Biology subjects

Moreira, R.

Publications and source records attributed to Moreira, R..

9 recordsLinked to original sources

bioRxiv2026

Structure and Mechanism of a Two-component Lanthipeptide Toxin

The enterococcal cytolysin is a two-component lanthipeptide natural product that co-operatively kills mammalian cells and bacteria. It is a virulence factor in typically commensal strains of gut-dwelling Enterococcus faecalis and causes a fatal form of alcoholic hepatitis. Despite its clinical significance, little is known about the mechanism of action. We present here the molecular details of cytolysins remarkable bioactivity. A high-resolution cryo-electron microscopy structure revealed highly ordered tubular assemblies comprising the two subunits. We further demonstrate these structures disrupt the membranes of eukaryotic and bacterial cells. These results provide the first high-resolution structure of two distinct lanthipeptides interacting with one another and offer an explanation for the unique bioactivity of the cytolysin toxin.

biochemistry↗

bioRxiv2026

NeoDBS: Open-Source Platform for Visualization and Analysis of Electrophysiological Recordings from Deep Brain Stimulation Systems

Optimization of deep brain stimulation (DBS) therapy for neurological and neuropsychiatric disorders depends on objective quantitative biomarkers that can guide stimulation parameter adjustments. With the recent introduction of new-generation DBS systems capable of simultaneously stimulating brain activity and recording local field potentials (LFP), there is increasing demand for platforms that enable efficient visualization and analysis of these signals for electrophysiological biomarkers identification. To address the limitations of currently available toolboxes that require advanced signal processing skills and rely on proprietary software, we present NeoDBS, an open-source Python platform designed for ingestion and advance signal visualization and processing of LFP signals from DBS systems through an easy-to-use graphical interface. NeoDBS is a user-centered platform that offers predefined analysis pipelines with the aim of facilitating electrophysiological biomarker investigation for DBS across different brain disorders. Custom analysis pipelines are also available for users to leverage the signal analysis tools to their research needs. Critical functionalities for longitudinal biomarker research are featured in NeoDBS, such as batch file processing and event-locked analysis for in-clinic and at-home recordings. This combination of accessibility, user-experience and advanced signal processing tools makes NeoDBS an environment that propels easy and fast electrophysiological biomarker research for DBS, across patients, sessions, and stimulation parameters.

bioengineering↗

bioRxiv2026

BODIPY-Tagged β-Lactams as Selective Quenched Activity-Based Probes to Target Human Neutrophil Elastase

Activity-based probes are indispensable tools for interrogating protease function, and quenched fluorescent variants enable dynamic, real-time imaging of enzymatic activity. Despite these advances, very few quenched activity-based probes (qABPs) have been reported for serine proteases, which constitute the largest and most diverse mechanistic class of proteases. {beta}-Lactams have been extensively used to develop molecular tools and drugs designed to bind or be hydrolysed by serine-dependent bacterial enzymes. Here, we report the first monocyclic {beta}-lactam-containing qABPs for detecting serine proteases. Both the enzyme-triggered activation mechanism and intrinsic reactivity of the probes were highly dependent on the relative position of the BODIPY-FL fluorophore and quencher moiety at the {beta}-lactam core. qABPs displaying the most efficient turn-on mechanism were shown to selectively target human neutrophil elastase (HNE) in different human cell lysates. The most successful qABP was rapidly internalised and targeted HNE in U937 cells and human neutrophils. These results demonstrate the potential of the modular {beta}-lactam warhead to develop turn-on probes to track neutrophil serine proteases in live cells

