Biology subjects

Gomez, N. O.

Publications and source records attributed to Gomez, N. O..

5 recordsLinked to original sources

bioRxiv2026

Loss of restriction-modification methyltransferases drives persistence to fluoroquinolones in Pseudomonas aeruginosa

The resurgence of phage therapy has renewed interest in the interplay between phage resistance and antibiotic susceptibility and has stimulated research in the emergent field of non-canonical cellular functions carried out by defence systems. Yet it remains largely unknown whether intracellular antiphage defence systems influence bacterial physiology, resistance or persistence to antibiotics. Here we discovered that besides its canonical antiphage defence function, the type I restriction modification (RM) system profoundly affects the physiology of the opportunistic pathogen Pseudomonas aeruginosa. Deletion of the type I RM methyltransferase HsdM reduces the size of the bacterial nucleoid and delays DNA replication initiation and exit from lag phase in P. aeruginosa PAO1. Crucially, P. aeruginosa strains isolated from patients with cystic fibrosis (CF) and lacking the RM type I system also display slower growth compared to strains isolated from other sites of infections and encoding this system. Deletion of HsdM selectively increases the levels of persisters that survive treatment with fluoroquinolones by displaying enhanced SOS response but without acquiring resistance. Importantly, we measured elevated persistence to fluoroquinolones also in P. aeruginosa CF isolates lacking the type I RM system, providing a functional link between RM systems, slow growth and persistence to fluoroquinolones. Together these findings open a new way of approaching bacterial susceptibility to antibiotics, bringing antiphage defence systems in a forward-facing position in this field.

microbiology↗

bioRxiv2025

Pseudogenization of the cntQ permease confers distinct yersinopine-metal uptake selectivity in Yersinia species

Yersinopine, a nicotianamine-like metallophore, was recently identified through biochemical analyses, but its in vivo production and functional role remain uncharacterized. In Yersinia pseudotuberculosis and its recent descendant Yersinia pestis, the cnt operon (cntPQRLMI) putatively encodes the biosynthesis and transport of yersinopine. In Y. pestis, however, two frameshift mutations disrupt cntQ, which encodes the predicted permease for yersinopine-metal complexes. This pseudogenization raises critical questions about the functional relevance of yersinopine in these closely related species. Here, we show that cnt operon expression is repressed by the zinc uptake regulator Zur and that both Y. pestis and Y. pseudotuberculosis secrete yersinopine under zinc-limited conditions. Unexpectedly, the operon mediates iron uptake in Y. pseudotuberculosis but supports zinc acquisition in Y. pestis. Moreover, targeted disruption of cntQ in Y. pseudotuberculosis shifts metal specificity from iron to zinc, mimicking the Y. pestis phenotype. Collectively, our results suggest that a single pseudogenization event could rewire metal uptake specificity. Our findings illustrate how evolutionary genome reduction can reshape bacterial physiology.

microbiology↗

bioRxiv2025

Pseudopaline-mediated zinc uptake by Pseudomonas aeruginosa determines specific clinically relevant phenotypes and infection outcome

AUTHOR SUMMARYThe host-pathogen interface is a biological niche in which two entities competes for essential resources. The hosts nutritional immunity restrict access to metals, while a successful pathogen overcomes these restrictions using dedicated uptake pathways. Pseudopaline is a high-affinity metallophore allowing Pseudomonas aeruginosa to acquire zinc in chelated environments. We demonstrate that this pathway is the last-resort solution to acquire zinc for this dreadful pathogen. The capacity to provide this metal to zinc-metalloproteins drives clinically relevant phenotypes, such as the capacity to form a mature and antibiotic-tolerant biofilm, or to affect the outcome of an infection. These results place pseudopaline as a potential drug target for blocking P. aeruginosa pathogenic capacity and resensitizing established biofilm to classic antibiotic treatment. ABSTRACTBiological metals are essential trace elements which are required by metalloproteins, involved in virtually every cellular, structural and catalytic function of the bacterial cell. Bacterial pathogenesis involves a tug-of-war between the host nutritional immunity, sequestering essential metals and the invading pathogens that deploy high-metal affinity uptake strategies in order to overcome these defence mechanisms. Metallophores are high-affinity, low-molecular mass metal chelators produced and secreted by bacteria to access chelated metals from the environment. Pseudopaline is a metallophore produced and secreted by Pseudomonas aeruginosa to acquire zinc when the bioavailability of this metal is severely restricted, as in the presence of a strong metal chelator such as EDTA, or during infections when the nutritional immunity of the host is active, in mammals through the production of the zing binding protein calprotectin. We show that under the conditions of metal deprivation, a pseudopaline-deficient P. aeruginosa strain exhibit a severe intracellular zinc deficiency, establishing that the pseudopaline pathway is the last-resort and unique pathway for the bacteria to acquire zinc under these restricted growth conditions. The present study explores the pleiotropic role of pseudopaline-mediated zinc acquisition on several clinically relevant phenotypes and its capacity to drive infection outcomes, placing this machinery as a promising therapeutic target for P. aeruginosas infection, acting synergistically as a pathogenicity determinant as well as an adaptative trait allowing the establishment of a mature and antibiotic resistance biofilm necessary for recalcitrant chronic infections.

