Biology subjects

Rodrigues, R.

Publications and source records attributed to Rodrigues, R..

7 recordsLinked to original sources

bioRxiv2026

Carbohydrate-active enzymes of giant viruses: Molecular and biochemical characterization of glycosyl hydrolases from algae-infecting chloroviruses

Microbial hydrolases are considered to be promising enzymes for pathogen control. Bacterial and viral chitinases of the glycosyl hydrolase (GH) 18 family are important biological macromolecules with antifungal and anti-insect activity. Chloroviruses, nucleocytoplasmic large DNA viruses (NCLDVs) that infect unicellular green algae have a considerable number of genes involved in carbohydrate metabolism, including the chitinase GH18 family. In this study, we investigated the abundance and diversity of chitinases in chlorovirus genomes using a combination of silico and in vitro strategies, and characterized these enzymes at a molecular and biochemical level. Different enzymatic profiles were observed in Chlorovirus subgenera revealing the different viral machinery related to host species. We performed a comprehensive biochemical characterization of three heterologous expressed GH18 domains, which revealed their endo and exochitinase activity and thermostability. Crystallographic analysis of the GH18 domain by X-ray diffraction yielded a structure at 1.0 [A] resolution, representing the highest-resolution structure reported to date for a giant viral protein and showing lower predominancy of residue coevolution compared GH18 chitinases from other organisms. Additionally, our binding site characterization predicted high conservation in betachloroviruses and gammachloroviruses, and less so in alphachloroviruses. Lastly, these enzymes did not inhibit fungal growth of medical and agricultural importance species in vitro but exhibited high inhibitory activity against different algae at nanogram/mL range. Together, our experimental and computational data show that evolutionary events may contribute to maintaining viral chitinases enzymatic activity and specificity. These findings highlight the potential of virus-derived enzymes as promising new biotechnological tools for microbial control against different algal strains.

microbiology↗

bioRxiv2026

IL-17RC signaling connects intestinal microbiota and neuroimmune interactions in atherosclerosis

While dysbiosis and inflammation were previously implicated in cardiovascular diseases, the circuits of how microbiota drives distant perivascular innervation, neuroinflammation and atherosclerosis remains unknown. Here, we report that IL-17RC signaling in intestine protects from atherosclerosis controlling intestinal barrier and microbiota, and loss of IL-17RC in intestinal epithelial cells alters microbiota, enhances perivascular innervation and aortic inflammation, augmenting the disease. Neuronal outgrowth is functionally dependent on microbiota and is essential for neuroinflammation and augmentation of atherosclerosis as chemical denervation reduces inflammation, macrophage activation and disease progression. Microbiota-dependent IL-17A producing {gamma}{delta} T cells accumulate in aorta to promote neuronal outgrowth and activation that can be reversed by {gamma}{delta} T cell blockade. Perivascular neuron activation is further dependent on cell autonomous IL-17 signaling as IL-17RC ablation in sympathetic neurons protected mice from microbiota-driven atherosclerosis. Together, our data illuminate how intestinal cytokine signaling distantly restrains neuroimmune interactions in aorta and uncovers a novel link between IL-17 signaling, microbiota, perivascular innervation and neuroimmune pro-inflammatory crosstalk instrumental for atherosclerosis progression. SummaryIL-17RC signaling regulates intestinal dysbiosis and perivascular neuronal outgrowth that modulates inflammation in atherosclerosis.

immunology↗

bioRxiv2025

Adaptively integrated sequencing and assembly of near-complete genomes

Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. Cornetto is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).

genomics↗

bioRxiv2022

Extracellular vesicles improve GABAergic transmission in Huntington's disease iPSC-derived neurons

