Eva Bastida-Martínez

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 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.

Summary: Light‐induced carotenogenesis in Myxococcus xanthus is controlled by the B ₁₂ ‐based CarH repressor and photoreceptor, and by a separate intricate pathway involving singlet oxygen, the B ₁₂ ‐independent CarH paralogue CarA and various other proteins, some eukaryotic‐like. Whether other myxobacteria conserve these pathways and undergo photoregulated carotenogenesis is unknown. Here, comparative analyses across 27 Myxococcales genomes identified carotenogenic genes, albeit arranged differently, with carH often in their genomic vicinity, in all three Myxococcales suborders. However, CarA and its associated factors were found exclusively in suborder Cystobacterineae, with carA ‐ carH invariably in tandem in a syntenic carotenogenic operon, except for Cystobacter/Melittangium , which lack CarA but retain all other factors. We experimentally show B ₁₂ ‐mediated photoregulated carotenogenesis in representative myxobacteria, and a remarkably plastic CarH operator design and DNA binding across Myxococcales. Unlike the two characterized CarH from other phyla, which are tetrameric, Cystobacter CarH (the first myxobacterial homologue amenable to analysis in vitro ) is a dimer that combines direct CarH‐like B ₁₂ ‐based photoregulation with CarA‐like DNA binding and inhibition by an antirepressor. This study provides new molecular insights into B ₁₂ ‐dependent photoreceptors. It further establishes the B ₁₂ ‐dependent pathway for photoregulated carotenogenesis as broadly prevalent across myxobacteria and its evolution, exclusively in one suborder, into a parallel complex B ₁₂ ‐independent circuit.

Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.

Distant cousin helps spot animal enzyme: In addition to forming the membranes that enclose cells, lipids are important signaling molecules. Plasmalogens, which contain a vinyl ether linkage, are an abundant group of lipids in animals. How these lipids are synthesized from precursors with an alkyl ether linkage has been a mystery. Gallego-García et al. found an enzyme, CarF, in the social bacterium Myxococcus xanthus that produces plasmalogens used in a signaling pathway for singlet oxygen, a marker of photooxidative stress. They then showed that the animal homolog could catalyze the final step in plasmalogen synthesis in bacterial and human cells, thus resolving a source for plasmalogens in animals. Science , this issue p. 128

Expression of CRISPR-Cas systems is a prerequisite for their defensive role against invading genetic elements. Yet, much remains unknown about how this crucial step is regulated. We describe a new mechanism controlling CRISPR-cas expression, which requires an extracytoplasmic function (ECF) σ factor (DdvS), its membrane-bound anti-σ (DdvA) and a global regulatory complex (CarD–CarG). Transcriptomic analyses revealed that the DdvS/CarD/CarG-dependent regulon comprises a type III-B CRISPR-Cas system in Myxococcus xanthus. We mapped four DdvS-driven CarD/CarG-dependent promoters, with one lying immediately upstream of the cas cluster. Consistent with direct action, DdvS and CarD–CarG localize at these promoters in vivo. The cas genes are transcribed as a polycistronic mRNA that reads through the leader into the CRISPR array, a putative σ^A-dependent promoter in the leader having negligible activity in vivo. Consequently, expression of the entire CRISPR-Cas system and mature CRISPR-RNA (crRNA) production is DdvS/CarD/CarG-dependent. DdvA likely uses its large C-terminal domain to sense and transduce the extracytoplasmic signal triggering CRISPR-cas expression, which we show is not starvation-induced multicellular development. An ECF-σ/anti-σ pair and a global regulatory complex provide an effective mechanism to coordinate signal-sensing with production of precursor crRNA, its processing Cas6 endoribonuclease and other Cas proteins for mature crRNA biogenesis and interference.