched by identifying direct regulatory targets of PhaR through a regulon-centric computational multi-step search for DNA binding site motifs combined with PhaR-DNA binding and promoter-reporter assays. We confirmed that the model of accumulated PHB sequestering PhaR and thereby relieving phasin and PHB depolymerase gene repression to control cellular PHB levels also applies to S. meliloti, and showed that PhaR-mediated regulation also occurs the symbiotic state. A comprehensive picture of the impact of PHB-mediated PhaR titration on cellular functions revealed exopolysaccharide production as well as central carbon metabolism (pdh and bkd), gluconeogenesis (ppdK and pyc), entry into the TCA cycle (gltA), and the initial steps of the Entner-Doudoroff pathway (zwf, pgl and edd) as major regulatory targets, and beyond carbon metabolism several target genes of yet unknown function. Our findings highlight a pivotal role for PhaR in orchestrating carbon metabolism.

microbiology↗

bioRxiv2024

Identification and functional analysis of recent IS transposition events in rhizobia

Rhizobia are alpha- and betaproteobacteria that, through the establishment of symbiotic interactions with leguminous plants, are able to fix atmospheric nitrogen as ammonium. The successful establishment of a symbiotic interaction is highly dependent on the availability of nitrogen sources in the soil, and on the specific rhizobia strain. Insertion sequences (ISs) are simple transposable genetic elements that can move to different locations within the host genome and are known to play an important evolutionary role, contributing to genome plasticity by acting as recombination hot-spots, and disrupting coding and regulatory sequences. Disruption of coding sequences may have occurred either in a common ancestor of the species or more recently. By means of ISComapare, we identified Differentially Located ISs (DLIS) in nearly related rhizobial strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium. Our results revealed that recent IS transposition events dont seem to be playing a major role in adaptation. Nevertheless, DLIS could have a role enabling the activation and inactivation of certain genes that could dynamically affect the competition and survival of rhizobia in the rhizosphere.

microbiology↗

bioRxiv2023

Supporting central nervous system neuroprotection and remyelination by specific TLR4 antagonism

ApTOLL is an aptamer specifically designed to antagonize Toll-Like Receptor 4 (TLR4), a relevant actor for innate immunity involved in inflammatory responses in multiple sclerosis (MS) and other diseases. MS is a primary demyelinating, chronic, inmune and neurodegenerative disease of the central nervous system that normally debuts in young adults. The currently available therapeutic arsenal to treat MS is composed of immunomodulators but, to date, there are no (re)myelinating drugs available in clinics. Our present study shows cells expressing TLR4 in demyelinating lesions of MS patients (postmortem samples from cerebral cortex) and, as a derivative, we studied the effect of TLR4 inhibition with ApTOLL in animal models of MS (experimental autoimmune encephalomyelitis -EAE- and the cuprizone). The treatment with ApTOLL positively impacted the clinical symptomatology, and this was associated with better preservation plus restoration of myelin and oligodendrocytes in the demyelinated lesions of these animals, which suggests not only an immunomodulatory but also a remyelinating effect of the treatment with ApTOLL. This latter was corroborated on purified cultures of rodent and adult human oligodendrocyte precursor cells (OPCs), confirming the expression of TLR4 in this cell type. Altogether, the molecular nature of ApTOLL and its mechanism/s of action strongly supports this compound as a novel candidate to treat MS and other demyelinating scenarios.

neuroscience↗

bioRxiv2022

Identification of Ensifer meliloti genes required for survival during peat-based bioinoculant maturation by STM-seq

