Biology subjects

Gomperts Boneca, I.

Publications and source records attributed to Gomperts Boneca, I..

8 recordsLinked to original sources

bioRxiv2026

The chemorepellent effect of metformin limits bacterial penetration into mammalian mucus by altering bacterial motility

Metformin improves metabolic health and remodels the intestinal microbiota, yet how these microbial changes contribute to therapeutic benefits remains incompletely understood. We combined human metagenomics, quantitative analyses of bacterial behavior and ex vivo mucus models to investigate how metformin modulates host-microbiota interactions. Human metagenomics revealed metformin-associated enrichment of chemotaxis- and motility-related genes. At millimolar concentrations, metformin acted as a bacterial chemorepellent, an effect abolished by deletion of the chemotaxis regulator CheY and dependent on the chemoreceptor Tsr. Direct metformin exposure or fecal water from metformin-treated individuals reduced bacterial penetration into mucin, an effect reproduced in intestinal mucus from pigs fed a moderate-fat diet. Metformin treatment was further associated with reduced fecal flagellin activity and increased anti-flagellin IgA. Together, these findings identify bacterial chemotaxis as a target of metformin and reveal a mechanism by which metformin may limit bacterial access to the intestinal mucus barrier.

microbiology↗

bioRxiv2026

Morphological transformation in Helicobacter pylori is a dynamic process leading to two types of coccoid

The helical shape of Helicobacter pylori is crucial for successful colonization of the human stomach. However, this pathogen can shapeshift into another form termed the "coccoid form" with a spherical shape, through a mechanism that remains elusive. Here, by a combination of fluorescence microscopy using fluorescent D-aminoacids, cryoelectron and atom force microscopy, we explored the dynamics of coccoid formation in H. pylori through interrogation of the peptidoglycan layer. Contrary to the widely held hypothesis, we showed that helical-rod H. pylori transformed into a coccoid without transiting through a U-form. We show that U-forms, characterized by a U-shaped peptidoglycan with enlarged periplasmic space, altered genetic material, and red autofluorescence, are the output of a parallel pathway, which, unlike the coccoid pathway, is independent of the HdpA/Csd3 peptidoglycan endopeptidase. Coccoid formation occurred along a rigid timeline, by bulging of the cytoplasmic membrane through a peptidoglycan crack, resulting in a spheroplast-like structure with the peptidoglycan stacked into a thick layer near the original cell poles. Resistance of that structure against lysis likely involves a switch in metabolic profile reminiscent of bacteria in dormancy, with a notable accumulation of lysophospholipids, demonstrated in this work. Altogether, the ultrastructure and properties of H. pylori coccoids evidenced here are compatible with a role of this form in relapse after antibiotic treatment. SIGNIFICANCE STATEMENTUpon prolonged growth, stomach pathogen Helicobacter pylori undergoes a morphological change from a helical to a spherical form called coccoid, which may be involved in bacterial persistence and immune evasion. The pathway leading to this form, as well as its precise architecture, were unclear. In this work, we show by different microscopy techniques that the transition to coccoid does not involve a U-shaped intermediate as proposed before, but is triggered by progressive thinning, due to the activity of endopeptidase HdpA/Csd3, of the peptidoglycan meshwork that normally protects the cell, eventually leading to rupture. Because of the hole thus created, peptidoglycan can no longer contain the osmotic pressure in the cytoplasm, which leaks out within a membrane bulge, to eventually give rise to a kind of sphaeroplast, expected to be insensitive to cell wall-targeted antibiotics.

microbiology↗

bioRxiv2025

Architecture of a peptidoglycan peptidase complex involved in morphological transition in Helicobacter pylori.

Peptidoglycan is a meshwork macromolecule, made of polysaccharide strands cross-linked by short peptides, which encases the cytoplasmic membrane of bacteria and protects them against turgor pressure. Peptidoglycan peptidases are membrane or periplasmic enzymes that cleave these peptides, either lowering the cross-linking level of peptidoglycan to sculpt bacterial shape or allowing cell elongation by making space for the insertion of neosynthesized glycan strands. In the pathogen Helicobacter pylori, shape is important for virulence, and transition to a coccoid form after prolonged growth enables immune evasion. One particular endopeptidase, HdpA, is known to be involved in the maintenance of cell shape and in the transition to coccoids. Here we show that along growth, HdpA is constantly associated with LhiA, an inner membrane chaperone lipoprotein that keeps it in check while protecting it from fast proteolysis. The crystal structure of the HdpA-LhiA complex suggests that this interaction freezes the autoinhibitory interaction between the first domain of HdpA and the third, catalytic domain. Analysis of the evolution of the HdpA and LhiA protein levels over growth suggests that transition to coccoids is not triggered by a burst in HdpA activity but rather by a gradual weakening of the sacculus caused by the small fraction of free HdpA in equilibrium with LhiA-sequestered HdpA. SIGNIFICANCE STATEMENTThe cell wall, the exoskeleton of bacteria, is the target of numerous antibiotics. Its principal component, peptidoglycan, is remodeled by an interplay between peptidoglycan synthases and hydrolases to accomodate bacterial growth. Because their activity can be harmful, hydrolases have to be tightly regulated. We discovered the dedicated inhibitory chaperone of a H. pylori peptidoglycan hydrolase and showed how the chaperone keeps the hydrolase in check in the cytoplasmic membrane and releases it slowly to allow it to perform its task, ultimately triggering a shape transition to a spherical form important for immune evasion. The crystal structure of the complex gives clues to the mechanism of peptidase activation, suggesting strategies to design agonists that could be used as antibacterials.

