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.

Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. Despite evidence to the contrary, DBDs are often assumed to be the primary mediators of transcription factor (TF) interactions with DNA and chromatin. Here, we used fast single-molecule tracking of transcription factors in living cells to show that short activation domains can control the fraction of molecules bound to chromatin. Stronger activation domains have higher bound fractions and longer residence times on chromatin. Furthermore, mutations that increase activation domain strength also increase chromatin binding. This trend was consistent in four different activation domains and their mutants. This effect further held for activation domains appended to three different structural classes of DBDs. Stronger activation domains with high chromatin-bound fractions also exhibited increased binding to the p300 coactivator in proximity-assisted photoactivation experiments. Genome-wide measurements indicate these activation domains primarily control the occupancy of binding rather than the genomic location. Taken together, these results demonstrate that very short activation domains play a major role in tethering transcription factors to chromatin. 

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.

Understanding why some traits are maintained whereas others are repeatedly lost is a central question in evolutionary biology. Here, we address this problem through an analysis of the evolutionary dynamics of autoregulation of the prfB, which encodes peptide-chain release factor 2 (RF2), a key factor in bacterial translation termination. RF2 recognizes UGA and UAA stop codons and catalyzes the release of the completed polypeptide. In many species, prfB contains an internal UGA stop codon, triggering premature translation termination by RF2 itself. Complete RF2 translation depends on a +1 programmed ribosomal frameshifting (PRF) event on the internal stop codon, which occurs more frequently when RF2 levels are low, resulting in autoregulation of prfB expression. While widespread, this autoregulatory mechanism has been lost in multiple bacterial lineages. We combined phylogenetics, experimental evolution and molecular genetics to investigate the evolutionary forces behind this loss. We found no significant correlation between PRF loss and stop codon usage using phylogenetically informed analyses, and PRF disruption in Pseudomonas fluorescens SBW25 had no detectable fitness effect. However, engineered mutations that reduced frameshifting caused fitness defects, which were compensated by two classes of mutation: (i) mutations that impair specific ribosomal proteins, and (ii) single-nucleotide deletions in prfB that adjust the reading frame and bypass the internal stop codon. These results suggest that compensatory mutations facilitate the loss of prfB autoregulation under RF2-limiting conditions. We discuss three potential scenarios that could account for this process.

Plants rely on specialized adaptive mechanisms to enhance resistance against environmental stress. One such mechanism, priming, enables faster and stronger defence responses upon subsequent stress exposure. This study examines whether the non-pathogenic Fusarium oxysporum Fo47 primes flax by colonizing roots and activating antioxidant defences. Flax plants primed with Fo47 and those treated with both Fo47 and the pathogenic strain F. oxysporum Foln were analysed for fungal colonization, PR genes expression and antioxidant systems: enzymatic (ROS metabolism-related genes expression, catalase and superoxide dismutase activity, hydrogen peroxide and superoxide anion levels) and non-enzymatic (phenolic compound content and antioxidant potential). The results demonstrate that Fo47 colonises host tissues, significantly reducing Foln penetration and colonisation, particularly in primed plants. Root-specific suppression of Foln by Fo47 was stronger than systemic suppression in shoots. Fo47 induced early chitinase and NADPH oxidases D transcript accumulation and reduced superoxide anion level in roots, likely triggering defence activation. Notably, Fo47 also activated both enzymatic and non-enzymatic antioxidant systems in shoots, suggesting a systemic priming effect. These findings underscore the potential of non-pathogenic F. oxysporum strains in sustainable plant protection strategies.