Montserrat Elías-Arnanz

26th international Biometals Webinars Noncanonical peroxide stress response regulation in bacteria by the hydrogen peroxide-sensing metalloprotein PexR Redox processes are essential in all aerobic organisms, but they involve the formation of reactive oxygen species, such as hydrogen peroxide (H₂O₂), which cause oxidative stress when they exceed physiological levels. Cells combat H₂O₂ through peroxiredoxins and catalases, whose expression in bacteria is usually controlled by OxyR or PerR. The study of how a soil bacterium responds to H₂O₂ has revealed a novel regulatory mechanism, dependent on PexR, a "bacterial enhancer binding protein" widely spread among myxobacteria, which possibly also operates in other bacteria. The work, published in Nucleic Acids Research, has been carried out by Eva Bastida and Irene del Rey, under the direction of Profs. Montserrat Elías-Arnanz (University of Murcia) and S. Padmanabhan (IQF-CSIC, Madrid), with the collaboration of Prof. Catherine Drennan (MIT, USA) and Naike Ye. Through genetic, transcriptomic, biochemical and structural analyses, it has been shown that PexR binds ATP, forms oligomers and exerts a dual regulation essential for cell viability. Without H₂O₂ stress, PexR represses the expression of a peroxiredoxin from a promoter dependent on the primary sigma factor. H₂O₂ causes the expulsion of the metal attached to the N-terminal domain of PexR, freeing it from autoinhibition by this module and allowing it to activate the expression of a peroxiredoxin and a catalase, from promoters that are dependent on the alternative sigma54 factor. PexR exemplifies a H₂O₂ response mechanism beyond established paradigms and expands the toolkit for generating H₂O₂ biosensors. The superoxide dismutases as a model for studying metalloprotein evolution It is estimated that around one-third of all proteins in nature require an essential metal cofactor to function. This abundance of metalloproteins makes the understanding of the molecular mechanisms that determine the selectivity and specificity of metal-protein interactions relevant to every aspect of modern biology, medicine and biotechnology. Most metalloproteins exhibit cofactor specificity, possessing reduced, or even abrogated activity when associated with the ‘wrong’ metal cofactor in vitro and in vivo. We are studying a ubiquitous family of metal-dependent enzymes, the manganese/iron-dependent superoxide dismutases (SODs), to interrogate how cofactor specificity is controlled by the protein architecture and how such specificity evolves. Published data will be described that demonstrate how a pair of closely related SODs from Staphylococcus aureus have evolved different metal specificities that enable this pathogen to circumvent host-imposed manganese starvation that it experiences during infection. The value of this unique SOD pair as a model system with which to study the fundamental mechanisms by which proteins regulate the reactivity of their metal cofactor to give rise to specificity will be demonstrated. Data will then be presented showing that the ubiquitous SODs can be leveraged through bioinformatic, biochemical and structural studies to study how evolution can adjust metal specificity over time, giving rise to distinct enzymes with varying metal usage adapted to the metal availability experienced in its host’s niche.

Plasmalogens are a unique class of glycerophospholipids defined by a distinctive vinyl ether bond. While these lipids are abundant in animals and important for human health, their evolutionary history remains enigmatic, mostly due to their absence in some major eukaryotic lineages like plants. Here, we resolve the origin and evolution of the aerobic plasmalogen biosynthesis pathway in eukaryotes. Through comprehensive phylogenomic analysis and experimental validation of enzyme activity and plasmalogen presence, we demonstrate that the essential desaturase plasmanylethanolamine desaturase 1 (PEDS1)—and likely the fatty acyl-CoA reductase (FAR) and glycerone phosphate O -acyltransferase (GNPAT) enzymes also critical in the pathway—were acquired by an early eukaryotic ancestor through horizontal gene transfer (HGT) from myxobacteria. Our data show that this bacterial pathway was retained in the Amorphea and Discoba supergroups but lost or replaced in others. The findings yield insights into how HGT shaped metabolic pathways in early eukaryotes.

Cells combat peroxide stress using peroxiredoxins and catalases. The paradigmatic H2O2-sensing OxyR or PerR transcription regulators typically control their expression in bacteria. Here, we report our discovery of a noncanonical mechanism for H2O2-signaled regulation of peroxiredoxin ahpC and catalase katB genes in Myxococcus xanthus by PexR, an ATP-binding bacterial enhancer binding protein that acts as a dual-function repressor-activator. PexR, a dimer capable of higher-order oligomerization, binds to dyad-symmetry repeats upstream of ahpC and katB, activating their H2O2-induced σ54-dependent expression. Under peroxide stress-free conditions, PexR downregulates housekeeping σA-dependent ahpC expression. Deleting ahpC causes pleiotropy, and synthetic lethality when eliminated with katB or pexR, indicating PexR-mediated co-regulation of AhpC and KatB as critical for normal growth. We show that resting state PexR is autoinhibited by its N-terminal Zn2+/Fe2+-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) domain, which senses H2O2 and releases its bound metal to trigger PexR-activated σ54-dependent expression. Our genomic analyses reveal conservation of PexR and its regulatory elements and, likely, mechanism across Myxococcota, frequently co-occurring with OxyR or PerR, showcasing this phylum’s remarkable diversity of potential peroxide stress response regulatory mechanisms. Moreover, PexR likely operates in phyla beyond Myxococcota, and its discovery expands the toolkit for genetically encoded H2O2 sensors.