Rhizobial inoculants are sold either as rhizobia within a liquid matrix; or as rhizobia adhered to granules composed of peat prill or finely ground peat moss. During the production of peat-based inoculants, immediately after mixing the rhizobia culture with partially dry sterile peat, the inoculant is stored for a period of 4-5 weeks, inducing a series of changes that results in an increased capability of the rhizobia to survive in the seeds. The number of viable rhizobia on preinoculated seeds at the point of sale, however, is often a limiting factor, as is the inefficiency of the inoculant bacteria to compete with the local rhizobia for the host colonization. In the present work, we used STM-seq for the genomewide screening of Ensifer meliloti mutants affected in the survival during the maturation of peat-based inoculant formulations. Through this approach, we identified hundreds of genes that proved to be relevant to this process. These results also provide a base knowledge that could be used to more completely understand the survival mechanisms used by rhizobia during the maturation of peat-based inoculants, as well as for the design of new inoculant formulations. HighlightsRhizobial inoculants provide an ecological means of nitrogen fertilization compatible with the implementation of sustainable agricultural practices. Their successful usage, however, suffers from two main limitations: the low number of viable rhizobia on preinoculated seeds at the point of sale, and the inefficiency to compete with the local rhizobia for host colonization. Here, we used a high-throughput mutant-screening technology, STM-seq, to uncover which rhizobial genes are involved in the rhizobial survival during the preparation and storage of peat-based inoculant formulations. Our findings provide useful information about the stresses faced by rhizobia during peat-inoculant maturation and storage, which could assist both for the selection of better rhizobial strains, and for the improvement of the inoculant formulations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/508585v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1433abdorg.highwire.dtl.DTLVardef@c54ff7org.highwire.dtl.DTLVardef@4fb2borg.highwire.dtl.DTLVardef@105e0c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Codon-usage optimization in the prokaryotic tree of life: How synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation.

Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29-different prokaryote families. The analysis of core-gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly-expressed genes presented the more optimized codon usage, the singletons contained the less selectively-favored codons. Results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C-bias in 2- to 3-fold codons, and a U-bias in 4-fold codons occurred in all families, irrespective of the global genomic-GC content. Furthermore, the U-biases suggested that U3-mRNA-U34-tRNA interactions were responsible for a prominent codon optimization in both the more ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved-(cr) or variable-(vr) translated products, with each one being under high- (HEP) and low- (LEP) expression levels, demonstrated that the efficiency was more relevant (by a factor of 2) than accuracy to modelling codon usage. Finally, analysis of the third position of codons (GC3) revealed that, in genomes of global-GC contents higher than 35-40%, selection favored a GC3 increase; whereas in genomes with very low-GC contents, a decrease in GC3 occurred. A comprehensive final model is presented where all patterns of codon usage variations are condensed in five-distinct behavioral groups. IMPORTANCEThe prokaryotic genomes--the current heritage of the more ancient life forms on earth-- are comprised of diverse gene sets; all characterized by varied origins, ancestries, and spatial-temporal-expression patterns. Such genetic diversity has for a long time raised the question of how cells shape their coding strategies to optimize protein demands (i.e., product abundance) and accuracy (i.e., translation fidelity) through the use of the same genetic code in genomes with GC-contents that range from less than 20 to over 80%. In this work, we present evidence on how codon usage is adjusted in the prokaryote tree of life, and on how specific biases have operated to improve translation. Through the use of proteome data, we characterized conserved and variable sequence domains in genes of either high- or low-expression level, and quantitated the relative weight of efficiency and accuracy--as well as their interaction--in shaping codon usage in prokaryotes.

microbiology↗

bioRxiv2018

Increased oxidative stress tolerance by Superoxide dismutase overexpression in Mesorhizobium loti.

Drought and salinity conditions are the major factors affecting nitrogen fixation by legume-rhizobium symbiosis. A global response to these stress conditions is the increase of intracellular ROS leading to activation of antioxidant system to ensure cellular homeostasis. Under the hypothesis that overexpression of sod gene in M. loti improve tolerance to oxidative stress we decide to investigate the response of constitutive overexpression of the Mesorhizobium loti MAFF303099 sod gene on tolerance to oxidative stress under free-living conditions. The gene mlr7636 was overexpressed constitutively under the nptII promoter of pFAJ1708 plasmid. Our study revealed that the sod overexpressing mutant had five-fold increased SOD activity in periplasmic space and a better tolerance to superoxide and hydrogen peroxide in bacterial killing assays.\n\nIMPORTANCEIn this study, we report that the homologous superoxide dismutase overexpression in Mesorhizobium loti improves its tolerance to oxidative stress under free-living conditions.

microbiology↗