pharmacology and toxicology↗

bioRxiv2025

Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho-Tyrosines

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that possess many activities that are of potential translational interest. Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), until recently termed domain of unknown function 692 (DUF692), have been gaining interest because of their involvement in a range of biochemical reactions that are remarkable from a chemical perspective. Over 13,500 putative MNIO-encoding biosynthetic gene clusters (BGCs) have been identified by sequence similarity networks (SSNs). In this study, we identified a set of precursor peptides containing a conserved FHAFRF-motif in MNIO-encoding BGCs. These BGCs follow a conserved synteny with genes encoding an MNIO, a RiPP recognition element (RRE)-containing partner protein, an arginase, and a B12-dependent radical SAM enzyme (rSAM). Using heterologous reconstitution of a representative BGC from Peribacillus simplex (pbs cluster) in E. coli, we demonstrated that the MNIO in conjunction with the partner protein catalyzes ortho-hydroxylation of each of the phenylalanine residues in the conserved FRF-motif, the arginase forms an ornithine by deguanidination of the arginine in the motif, and the B12-rSAM crosslinks the ortho-Tyr side side chains by a C-C linkage forming a novel macrocyclic molecule. Substrate scope studies suggested tolerance of the MNIO and the B12-rSAM towards substituting the Phe residues with tyrosines in the conserved motif with the position of hydroxylation and crosslinking being maintained. Overall, this study expands the diverse array of posttranslational modifications catalyzed by MNIOs and B12-rSAM enzymes. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/647296v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@37d9c8org.highwire.dtl.DTLVardef@baf547org.highwire.dtl.DTLVardef@3d0ed8org.highwire.dtl.DTLVardef@99aaee_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

External and Internal Load Profiles of Male and Female Participants during a Walking Football Practice

BACKGROUNDHigh levels of sedentary behavior among older adults highlight the importance of walking football (WF) in promoting physical activity for healthy aging. This study examines the external and internal load profiles of male and female participants during a WF tournament, addressing a gap in research on game demands and induced load. METHODSThe study involved 176 players aged 50+ participating in a 40-min, 5v5 WF tournament with unlimited substitutions. External load (total and categorized distances) was measured using Global Positioning System (GPS), while heart rate (HR) monitors assessed internal load, including absolute HR and intensity zones based on %HRmax. RESULTSThe proportion of male participants (n=123; 70.3%) was higher than females (n=52; 29.7%), p<.001. They were similar in age (61.6{+/-}8.6 and 60.8{+/-}6.9, respectively). Males covered a higher distance per minute than females, with sex showing a moderate effect (63.3{+/-}10.7 m/min vs. 54.7{+/-}15.8 m/min; p < .001; Cohens dunbiased = 0.69 [0.36; 1.03]), especially in fast walking (41.7{+/-}12.2 m/min vs. 32.6{+/-}16.7 m/min; p < .001; Cohens dunbiased = 0.66 [0.33; 1.00]). Males played more time than females (22:26{+/-}09:47 min:ss vs. 15:41{+/-}07:46 min:ss; p<.001), with moderate effect (Cohens dunbiased = 0.73 [0.40; 1.06]). However, no differences between sexes were identified in the internal load variables, such that the female average %HRmax was 80{+/-}11% and the male was 82{+/-}8% during the practice. CONCLUSIONSOverall, while males generally exhibit higher external loads in WF, both sexes experience similar internal load demands, highlighting WFs potential as a scalable, health-promoting intervention for aging populations.

physiology↗

bioRxiv2024

Bibacillin 1: A two-component lantibiotic from Bacillus thuringiensis

Here we describe bibacillin 1 - a two-component lantibiotic from Bacillus thuringiensis. The peptides that comprise bibacillin 1 are modified by a class II lanthipeptide synthetase Bib1M producing two peptides with non-overlapping ring patterns that are reminiscent of cerecidin and the short component of the enterococcal cytolysin (CylLS"), a virulence factor associated with human disease. Stereochemical analysis demonstrated that each component contains LL-methyllanthionine and DL-lanthionine. The mature bibacillin 1 peptides showed cooperative bactericidal activity against Gram-positive bacteria, including members of ESKAPE pathogens, and weak hemolytic activity. Optimal ratio studies suggest that bibacillin 1 works best when the components are present in a 1:1 ratio, but near optimal activity was observed at ratios strongly favouring one component over the other, suggesting that the two peptides may have different but complementary targets. Mechanism of action studies suggest a lipid II-independent killing action distinguishing bibacillin 1 from two other two-component lantibiotics haloduracin and lacticin 3147. One of the two components of bibacillin 1 showed cross reactivity with the cytolysin regulatory system. These result support the involvement of bibacillin 1 in quorum sensing and raise questions about the impact of CylLS"-like natural products on lanthipeptide expression in diverse bacterial communities.