microbiology↗

bioRxiv2020

Involvement of the Pseudomonas aeruginosa MexAB-OprM efflux pump in the secretion of the metallophore pseudopaline

The ability for all organisms to acquire metals from their environment is essential for life. To overcome the metal restriction imposed by the hosts nutritional immunity, bacterial pathogens exploits the use of small high metal affinity molecules called metallophores. Metallophores are first synthetized in the cytoplasm, then secreted into the medium where they sequester the metal. The metal-metallophore complex is then imported into the bacterium following binding to dedicated cell surface receptors. Recently, a new family of metallophores has been discovered in pathogenic bacteria called staphylopine in Staphylococcus aureus and pseudopaline in Pseudomonas aeruginosa. Here, we are expending the molecular understanding of pseudopaline secretion/recovery cycle across the double-membraned envelope of the Gram-negative bacterium Pseudomonas aeruginosa. We first revealed that pseudopaline is secreted in a two-step process including export across the inner membrane by the CntI exporter followed by a specific transport across the outer membrane by the MexAB-OprM efflux pump. Such involvement of MexAB-OprM in pseudopaline secretion, reveal a new natural function that extends its spectrum of functions and therefore reasserts its interest as antibacterial target. We then addressed the fate of the recovered metal-loaded pseudopaline by combining in vitro reconstitution experiments using radio-labeled pseudopaline subjected to bacterial lysates, and in vivo phenotyping in absence of pseudopaline transporters. Our data support the existence of a pseudopaline degradation/modification mechanism, possibly involved in metal release following pseudopaline recovery. All together our data allowed us to provide an improved molecular model of secretion, recovery and fate of this important metallophore by P. aeruginosa. IMPORTANCEPseudopaline is a broad spectrum metallophore produced and used by Pseudomonas aeruginosa to supply the bacterium in metal in metal scarce environments. Here we are investigating the pseudopaline transport/recovery cycle across the bacterial envelope. We are first demonstrating that pseudopaline secretion in the medium is achieved by a specific efflux pump, usually dedicated to the release of toxic compounds such as antibiotics, thus revealing a new natural function for this efflux pump reasserting its interest as antibacterial target. Additional experiments also revealing the existence of an intracellular pseudopaline degradation mechanism providing new clues to another obscure step of the pseudopaline cycle which is the intracellular metal liberation from the imported metal-pseudopaline complex. All together our data allowed us to disclose important aspects of the secretion, recovery and fate of this essential molecule used by P. aeruginosa to survive during infections thus constituting new potential targets for antibacterial development.

microbiology↗

bioRxiv2017

Pseudopaline, a staphylopine-like metallophore involved in zinc and nickel uptake in Pseudomonas aeruginosa

Metal uptake is vital for all living organisms. In metal scarce conditions, a common bacterial strategy consists in the biosynthesis of metallophores, their export in the extracellular medium and the recovery of a metal-metallophore complex through dedicated membrane transporters. Staphylopine is a recently described metallophore distantly related to plant nicotianamine that contributes to the broad-spectrum metal uptake capabilities of Staphylococcus aureus. Here, we characterize a four genes operon (PA4837-PA4834) in Pseudomonas aeruginosa involved in the biosynthesis and trafficking of a staphylopine-like metallophore named pseudopaline. Pseudopaline differs from staphylopine with regard to the stereochemistry of its histidine moiety associated to an alpha ketoglutarate moiety instead of pyruvate. In vivo, the pseudopaline operon is regulated by zinc through the Zur repressor. The metal-uptake property of the pseudopaline system appears different from that of staphylopine with a predominant effect on nickel uptake, and on zinc uptake in metal scarce conditions mimicking a chelating environment, thus reconciling the regulation of the cnt operon by zinc with its function as a zinc importer under metal scarce conditions.\n\nAUTHOR SUMMARYZinc is an essential micronutrients for bacteria, particularly important at the host-pathogen interface where the host tends to sequester metals in a so called nutritional immunity framework, and the pathogenic bacterium increases its metal uptake efforts in order to keep up with its metal requirements. Here we reveal a novel metallophore, named pseudopaline, which is synthesized and exported by Pseudomonas aeruginosa and serves for the uptake of nickel in metal poor media, and for the uptake of zinc in metal scarce conditions that mimic the chelating environment that presumably prevails within a host.

microbiology↗