microbiology↗

bioRxiv2025

Arm and head domain in highly conserved lipoprotein modification enzyme Lgt determine functional diversity among bacterial pathogens

Lipoproteins are important components of the bacterial cell envelope that itself is an excellent target for antibiotics. The post-translational lipoprotein modification pathway is conserved in bacteria in which prolipoprotein phosphatidylglycerol diacylglyceryl transferase (Lgt) catalyses the first and committed step. Due to its essentiality for cell viability in proteobacteria its membrane localisation and relative accessibility, Lgt is proposed as promising target for the development of novel antibiotics. To answer the question of the degree of conservation between Lgt homologues of WHO-listed pathogenic species we performed evolutionary, structural and functional analyses. Our data show that Lgt is present in all bacteria and absent from archaea. Alpha Fold structural models are similar to the X-ray structure of Lgt from E. coli with most variability and less conserved residues in the arm- and head domains. Lgt of proteobacteria but not of firmicutes restore growth and viability of a Lgt depletion strain in E. coli. Sequence alignments and site-directed mutagenesis demonstrate that unique conserved residues on arm-2 together with histidine 103 determine protein substrate specificity. This large-scale analysis led to the definition of a 13-residue Lgt motif and an alternative catalytic mechanism. Our results highlight similarities in catalytic mechanism and differences in substrate specificity between Lgt homologues from pathogenic species with impact on strategies to develop narrow-spectrum antibiotics targeting Lgt. Author summaryAntimicrobial resistance is a major threat to public health for which novel targets to develop new therapies is urgently needed. The bacterial lipoprotein modification pathway is promising for exploration of new antibiotics since it is unique to bacteria, it is essential for bacterial viability and virulence, and it is accessible to drugs due to the exposed domains of the modification enzymes. In this study we explored large-scale sequence analysis, structural modelling and functional assays of the first enzyme in the pathway. Our findings show that the enzyme is highly conserved across distant phyla, that homologous enzymes have similar structures and contain a signature motif composed of invariant essential residues, but functional conservation divides monoderm and diderm pathogenic bacteria. This correlates with structural variation and differences in substrate specificity, illustrating the potential for the development of narrow spectrum antibiotics targeting the lipoprotein modification pathway.

microbiology↗

bioRxiv2021

PGfinder, a novel analysis pipeline for the consistent, reproducible and high- resolution structural analysis of bacterial peptidoglycans

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan, the essential and major component of bacterial cell envelopes. It is comprised of glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGfinder for the analysis of peptidoglycan structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial peptidoglycans. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.

microbiology↗

bioRxiv2020

A secreted NlpC/P60 endopeptidase from Photobacterium damselae subsp. piscicida cleaves the peptidoglycan of potentially competing bacteria

Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. Here, it is described the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA (Photobacterium NlpC-like Protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the {gamma}-D-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp and neither PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and V. vulnificus. This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA, showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG. IMPORTANCEPeptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, originating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or joint its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either for gaining competitive advantages and/or to get nutrients. The specificity of PnpA to the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.

microbiology↗

bioRxiv2019

The impact of gut microbiota on depressive-like behaviors and adult hippocampal neurogenesis requires the endocannabinoid system

Depression is the leading cause of disability worldwide. Recent observations have revealed an association between mood disorders and alterations of the intestinal microbiota, but causality remains yet to be established. Here, using unpredictable chronic mild stress (UCMS) as a mouse model of depression, we show that the UCMS mice display phenotypic alterations -- characterized by an altered gut microbiota composition, a reduced adult hippocampal neurogenesis and a depressive-like behaviors -- which could be transferred from UCMS donors to naive recipient mice by fecal microbiota transplantation. The cellular and behavioral alterations observed in recipient mice were accompanied by a decrease in the endocannabinoid (eCB) signaling due to lower peripheral levels of fatty acid precursors of eCB ligands. The adverse effects of UCMS-transferred microbiota on adult neurogenesis and behavior in naive recipient mice were alleviated by selectively enhancing the central eCB tone or by adding arachidonic acid, a fatty acid precursor of eCB ligands, to the diet. In the gut of both UCMS donors and recipients, the microbiota composition was characterized by a relative decrease in Lactobacilli abundance, and complementation of the UCMS recipient microbiota with a strain of the Lactobacilli genus was sufficient to restore normal eCB brain levels, hippocampal neurogenesis and to alleviate depressive-like behaviors. Our findings provide a mechanistic scenario for how chronic stress, diet and gut microbiota dysbiosis generate a pathological feed-forward loop that contributes to despair behavior via the central eCB system.

neuroscience↗

bioRxiv2019

Innate immune recognition of a bacterial MAMP leads to conditional activation of pro- or anti-inflammatory responses

Microbe-associated molecular patterns (MAMPs) are recognized by pattern recognition receptors (PRRs) of the innate immune system. Flagellin, the primary component of bacterial flagella, is recognized by membrane TLR5 and cytoplasmic NLRC4 receptors, which promote a vigorous pro-inflammatory response typically associated with bacterial infection. However, herein, we report that the nature of the flagellin-induced response is highly dependent on the physiological state of the tissue. Specifically, in the steady state, epithelial cell detection of flagellin orchestrates an anti-inflammatory response mediated by IL-33-dependent type 2 regulatory T cells while, in the context of injury, it induces a pro-inflammatory response mediated by myeloid cells, IL-18 and Th17 cells. Likewise, in the absence of infection, bacterial symbionts expressing high levels of flagellin induce a type 2 response. These data demonstrate that, depending on the inflammatory state of the milieu, MAMPs can function both as immunogens or tolerogens.

immunology↗