biochemistry↗

bioRxiv2024

Polyphosphate mobilization influences the ability of Cryptococcus neoformans to cause disease in a murine model of cryptococcosis

Cryptococcus neoformans, an invasive basidiomycete fungal pathogen, causes one of the most prevalent, life-threatening diseases in immunocompromised individuals and accounts for [~]15% of AIDS-associated deaths. A dire need for the development of novel antifungal drugs, vaccines, and improved diagnostics has emerged with the increased frequency of fungal infections. Therefore, understanding the pathogenesis of C. neoformans and its interactions with the host immune system is critical for the development of therapeutics against cryptococcosis. Previous research demonstrated that C. neoformans cells lacking polyphosphate (polyP), an immunomodulatory polyanionic storage molecule, display altered cell surface architecture. However, the relevance of surface changes and the role of polyP in the virulence of C. neoformans remain unclear. Here we show that mutants lacking the polyphosphatases (Xpp1 and Epp1) are attenuated for virulence in a murine inhalational model of cryptococcosis, demonstrate reduced proliferation in host tissue, and provoke an altered immune response. An analysis of mutants lacking the polyphosphatases and the Vtc4 protein for polyP synthesis indicated that the Xpp1 and Epp1 contribute to the organization of the cell surface, virulence factor production, the response to stress, and mitochondrial function. Overall, we conclude that polyP mobilization plays a multifaceted role in the pathogenesis of C. neoformans. Author SummaryCryptococcus neoformans causes one of the most prevalent fungal diseases in people with compromised immune systems and accounts for 15-20% of AIDS-associated deaths worldwide. The continual increase in the incidence of fungal infections and limited treatment options necessitate the development of new antifungal drugs and improved diagnostics. Polyphosphate (polyP), an under-explored biopolymer, functions as a storage molecule, modulates the host immune response, and contributes to the ability of many fungal and bacterial pathogens to cause disease. However, the role of polyP in cryptococcal disease remains unclear. In this study, we report that the enzymes that regulate polyP synthesis and turnover contribute to the virulence of C. neoformans in a mouse model of cryptococcosis. The polyphosphatases, Xpp1 and Epp1, influenced the survival of C. neoformans in macrophages and altered the host immune response. The loss of Xpp1 and Epp1 led to changes in cell surface architecture, cell size, impaired growth, and defects in both mitochondrial function and the stress response of C. neoformans. Thus, our work establishes polyP as a key factor in the disease caused by C. neoformans, and identifies polyP mobilization as a novel target to support new therapeutic approaches.

microbiology↗

bioRxiv2022

THE MAJOR ROLE OF JUNCTIONAL DIVERSITY IN THE HORSE ANTIBODY REPERTOIRE

The sequencing of the antibody repertoire (Rep-seq) revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis of diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-immunized horses using HTS technology. In this study, we obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 and 82% in IgM and IgG isotypes. We observed that besides horses antibody can use all of the functional IGHV genes, around 80% of their antibodies use only three IGHV gene segments, and around 55% use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horses antibodies is highly frequent, present in more than 90% of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45% of the antibody clones have more than ten nucleotides in both N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and in other species to better understand antibody repertoire characteristics.

immunology↗

bioRxiv2019

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Mussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes ([~]15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few non-metazoan eukaryotes, but that might also characterize other marine invertebrates.\n\nSignificance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding protein-coding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

genetics↗