Biology subjects

Valente, C.

Publications and source records attributed to Valente, C..

7 recordsLinked to original sources

bioRxiv2026

Scalable longitudinal imaging and transcriptomics of cells in dynamic enclosures

Dynamic transitions between cell states underlie both normal physiology and disease. However, most single-cell technologies capture only static snapshots. To address this gap, we developed a platform that integrates light-guided hydrogel polymerization with computer vision to generate on-demand compartments around live cells, enabling longitudinal imaging of cellular behavior paired with whole-transcriptome profiling of the same cells at scale. These data link dynamic phenotypes with molecular programs, enabling deeper characterization of cellular states. This approach revealed an adaptive, drug-resistant state in lung cancer cells characterized by potassium channel upregulation and p53-dependent quiescence. In models of adipogenesis and microglial phagocytosis, joint analysis of imaging and transcriptomic data identified key drivers of cellular function that were missed by transcriptomic clustering alone. These results establish the value of paired functional and transcriptomic analysis to resolve molecular drivers of complex cellular behaviors.

systems biology↗

bioRxiv2025

Coexistence of two divergent TprA/PhrA cell-cell communication systems in Streptococcus mitis coordinate bacteriocin production, competence, oxidative stress responses, and interspecies competition with S. pneumoniae

Cell-cell communication (CCC) systems are key regulators of bacterial behaviors and adaptation. The human upper respiratory tract is co-colonized by commensal and pathogenic streptococci, but how CCC systems mediate their interactions remains unclear. Here, we investigated the TprA/PhrA quorum-sensing system, composed of the transcription factor TprA and its cognate signaling peptide PhrA, across Streptococcus mitis and S. pneumoniae. Comparative genomics showed that this system is broadly distributed across both species, with most strains sharing identical phrA alleles that enable interspecies signaling. In both species, the tprA/phrA module is commonly linked to the streptococcin E (sce) locus, encoding a putative bacteriocin. We show that activation of the sce operon enhances the competitive fitness of S. mitis in biofilm and infection models. In S. mitis strain C22, two diverse copies of tprA/phrA are present and differentially regulated, coordinating expression of tprA/phrA and the downstream sce locus through both shared and independent pathways. Transcriptomic analyses revealed redundancy, additivity, and cross-regulation between the two systems, linking them to the control of bacteriocin production, competence, and oxidative stress responses. Distinct promoter architectures and TprA-binding motifs underlie the functional divergence of these paralogues, highlighting how regulatory diversification can expand quorum-sensing outputs. Together, our findings show that S. mitis has evolved a flexible and layered communication network that integrates population sensing with antimicrobial and competence responses, providing a molecular basis for its competitive interactions with S. pneumoniae during colonization of the human respiratory tract.

microbiology↗

bioRxiv2025

Network rewiring of a pneumococcal communication system promotes stress adaptation in a globally successful lineage

Cell-cell communication (CCC) systems regulate bacterial behaviors and shape social interactions within microbial communities. In Streptococcus pneumoniae, several CCC systems coordinate intra- and inter-strain signaling, yet the genetic plasticity of their components and regulons remains underexplored. Here, we investigate a divergent allelic variant of the TprA/PhrA CCC system, a regulator-pheromone pair widely conserved in S. pneumoniae. We characterize PhrA1.2, the second most prevalent PhrA pheromone, as a non-signaling variant found in the globally distributed GPSC6 lineage, with presence in isolates dating back to the 1960s. In GPSC6, PhrA1.2 co-occurs with TprA1.2, a truncated transcriptional regulator carrying premature stop codons that eliminate the predicted pheromone-binding domain. Functional assays show that PhrA1.2 is non-functional, both when paired with the truncated TprA1.2 and when paired with the canonical regulator allele TprA1.1. Unexpectedly, despite its truncation, TprA1.2 activates genes involved in oxidative stress responses, including those related to iron-sulfur cluster formation and redox homeostasis. Loss of tprA1.2 impairs growth and increases hydrogen peroxide sensitivity, while in vivo experiments reveal a fitness defect during nasopharyngeal colonization. Together, our findings show that the TprA1.2 allele represents a regulator that has lost its communication component while modifying its regulon. This variant promotes adaptation to oxidative stress and contributes to colonization, demonstrating circuit rewiring of a peptide-regulator CCC system in an epidemiologically relevant S. pneumoniae lineage.

