Biology subjects

Berrios-Pasten, C.

Publications and source records attributed to Berrios-Pasten, C..

6 recordsLinked to original sources

bioRxiv2026

Linking immunity and nutrition: Vital DNA extracellular trap formation in Dictyostelium discoideum reveals an ancestral strategy for microbial management

Extracellular traps (ETs) were originally described in neutrophils as DNA-based structures that immobilize microbes and contribute to innate immunity. Subsequent studies revealed that ET formation occurs across diverse immune cell types and can proceed through non-lytic mechanisms involving mitochondrial DNA release. Whether ETosis also operates outside classical immune contexts and what its ancestral functions may be remain incompletely understood. Here, we show that vegetative, phagocytic cells of the social amoeba Dictyostelium discoideum, a professional bacterial predator with phagocytic mechanisms conserved with those of mammalian innate immune cells, deploy extracellular DNA traps in response to bacterial cues. ET formation is selectively induced by specific lipopolysaccharide variants, is not triggered by canonical neutrophil NET inducers, and occurs through a vital ETosis mechanism that preserves membrane integrity and feeding capacity. Ultrastructural analyses provide the first visualization of extracellular traps in Amoebozoa, revealing extracellular filamentous networks that physically capture bacteria. Molecular characterization demonstrates that amoeboid ETs are enriched in mitochondrial DNA and harbor a dynamic proteomic repertoire dominated by mitochondrial components, DNA-associated proteins, and multiple antibacterial effectors. Notably, ET composition varies with the bacterial stimulus, indicating that ETs are not static structures but rather responsive extracellular assemblies. Together, these findings establish ET formation as a regulated response in a unicellular phagocyte and suggest that extracellular traps may have originally functioned in microbial management during feeding, prior to their elaboration as immune effectors in multicellular organisms. HighlightsO_LIVegetative Dictyostelium discoideum cells deploy mitochondrial DNA-based extracellular traps in response to bacterial cues. C_LIO_LIET formation occurs through a vital, non-lytic mechanism that preserves membrane integrity and feeding capacity. C_LIO_LIExtracellular traps exhibit stimulus-dependent composition and are enriched in mitochondrial and antimicrobial proteins. C_LIO_LIETosis functions as an ancestral strategy for microbial containment and management beyond canonical immune contexts. C_LI

microbiology↗

bioRxiv2026

Intrinsic class C extended-spectrum β-lactamases mediate resistance to oxyimino-cephalosporins in Antarctic Pseudomonas fluorescens complex bacteria

From a One Health perspective, identifying environmental reservoirs of antibiotic resistance determinants with potential clinical relevance is increasingly important. Among resistance mechanisms, {beta}-lactamases are of particular concern because they compromise the efficacy of {beta}-lactam antibiotics, the most widely used class in clinical practice. Antarctic soils harbor thousands of putative {beta}-lactamase genes, yet the functional properties and resistance contributions of these enzymes remain largely unexplored. Here, we investigated the distribution, diversity, and functional impact of intrinsic class C {beta}-lactamases (AmpC-type) in Antarctic members of the Pseudomonas fluorescens species complex, a lineage widely distributed in Antarctic soils and increasingly recognized as an opportunistic pathogen of humans, animals, and plants. Genome-scale analyses revealed that class C {beta}-lactamases are intrinsic, widespread, and highly diverse within this lineage. Phenotypic assays demonstrated that Antarctic isolates exhibit elevated resistance to {beta}-lactam antibiotics, particularly oxyimino-cephalosporins such as cefotaxime and ceftazidime, and that this phenotype is largely attenuated by {beta}-lactamase inhibition. Heterologous expression of selected Antarctic AmpC variants in a susceptible Escherichia coli host confirmed their ability to increase minimum inhibitory concentrations to oxyimino-cephalosporins. Notably, several Antarctic {beta}-lactamases harbor amino acid substitutions previously associated with extended-spectrum AmpC (ESAC) variants, including M174L and N346I, while others display broader substrate profiles despite lacking known ESAC-associated signatures. Comparative analyses further showed that the sequence diversity of Antarctic class C {beta}-lactamases exceeds that reported for clinical PDC variants from Pseudomonas aeruginosa. Together, these findings provide functional evidence that pristine Antarctic environments constitute reservoirs of naturally occurring class C {beta}-lactamases with extended-spectrum potential. Our results highlight the evolutionary depth and functional diversity of environmental {beta}-lactamases and underscore the importance of incorporating remote ecosystems into One Health-oriented antimicrobial resistance surveillance frameworks.

microbiology↗

bioRxiv2025

A structure-guided pipeline to uncover the underexplored beta-lactamases from Antarctic and Subantarctic soil microbiota

As the One Health approach points out, the environment can significantly affect human health, particularly having diverse and profound implications in the ongoing antimicrobial resistance crisis. One central aspect is the potential role of environmental microorganisms as a source of resistance genes that could emerge among pathogens aided by horizontal transfer. In this context, previous reports showed that the Antarctic soil microbiota hosts a rich resistome, including putative beta-lactamases conferring resistance to beta-lactams, the most widely used antibiotics for treating bacterial infections worldwide. However, the diversity of beta-lactamases across different areas of Antarctica and Subantarctic islands and their associated microbiota remains largely unexplored. In this study, we analyzed an extensive collection of Antarctic soil metagenomes, applying a novel bioinformatic pipeline based on combining sequence identity and structural similarity criteria to search for bona fide distant beta-lactamase orthologs. We found several classes and families, with a notable predominance of class-B metallo-beta-lactamases, including proposed novel families and variants of known families. The beta-lactamase diversity and dominant classes varied across sites following changes in the microbial community, observing three main sample groups: 1) Subantarctic islands, 2) Antarctic Peninsula and surrounding islands; and 3) Cold-desert environments. The most prevalent beta-lactamases corresponded to subclass B3. We reconstructed more than 3500 metagenome-assembled genomes (MAGs) and searched for beta-lactamases among them. The main taxa encoding the beta-lactamases were Pseudomonadota and Bacteroidota. Moreover, a certain proportion of beta-lactamases was associated with mobile genetic elements, especially integrons and insertion sequences, suggesting their potential dissemination by horizontal transference. This evidence reinforces the role of the environment, and especially (sub)Antarctic soils, as a reservoir of resistance genes, in particular, beta-lactamases.

