Biology subjects

Costa, A. R.

Publications and source records attributed to Costa, A. R..

10 recordsLinked to original sources

bioRxiv2025

Discovery of phage defense systems through component modularity networks

Phage defense systems in bacteria exhibit high degrees of modularity, with sensing, signal transmission, and effector enzymes frequently being exchanged among phage defense gene clusters. In this study, we capitalized on this modularity to discover phage defense systems by searching for defense-associated modules in new gene contexts. This approach revealed a large and interconnected network of modular components distributed across diverse gene clusters. From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system. Collectively, we demonstrate that leveraging the modular architecture of phage defense systems is an effective approach to their discovery.

microbiology↗

bioRxiv2025

Glioblastoma cells taste temozolomide via TAS2R43

Bitter taste receptors (TAS2Rs) have a widespread expression in various extraoral organs where they detect the chemical composition of body fluids and trigger biological responses accordingly. Among the chemicals recognised by TAS2Rs there are natural and synthetic compounds including therapeutic drugs. We have shown that TAS2Rs are expressed in the blood-cerebrospinal fluid barrier where they regulate efflux transporters, thereby controlling the transport of compounds into the cerebrospinal fluid. More recently, we assessed the expression of these receptors in human glioblastoma cells, where 20 out of the 26 human TAS2Rs were identified. In this study, we investigated if temozolomide, the standard chemotherapy for glioblastoma, activates the bitter signalling pathway with impact in its therapeutic efficacy. Notably, we found that blocking the bitter taste signalling pathway significantly reduced the anti-proliferative and pro-apoptotic effects of temozolomide, and identified TAS2R43 as the receptor mediating these effects. We propose that upon ligand binding, TAS2R43 modulates multidrug resistance proteins (MDRs) activity, facilitating temozolomide entrance into glioblastoma cells. These findings underscore the importance of the taste transduction pathway in evaluating the chemical composition of the glioblastoma microenvironment. Furthermore, our data suggest that TAS2R43 could serve as a biomarker for the efficacy of temozolomide and other drugs that are substrates of MDRs.

cancer biology↗

bioRxiv2025

Sweet taste receptor regulates proliferation and glucose uptake in glioblastoma cells

Glioblastoma is a brain tumour classified by the World Health Organization as grade 4 due to its aggressiveness, invasiveness, and poor differentiation. Current standard therapies remain largely ineffective, reinforcing the need for novel targets to improve glioblastoma prognosis. Reprogramming of cellular metabolism is an important hallmark of cancer, marked by a shift from oxidative phosphorylation to glycolysis as the primary energy source. This metabolic switch, known as the Warburg effect, is exacerbated by the reduced oxygen and glucose availability in the tumour microenvironment. The sweet taste receptor (STR) is an important glucosensor with recognised role in the regulation of glucose uptake in several organs and in astrocytes, the glioblastoma precursor cells. We hypothesised that STR may regulate glucose uptake and metabolism in glioblastoma, representing a potential anticancer target. To test this, we investigated the effects of STR inhibition with lactisole, a specific TAS1R3 inhibitor, in three glioblastoma cell lines (U-87MG, SNB-19 and U-373MG) and in the UPCI-SCC-154 tongue cancer cell line. We provided evidence that STR inhibition consistently reduced cell viability and migration, without inducing apoptosis or necrosis, and impaired glucose uptake and L-lactate production, particularly in tongue cancer UPCI-SCC-154, and glioblastoma U-87MG and SNB-19 cells. Moreover, in a 3D spheroid model, lactisole reduced the invasion capacity of U-87MG glioblastoma spheroids. These results suggest that STR contributes to glioblastoma cell metabolism and behaviour and may represent a promising therapeutic target.

cancer biology↗

bioRxiv2025

Taste receptors' profiling in glioblastoma

Glioblastoma is the most common and aggressive form of primary brain cancer. Despite significant progress in the development of promising therapeutic agents, cancer-targeting therapies often fail to achieve effective concentrations in the brain, limiting their therapeutic efficacy. As such, a deeper understanding of how glioblastoma tumours interact with their microenvironment and assess the chemical composition therein can reveal novel therapeutic strategies. Recent studies have highlighted the critical role of taste receptors, particularly bitter taste receptors (TAS2Rs) and their ligands in cancer progression and metastasis. Activation of TAS2Rs by both natural and synthetic compounds has been associated with drug resistance, apoptosis, and the proliferation of malignant tumours. The sweet taste receptor TAS1R2/TAS1R3, or the umami receptor TAS1R1/TAS1R3, as recognised sensors of glucose levels and aminoacids, respectively, are also of interest in the context of cancer metabolism. In this study, we investigated the expression and function of TAS2Rs, TAS1R2/TAS1R3 and TAS1R1/TAS1R3 and all the taste signalling pathway machinery in glioblastoma. Our findings demonstrate that TAS1R2/TAS1R3, TAS1R1/TAS1R3, and 20 out of the 26 human TAS2Rs are present and active in glioblastoma cells, with expression differences in glioblastoma cells and human tumours. The expression of such a large number of members of this family of receptors, highlight the significance of the taste transduction pathway in this form of brain cancer, where these receptors might be essential for the crosstalk between glioblastoma and its microenvironment.

