The dark-operative protochlorophyllide oxidoreductase (DPOR) catalyzes the light-independent reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key step in photosynthetic pigment biosynthesis. Structurally and mechanistically related to nitrogenase, DPOR consists of a reductase (BchL) and a catalytic component (BchNB) homologous to the reductase (NifH) and catalytic component (NifDK) of Mo-nitrogenase. Structural alignment of Rhodobacter capsulatus (Rc) BchNB with Azotobacter vinelandii (Av) NifDK and the cofactor maturase NifEN reveals a conserved α2β2 architecture and a shared cofactor-insertion path linking their respective prosthetic-like group/cofactors (Pchlide, M-cluster, L-cluster), suggesting the possibility of generating chimeric proteins with novel reactivities. Herein, Pchlide-free RcBchNB (RcBchNBapo) is reconstituted with the L-cluster extracted from AvNifEN to yield a hybrid protein (RcBchNBL) capable of reducing N2 and C1 substrates (CN−, CO) to NH3 and hydrocarbons, respectively, in the presence of a strong reductant (EuII-DTPA). In contrast, reconstituting Pchlide-bound RcBchNB with the L-cluster yields minimal activity, indicating that Pchlide and the L-cluster compete for a common binding site, as supported by Boltz-2 modeling. These findings support the hypothesis of an intertwined evolution of photosynthetic and nitrogen-fixing enzymes and outline a framework for engineering chimeric metalloenzymes that couple light capture with nitrogenase-like catalysis in the future.

Plasmids are key drivers of bacterial adaptation, yet the mechanisms that generate their diversity remain poorly understood. Here, we show that mobile genetic elements (MGEs) orchestrate a fusion-deletion life cycle that drives the emergence of multireplicon, multidrug-resistant plasmids in Staphylococcus aureus. Large-scale genomic analyses reveal that multireplicon plasmids are widespread and strongly enriched in transposases. Using experimental assays, we demonstrate that rare MGE-mediated fusion events, via homologous recombination or transposition, combine distinct plasmids into single multireplicon elements, expanding gene content and transfer potential. Antibiotic pressure selectively enriches these fused plasmids, rescuing bacterial populations under stress, whereas opposing selective forces, including phage predation, favor deletion derivatives that preserve essential functions and transmissibility. This cyclical process generates dynamic plasmid repertoires with conserved backbones and diverse accessory modules. We propose that MGE-driven fusion-deletion cycles represent a general principle of plasmid evolution, explaining the rapid emergence and persistence of multidrug-resistant plasmids across bacterial pathogens.

Antibiotics have revolutionized human health by significantly reducing morbidity and mortality associated with bacterial infections. Antibiotics exert bactericidal or bacteriostatic effects through inhibition of cell wall synthesis and disruption of cell membrane integrity, inhibition of protein, nucleic acid synthesis, and other metabolic pathways. Despite their remarkable success since the mid-20th century, antimicrobial resistance (AMR) has emerged as a major global health concern, undermining current treatments and complicating infection management. Key drivers of AMR include the overuse and misuse of antibiotics in clinical settings as well as bacterial adaptations such as genetic mutations and horizontal gene transfer. Mechanistically, these changes can lead to enzymatic inactivation of antibiotics, modification of drug targets, changes in permeability, and active efflux of antimicrobial agents. As resistance rises, antibiotic discovery and development have lagged, creating an urgent need for novel therapeutic strategies and chemical scaffolds. This review examines the antibiotic mechanisms and antibiotic evasion strategies, highlighting genetic and omics approaches used to identify high-priority targets for future drug discovery.

Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli delta-rimM strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this arrested state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a significantly longer delay in recovery than other 30S maturation factors, including RbfA - the presumed primary factor in 30S maturation. Cryo-EM analysis of delta-rimM ribosomes revealed a delayed recruitment of ribosomal proteins to the 30S head domain and increased occupancy of the initiation factors IF1 and IF3, as well as recruitment of the silencing factor RsfS to the 50S subunit. These coordinated changes provide a safeguarding mechanism to block the assembly of premature 70S ribosomes. Notably, while the delayed 30S assembly in delta-rimM reduces the activity of global protein synthesis during the recovery phase, bacteria attempt to compensate for this deficiency by producing higher levels of the ribosomal machinery, indicating a programmatic change in energy allocation to generate the ribosome machinery. These findings highlight the importance of the RimM-assisted assembly of the ribosomal head domain for bacterial recovery from growth arrest.

Microbial communities often rely on metabolic cooperation, especially under nutrient limitation, but how antibiotics influence these interactions remains unclear. Here, we show that exposure to chloramphenicol, a ribosome-targeting bacteriostatic antibiotic, promotes cooperation in auxotrophic Escherichia coli consortia. Using a proteome-partition model, we find that chloramphenicol-induced growth inhibition elevates levels of the alarmone ppGpp, shifting proteome allocation toward amino acid biosynthesis and export. This regulatory response enhances cross-feeding and supports cooperative growth, even under antibiotic stress. Laboratory experiments confirm that, under low amino acid availability, co-cultures of leucine and phenylalanine auxotrophs display greater tolerance to chloramphenicol than monocultures. Both our theoretical and experimental results reveal a feedback loop in which antibiotic stress strengthens metabolic interdependence, buffering growth inhibition and enhancing community-level tolerance.

The rapid global spread of antibiotic resistance is mediated by conjugative plasmids, yet how these elements establish immediately after entering new bacterial hosts remains poorly understood. Here we show that plasmids actively coordinate DNA processing with early gene expression to promote their own establishment. Using single-cell measurements of plasmid conversion dynamics, we demonstrate that the F plasmid selectively delays complementary strand synthesis within its leading region, creating a transient single-stranded DNA window that prolongs zygotic induction. This delay is imposed by a single-stranded DNA promoter that forms a structural roadblock to complementary strand DNA synthesis and is resolved by the host helicase UvrD. By extending the single-stranded state of the leading region, plasmids enhance early expression of protective genes that counter host defence responses and promote survival during entry, particularly in non-isogenic hosts. Together, these findings identify early post-entry regulation as a critical determinant of plasmid establishment and reveal how coupling DNA conversion to transient protective gene expression enables conjugative plasmids to overcome host barriers and disseminate antibiotic resistance.