microbiology↗

bioRxiv2025

Streptolancidin D mediates intra-species competition in Streptococcus pneumoniae through the Rgg144/SHP144 quorum-sensing system

Streptococcus pneumoniae is a major colonizer of the human nasopharynx, where inter- and intra-strain competition plays a critical role in shaping population structure and influencing vaccine outcomes. Bacteriocins are key mediators of intra-species competition, yet many of their functions and regulatory mechanisms remain poorly understood. Here, we identify and characterize streptolancidin D, a previously uncharacterized bacteriocin encoded by the sldA-T locus and demonstrate its contribution to pneumococcal competition. Using isogenic streptolancidin-producing and non-producing variants of a naturally colonizing strain, we show that sldA-T contributes to inhibition of competitor strains in in vitro biofilms and during murine co-colonization. Importantly, streptolancidin D also inhibited a subset of genetically diverse pneumococcal isolates representing multiple serotypes, whereas non-producing variants showed no activity. This indicates that its effect is broad and not restricted to isogenic interactions. Genomic analysis of over 7,500 pneumococcal genomes revealed that sldA-T is present in [~]12% of isolates, with lineage-associated distribution patterns, and is consistently encoded downstream of the Rgg144/SHP144 quorum sensing system. We further demonstrate that sldA-T is regulated by this system, with sldA-T promoter activity abolished in a SHP-deficient background and partially restored by exogenous peptide stimulation. Finally, we show that streptolancidin D acts in concert with other bacteriocin systems and competence-mediated fratricide, highlighting a multifactorial antimicrobial strategy that enhances pneumococcal competitiveness. Overall, our findings identify a quorum sensing-regulated bacteriocin that contributes to pneumococcal competition and helps shape population dynamics. IMPORTANCEBacteriocins are central to bacterial competition and niche occupation, particularly in structured environments like the human nasopharynx. While several pneumococcal bacteriocins have been characterized, the functions of many remain unknown, limiting our understanding of how these systems shape strain fitness and population dynamics. We characterize streptolancidin D, a bacteriocin that enhances intraspecies competitiveness in vitro and in vivo and contributes to inhibition of genetically diverse pneumococcal strains. We demonstrate that its expression is tightly regulated by the conserved Rgg144/SHP144 quorum sensing system and that the locus is distributed and shows synteny across multiple pneumococcal lineages. Our findings reveal that streptolancidin D operates within a broader network of bacteriocins and competence-associated mechanisms that collectively shape competitive interactions. By integrating genomic, functional, and regulatory analyses, this work expands the known repertoire of pneumococcal antimicrobial systems and provides new insights into the mechanisms underpinning competition and population structure in S. pneumoniae.

microbiology↗

bioRxiv2025

Bacteriocin-mediated prevention of secondary pneumococcal pneumonia by a human commensal Streptococcus mitis strain