Plasmalogens, a unique class of membrane lipids defined by a distinctive vinyl ether bond, are critical for human health, with their altered levels linked to various diseases. Despite their importance, their origin and evolutionary history remain enigmatic. Here, we uncover the evolutionary history of the aerobic plasmalogen biosynthesis pathway in eukaryotes, focusing on the four essential enzymes responsible for their formation. Through comprehensive phylogenetic analyses and experimental validation, we demonstrate a significant divide in plasmalogen synthesis capabilities across major eukaryotic lineages. Our study also suggests that the acquisition of these plasmalogen biosynthesis genes by an early eukaryotic ancestor was through horizontal gene transfer (HGT) from Myxobacteria. The findings yield insights into how HGT shapes metabolic pathways and illuminate a critical step in the genesis of eukaryotic cell complexity.

From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.

How CRISPR-Cas and cyclic oligonucleotide–based antiphage signaling systems (CBASS) are coordinately deployed against invaders remains unclear. We show that a locus containing two CBASS and one type III-B CRISPR-Cas system, regulated by the transmembrane anti-σ DdvA and its cognate extracytoplasmic function (ECF) σ DdvS, can defend Myxococcus xanthus against a phage. Cryo–electron microscopy reveals DdvA-DdvS pairs assemble as arrow-shaped transmembrane dimers. Each DdvA periplasmic domain adopts a separase/craspase-type tetratricopeptide repeat (TPR)–caspase HetF–associated with TPR (TPR-CHAT) architecture with an incomplete His-Cys active site, lacking three α-helices conserved among CHAT domains. Each active site faces the dimer interface, raising the possibility that signal-induced caspase-like DdvA autoproteolysis in trans precedes RseP-mediated intramembrane proteolysis and DdvS release. Nuclear magnetic resonance reveals a DdvA cytoplasmic CHCC-type zinc-bound three-helix bundle that binds to DdvS σ ₂ and σ ₄ domains, undergoing σ ₄ -induced helix extension to trap DdvS. Altogether, we provide structural-mechanistic insights into membrane anti–σ-ECF σ regulation of an antiviral CBASS-CRISPR-Cas defense island.

Plasmalogens are glycerophospholipids with a vinyl ether bond that confers unique properties. Recent identification of the gene encoding PEDS1, the desaturase generating the vinyl ether bond, enables evaluation of the role of plasmalogens in health and disease. Here, we report that Peds1-deficient zebrafish larvae display delayed development, increased basal inflammation, normal hematopoietic stem and progenitor cell emergence, and cell-autonomous myeloid cell apoptosis. In a sterile acute inflammation model, Peds1-deficient larvae exhibited impaired inflammation resolution and tissue regeneration, increased interleukin-1β and NF-κB expression, and elevated ROS levels at the wound site. Abnormal immune cell recruitment, neutrophil persistence, and fewer but predominantly pro-inflammatory macrophages were observed. Chronic skin inflammation worsened in Peds1-deficient larvae but was mitigated by exogenous plasmalogen, which also alleviated hyper-susceptibility to bacterial infection, as did pharmacological inhibition of caspase-3 and colony-stimulating factor 3-induced myelopoiesis. Overall, our results highlight an important role for plasmalogens in myeloid cell biology and inflammation.

Myxococcus xanthus is the best-studied member of the phylum Myxococcota, but the bacteriophages infecting it and their characterization remain limited. Here, we present complete genomes of Mx1, the first Myxococcus phage isolated, and of an Mx4 derivative widely used for generalized transduction, both unclassified Caudoviricetes with long, contractile tails.

Plasmalogens are glycerophospholipids with a vinyl ether bond that confers unique properties. Recent identification of the gene encoding PEDS1, the desaturase generating the vinyl ether bond, enables evaluation of the role of plasmalogens in health and disease. Here, we report that Peds1-deficient zebrafish larvae display delayed development, increased basal inflammation, normal hematopoietic stem and progenitor cell emergence, and cell-autonomous myeloid cell apoptosis. In a sterile acute inflammation model, Peds1-deficient larvae exhibited impaired inflammation resolution and tissue regeneration, increased interleukin-1β and NF-κB activities, and elevated ROS levels at the wound site. Abnormal immune cell recruitment, neutrophil persistence, and fewer but predominantly pro-inflammatory macrophages was observed. Chronic skin inflammation worsened in Peds1-deficient larvae but was mitigated by exogenous plasmalogen, which also alleviated hyper-susceptibility to bacterial infection, as did pharmacological inhibition of caspase-3 and colony-stimulating factor 3-induced myelopoiesis. Overall, our results highlight an important role for plasmalogens in myeloid cell biology and inflammation. Keypoints: Plasmalogens are crucial for cell autonomous survival, recruitment and activation of neutrophils and macrophages. Plasmalogen production aids inflammation resolution, while supplementation reduces inflammation and boosts bacterial clearance.

Myxococcus xanthus is a social Gram-negative soil bacterium and the best studied member of the order Myxococcales in the class Deltaproteobacteria, which was recently reclassified as the phylum Myxococcota. Here, we report complete genomes, obtained using Illumina and PacBio sequencing, of M. xanthus strains DK1050 and DK101 (GenBank accession numbers CP104804 and CP104803, respectively).