Extracellular vesicles (EVs) carry bioactive molecules associated with various biological processes, including miRNAs. In both Huntingtons disease (HD) models and human samples, altered expression of miRNAs involved in synapse regulation were reported. Recently, the use of EV cargo to reverse phenotypic alterations in disease models with synaptopathy as the end-result of the pathophysiological cascade has become an interesting possibility. Here, we assessed the contribution of EVs to GABAergic synaptic alterations using a human HD model and studied the miRNA content of isolated EVs. After differentiating HD human induced-pluripotent stem cells into electrophysiologically active striatal-like GABAergic neurons, we found that HD-derived neurons displayed reduced density of inhibitory synapse markers and of GABA receptor-mediated ionotropic signaling. Treatment with EVs secreted by control (CTR) fibroblasts reversed the deficits in GABAergic synaptic transmission and increased the density of inhibitory synapses on HD-neuron cultures, while EVs from HD-derived fibroblasts had the opposite effects on CTR-neurons. Moreover, analysis of miRNAs from purified EVs identified a set of differentially expressed miRNAs between manifest HD, premanifest and CTR lines with predicted synaptic targets. The EVs-mediated reversal of the abnormal GABAergic phenotype in HD-derived neurons reinforces the potential role of EVs-miRNAs on synapse regulation.

neuroscience↗

bioRxiv2022

Suppression of Betacellulin expression is a key mechanism for omega-3 fatty acid mediated attenuation of nonalcoholic steatohepatitis

Clinical and preclinical studies have established that supplementing diets with {omega}3 polyunsaturated fatty acids (PUFA) can reduce hepatic dysfunction in nonalcoholic steatohepatitis (NASH). Herein, we used multi-omic network analysis to unveil novel mechanistic targets of {omega}3 PUFA effects in a preclinical mouse model of western diet induced NASH. After identifying critical molecular processes responsible for the effects of {omega}3 PUFA, we next performed meta-analysis of human liver cancer transcriptomes and uncovered betacellulin as a key EGFR-binding protein that was induced in liver cancer and downregulated by {omega}3 PUFAs in animals with NASH. We then confirmed that betacellulin acts by promoting proliferation of quiescent hepatic stellate cells, stimulating transforming growth factor-{beta}2 and increasing collagen production. When used in combination with TLR2/4 agonists, betacellulin upregulated integrins in macrophages thereby potentiating inflammation and fibrosis. Taken together, our results suggest that suppression of betacellulin is one of the key mechanisms associated with anti-inflammatory and antifibrotic effects of {omega}3 PUFA during NASH. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/510635v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b8ebe7org.highwire.dtl.DTLVardef@879e8dorg.highwire.dtl.DTLVardef@1ba56f3org.highwire.dtl.DTLVardef@a26c67_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIMulti-omic network analysis points to mitochondrial cardiolipin precursors as candidate key lipids whereby {omega}3 fatty acids restore mitochondrial functioning. C_LIO_LIMulti-omic network analysis suggests betacellulin (BTC) as one of the key mediators of NASH suppressed by {omega}3 polyunsaturated fatty acids. C_LIO_LIReduction of liver fibrosis by omega-3 fatty acids (especially by docosahexaenoic acid, DHA) is accomplished by simultaneous inhibition of betacellulin and TLR agonists. C_LIO_LIBTC promotes collagen production and induces TGFB2 in hepatic stellate cells. C_LIO_LIBTC together with TLR2/4 agonists stimulate expression of integrins in macrophages. C_LIO_LIDHA suppresses BTC-EGFR pathway in NASH animal model potentially preventing progression to hepatocellular carcinoma. C_LI

systems biology↗

bioRxiv2021

merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures, while leveraging the users expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and non-template based draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

bioinformatics↗

bioRxiv2019

Engineering the smallest transcription factor: accelerated evolution of a 63-amino acid peptide dual activator-repressor

Transcription factors control gene expression in all life. This raises the question of what is the smallest protein that can support such activity. In nature, Cro from bacteriophage {lambda} is the smallest known repressor (66 amino acids; a.a.) but activators are typically much larger (e.g. {lambda} cI, 237 a.a.). Indeed, previous efforts to engineer a minimal activator from Cro resulted in no activity in vivo. In this study, we show that directed evolution results in a new Cro activator-repressor that functions as efficiently as {lambda} cI, in vivo. To achieve this, we develop Phagemid-Assisted Continuous Evolution: PACEmid. We find that a peptide as small as 63-a.a. functions efficiently as an activator and/or repressor. To our knowledge, this is the smallest protein gene regulator reported to date, highlighting the capacity of transcription factors to evolve from very short peptide sequences.

synthetic biology↗