cancer biology↗

bioRxiv2024

KlebPhaCol: A community-driven resource for Klebsiella research identified a novel gut phage order associated with the human gut

The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation of Klebsiella-targeting phages, clinical applications remain limited, with key phage-bacteria interactions still poorly understood. A major obstacle is fragmented access to well-characterised phage-bacteria pairings, restricting the collective advancement of therapeutic and mechanistic insights. To address this gap, we created the Klebsiella Phage Collection (KlebPhaCol), an open-source resource comprising 53 phages and 74 Klebsiella isolates, all fully characterised. These phages span five families - including a novel order, Felixvirales, associated with the human gut - and target 27 sequence types (including ST258, ST11, ST14) and 28 capsular-locus types (including KL1 and KL2), across six Klebsiella species. Freely accessible at www.klebphacol.org, KlebPhaCol invites the scientific community to both use and contribute to this resource, fostering collaborative research and a deeper understanding of Klebsiella-phage interactions beyond therapeutic use.

microbiology↗

bioRxiv2022

Accumulation of defense systems drives panphage resistance in Pseudomonas aeruginosa

Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems are specific to phage genera, and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.

microbiology↗

bioRxiv2022

High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

The Klebsiella jumbo myophage {phi}Kp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combined cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, and machine learning approaches to explore the capsid, tail, and tail fibers of this phage at high resolution. We determined the structure of the capsid and tail at 4.3[A] and 4.1[A] resolution. We observed that the tail fibers were highly branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide {phi}Kp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Taken together, our study provides structural and functional insight into how {phi}Kp24 adapts to the highly variable surfaces of capsulated bacterial pathogens, which will be useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.

microbiology↗

bioRxiv2021

Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae

Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0-13%) identity to genomic phage sequences deposited in the Genbank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.

microbiology↗

bioRxiv2018

Coherent-hybrid STED: a tunable photo-physical pinhole for super-resolution imaging at high contrast

Resolution in microscopy is not limited by diffraction as long as a nonlinear sample response is exploited. In a paradigmatic example, stimulated-emission depletion (STED) fluorescence microscopy fundamentally breaks the diffraction limit by using a structured optical pattern to saturate depletion on a previously excited sample area. Two-dimensional (2D) STED, the canonical low-noise STED mode, structures the STED beam by using a vortex phase mask, achieving a significant lateral resolution improvement over confocal fluorescence microscopy. However, axial resolution and optical sectioning remain bound to diffraction. Here we use a tunable coherent-hybrid (CH) beam to improve optical sectioning, markedly reducing background fluorescence. CH-STED, which inherits the 2D-STED immunity to spherical aberration, diversifies the depletion strategy, allowing an optimal balance between two key metrics (lateral resolution and background suppression) to be found. CH-STED is used to perform high-contrast imaging of complex biological structures, such as the mitotic spindle and the neuron cell body.

biophysics↗

bioRxiv2018

Genomic analysis of Acinetobacter baumannii prophages reveals remarkable diversity and suggests profound impact on bacterial virulence and fitness

The recent nomination by the World Health Organization of Acinetobacter baumannii as the number one priority pathogen for the development of new antibiotics is a direct consequence of its fast evolution of pathogenicity, and in particular of multidrug resistance. While the development of new antibiotics is critical, understanding the mechanisms behind the crescent bacterial pathogenicity is equally relevant. Often, resistance and other bacterial virulence elements are contained on highly mobile pieces of DNA that can easily spread to other bacteria. Prophages are one of the mediators of this form of gene transfer, and have been frequently found in bacterial genomes, often offering advantageous features to the host. Here we question the contribution of prophages for the evolution of A. baumannii pathogenicity. We found prophages to be notably diverse and widely disseminated in A. baumannii genomes. Also remarkably, A. baumannii prophages encode for multiple putative virulence factors that may be implicated in the bacteriums capacity to colonize host niches, evade the host immune system, subsist in unfavorable environments, and tolerate antibiotics. Overall our results point towards a significant contribution of prophages for the dissemination and evolution of pathogenicity in A. baumannii, and highlight their clinical relevance.

microbiology↗