bioinformatics↗

bioRxiv2025

Pseudomonas species from Antarctica and other environments host diverse genes encoding structurally conserved polyhydroxyalkanoate synthases linked with different mobile genetic elements

Polyhydroxyalkanoates (PHAs) are industrial microbial biopolymers offering a sustainable and biodegradable alternative to petroleum-based plastics. The PHA polymerization process is primarily mediated by PHA synthases (PhaCs), which determine the molecular and physical properties of the synthesized polymers. Previous reports have described Antarctic Pseudomonas isolates with unique PhaCs and capabilities for PHA production. However, the genes encoding PhaCs in Pseudomonas from Antarctica and other environments have not been investigated systematically. Here, we studied the diversity and phylogenetic distribution of phaC genes in 186 Pseudomonas species, including 33 isolates from Antarctica. Most species encode two class II PhaCs, with some displaying additional class II and class I enzymes, especially in Antarctic isolates. Different PhaC subclasses were proposed based on this diversity. Some phaC genes are in putative genomic islands, phages, plasmids, or close to insertion sequences, supporting their acquisition by multiple routes of horizontal gene transfer. Remarkably, the Antarctic strain P. frigusceleri MPC6 harbors five PhaCs, including one from a potential novel class. These findings underscore the unique attributes and potential use of Antarctic Pseudomonas for biopolymer production. Future research is essential to elucidate the enzymatic properties of this underexplored PhaC diversity. Impact StatementA few Pseudomonas strains have been widely used to produce polyhydroxyalkanoates (PHAs), biopolymers constituting a sustainable alternative to petroleum-based plastics whose synthesis and properties primarily rely on PHA synthase enzymes (PhaCs). We showed that less-studied Pseudomonas species, especially from Antarctica, host a remarkable diversity of PhaCs, some likely acquired by horizontal transfer, including a potential novel class with yet-to-be-explored functional features and biotechnological potential.

microbiology↗

bioRxiv2022

Population genomics, resistance, pathogenic potential, and mobile genetic elements of carbapenem-resistant Klebsiella pneumoniae causing infections in Chile

Multidrug and carbapenem-resistant K. pneumoniae (CR-Kp) are considered critical threats to global health and key traffickers of resistance genes to other pathogens. In Chile, although a sustained increase in CR-Kp infections has been observed, few strains have been described at the genomic level, lacking molecular details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial resistance and performed a comparative genomics analysis of ten CR-Kp isolates from the Chilean surveillance of carbapenem-resistant Enterobacteriaceae. High resistance to most of the antibiotics tested was observed among the isolates, five ST25, three ST11, one ST45, and one ST505, which harbored a total of 44 plasmids, many of them predicted to be conjugative and carrying genes conferring resistance to a variety of antibiotic, metals, and disinfectants. Ten plasmids encoding either KPC-2, NDM-1, or NDM-7 carbapenemases were characterized, including novel plasmids with increased resistance gene load and a novel genetic environment for blaKPC-2 gene. This corresponds to the first report of ST25 and ST45 Kp producing NDM-7 in South America, and of an ST505 CR-Kp worldwide, producing both NDM-7 and KPC-2. Moreover, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for the detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of K. pneumoniae in Chile and South America.

microbiology↗

bioRxiv2020

Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae

The evolution of traits including antibiotic resistance, virulence, and increased fitness in Klebsiella pneumoniae and related species has been linked to the acquisition of mobile genetic elements through horizontal transfer. Among them, genomic islands (GIs) preferentially integrating at genes encoding tRNAs and the tmRNA (t(m)DNAs) would be significant in promoting chromosomal diversity. Here, we studied the whole set of t(m)DNAs present in 66 Klebsiella chromosomes, investigating their usage as integration sites and the properties of the integrated GIs. A total of 5,624 t(m)DNAs were classified based on their sequence conservation, genomic context, and prevalence. 161 different GIs and prophages were found at these sites, hosting 3,540 gene families including various related to virulence and drug resistance. Phylogenetic analyses supported the acquisition of several of these elements through horizontal gene transfer, likely mediated by a highly diverse set of encoded integrases targeting specific t(m)DNAs and sublocations inside them. Only a subset of the t(m)DNAs had integrated GIs and even identical tDNA copies showed dissimilar usage frequencies, suggesting that the genomic context would influence the integration site selection. This usage bias, likely towards avoiding disruption of polycistronic transcriptional units, would be conserved across Gammaproteobacteria. The systematic comparison of the t(m)DNAs across different strains allowed us to discover an unprecedented number of K. pneumoniae GIs and prophages and to raise important questions and clues regarding the fundamental properties of t(m)DNAs as targets for the integration of mobile genetic elements and drivers of bacterial genome evolution and pathogen emergence.

genomics↗