Streptococcus pneumoniae remains a major public health threat despite widespread use of vaccines and antibiotics. Its well-established synergy with influenza A virus (IAV) often results in secondary bacterial pneumonia, a condition associated with high morbidity and mortality. As pneumococcal pneumonia is invariably preceded by nasopharyngeal colonization, preventing colonization represents a promising intervention strategy. Current approaches, including pneumococcal conjugate vaccines and antibiotics, can drive serotype replacement and antimicrobial resistance, underscoring the need for novel, targeted, and serotype-independent alternatives. We previously identified seven commensal streptococcal strains (S. oralis A22 and S. mitis B22-G22) that robustly inhibit S. pneumoniae growth and biofilm formation in vitro. Here, using a murine model, we demonstrate that colonization with the commensal strain F22Ad significantly reduces pneumococcal density in the nasopharynx by day 10 post-infection and prevents pneumococcal dissemination to the lungs following IAV co-infection. This protective effect was dependent on bacteriocins encoded at the blp1 locus. Among these, Bac2v1 (alone or in combination with Bac1) significantly reduced pneumococcal colonization. Notably, Bac2v1 exerted serotype-independent inhibitory activity, impairing the growth of diverse pneumococcal strains. Our findings provide the first in vivo proof-of-concept that commensal streptococci, and specifically their bacteriocins, can disrupt S. pneumoniae colonization and prevent progression to secondary bacterial pneumonia. This work introduces a previously unrecognized precision-based approach to pneumococcal disease prevention, offering a potential complement to current strategies.

microbiology↗

bioRxiv2022

Changes in adenosine and neurotrophic signaling in the SOD1G93A mouse model of amyotrophic lateral sclerosis: modulation by chronic caffeine intake

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of corticospinal tract motor neurons. Previous studies showed that adenosine-mediated neuromodulation is disturbed in ALS and that vascular endothelial growth factor (VEGF) has a neuroprotective function in ALS mouse models. We evaluated how adenosine (A1R and A2AR) and VEGF (VEGFA, VEGFB, VEGFR-1 and VEGFR-2) system markers are altered in the cortex and spinal cord of pre-symptomatic and symptomatic SOD1G93A mice. We then assessed if/how chronic treatment of SOD1G93A mice with a widely consumed adenosine receptor antagonist, caffeine, modulates VEGF system and/or the levels of Brain-derived Neurotrophic Factor (BDNF), known to be under control of A2AR. We found out decreases in A1R and increases in A2AR levels even before disease onset. Concerning the VEGF system, we detected increases of VEGFB and VEGFR-2 levels in the spinal cord at pre-symptomatic stage, which reverses at the symptomatic stage, and decreases of VEGFA levels in the cortex, in very late disease states. Chronic treatment with caffeine rescued cortical A1R levels in SOD1G93A mice, bringing them to control levels, while rendering VEGF signaling nearly unaffected. In contrast, BDNF levels were significantly affected in SOD1G93A mice treated with caffeine, being decreased in the cortex and increased in spinal the cord. Altogether, these findings suggest an early dysfunction of the adenosinergic system in ALS and highlights the possibility that the negative influence of caffeine previously reported in ALS animal models results from interference with BDNF rather than with the VEGF signaling molecules.

neuroscience↗

bioRxiv2020

PARP12-catalyzed mono-ADP-ribosylation of Golgin-97 controls the transport of E-cadherin

ADP-ribosylation is a post-translational modification involved in physiological and pathological events catalyzed by Poly-ADP-Ribosyl-Polymerase (PARP) enzymes. Substrates of this reaction have been identified by mass-spectrometry, but the definition of PARPs-regulated cellular functions remains scarce. Here, we have analyzed the control of intracellular membrane traffic by the mono-ADP-ribosyl-transferase PARP12, motivated by its localization at the trans-Golgi network. By using bioinformatics, mutagenesis and cell biology approaches we identified Golgin-97, a protein regulating exocytosis, as a PARP12-specific substrate. Mono-ADP-ribosylation of Golgin-97 residues E558-E559-E565 is required for supporting traffic from the trans-Golgi network to the plasma membrane. This step is halted when PARP12 is deleted or when the Golgin-97 ADP-ribosylation-defective mutant is expressed. Under these conditions E-cadherin, whose transport is controlled by Golgin-97, does not reach the plasma membrane but accumulates in a trans-Golgi proximal compartment. Thus, we demonstrate that the ADP-ribosylation of Golgin-97 is required for E-cadherin exocytosis and thus this event may regulate the sorting of exocytic carriers as well as epithelial-to-mesenchymal transition.

cell biology↗