Paul A. Hoskisson

How conserved proteins acquire new physiological functions is a central question in molecular evolution. Rather than inventing new architectures, evolution often repurposes existing scaffolds, preserving core structural features while retuning the molecular logic that connects mechanism to physiology. Membrane transporters offer a powerful test of this principle because substrate selectivity, directionality, flux and energetic cost must be coordinated at the interface between the cell and its environment. The Amt/Mep/Rh superfamily controls one of the most fundamental requirements of cellular life: the movement of reduced nitrogen across biological membranes. Despite sharing a highly conserved ammonium-conducting pore, these proteins support distinct physiological roles, including nitrogen acquisition, sensing and homeostatic control. Here, we combined targeted mutagenesis, electrophysiology, yeast complementation and molecular dynamics simulations to define the transport logic of NeRh50, a bacterial Rhesus protein from the ammonia-oxidising bacterium Nitrosomonas europaea . We show that NeRh50 is not simply an AmtB-like ammonium importer. Instead, it uses the conserved Amt/Mep/Rh pore as a branched transport system in which inward uptake and export-linked transport can be separated genetically and mechanistically. Two conserved pore residues define this division of labour. A residue at the external entrance couples ammonium recruitment to productive inward uptake, whereas a second residue deeper in the pore enables a distinct transport mode required for substrate release when intracellular nitrogen accumulates. Thus, conserved Amt/Mep/Rh pore landmarks do not impose a single mechanism. Their local chemistry can be reassigned to generate different transport outputs, allowing NeRh50 to function as a reversible nitrogen valve. These findings reveal how minimal retuning within an ancient membrane-protein scaffold can rewire transport directionality and adapt nitrogen handling to ecological and physiological demand.

Nitrification is a major process in the global nitrogen cycle, initiated by the oxidation of ammonia to nitrite. The ammonia-oxidising bacterium Nitrosomonas europaea catalyses this first and rate-limiting step and depends on ammonium both as an energy substrate and as a nitrogen source, making ammonium acquisition central to its physiology. Cellular ammonium transport is mediated by the Amt/Mep/Rh superfamily, whose members share a conserved fold despite divergent physiological roles. Remarkably, N. europaea lacks a canonical prokaryotic Amt transporter and instead expresses NeRh50, a Rh-family protein proposed to have been acquired from a eukaryotic lineage. Here, we determine a cryo-EM structure of NeRh50 that reveals tightly associated lipids at the monomer–monomer interfaces, including density consistent with an unusual inverted lipid orientation. Native mass spectrometry and molecular dynamics simulations further support persistent lipid association at these interfaces. NeRh50 also differs functionally from canonical AmtB, selectively mediating electrogenic ammonium transport with ∼70-fold lower apparent affinity. Transport is enhanced under alkaline conditions but not by an imposed proton gradient, suggesting membrane-potential dependence. Together, these findings reveal divergence from canonical Amt proteins in both membrane-associated architecture and transport properties, providing insight into the functional and evolutionary diversification of the Amt/Mep/Rh superfamily.

The domestication of Streptomyces species for antibiotic production involves long-term, iterative mutagenesis and selection, yet the genomic changes driving enhanced production remain unclear. Analysis of five strains from an industrial lineage of Streptomyces clavuligerus using comparative genomics, transcriptomics and phenotypic profiling for dynamic genome architectures with plasmid integration events and chromosomal rearrangements, alongside the accumulation of mutations affecting metabolic pathways and global gene regulation. These changes increased precursor supply and reprogrammed transcription leading to enhanced clavulanic acid production but reduced catabolic flexibility. Complementation experiments confirmed the functional impacts of specific mutations. These findings reveal that artificial selection shapes genome evolution in industrial strains, balancing production gains with metabolic trade-offs. This work will likely inform rational design of Streptomyces strains for improved natural product production in industry while highlighting the constraints imposed by domestication on metabolic versatility. More broadly it shows that many of the evolutionary processes in industrial strain improvement programmes mirror those at play during natural selection.

Reshaping pathogen ecology in the Anthropocene

The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts—natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as ‘greenbeards’ (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.

Streptococcus suis is a Gram-positive bacterium with a dual role as a commensal member of the porcine nasal microbiota and a pathogen causing systemic disease in pigs and humans. Mounting evidence suggests that metabolism is a key driver of S. suis pathogenicity. Given the species' high genetic variability, we hypothesize that differences in metabolic networks could explain the diverse pathogenic phenotypes observed across different strains. To test this, we generated an atlas of over 3000 strain-specific and automatically curated genome-scale metabolic models that cover the breadth of pathogenic and commensal S. suis lineages. Using this model atlas, we performed the first species-level examination of metabolic traits in S. suis. Our simulations, supported by experimental validation, revealed three key insights. First, while metabolic traits are broadly conserved in S. suis, there are nevertheless lineage-dependent differences in amino acid auxotrophies and carbon utilization patterns that point towards distinct in vivo niches. Second, most strains are predicted to grow in different plausible in vivo environments regardless of their virulence phenotype, suggesting that metabolism is a weak barrier to systemic infection. Third, by systematically predicting reaction essentiality in more than 15 million reaction-strain-condition combinations, we identify a subset of 17 reactions, largely in nucleotide metabolism, that are conditionally essential in vivo and may serve as new targets for the development of new antimicrobials or vaccines. Overall, this study provides a valuable new resource for broadly examining S. suis metabolism and its role in pathogenicity.

Most antibiotics are derived from Streptomyces bacteria and produced industrially via fermentations relying on food-grade feedstocks, which have a substantial environmental impact. Efficient utilization of starch-rich organic wastes, such as bread and potato waste, as alternative feedstocks, remains limited by incomplete knowledge of starch metabolism in Streptomyces . Here, a genus-wide analysis of 295 Streptomyces strains was performed, identifying 645 amylases grouped into pullulanases, α -1,4-amylases and cyclomaltodextrin-like amylases, alongside biosynthetic gene clusters encoding amylase inhibitors such as acarbose and tendamistat. Structural and sequence analyses revealed that inhibitor resistance may arise from subtle modifications in the α -amylase catalytic pocket. This comprehensive analysis of amylases and inhibitors provides a foundation for engineering inhibitor-resistant enzymes tailored to diverse starch substrates, facilitating the development of sustainable, starch-based Streptomyces fermentations.

Members of the genus Streptomyces are prolific producers of antibiotics and bioactive natural products, whose biosynthesis is intricately linked to complex social and ecological interactions. Understanding how these bacteria adaptively regulate development and natural product biosynthesis in response to diverse environmental cues remains incomplete. Here, recent advances are synthesised revealing that phenotypic plasticity in Streptomyces is underpinned by regulatory networks integrating physiological and social signals, enabling multicellular differentiation, division of labour, and alternative growth modes such as exploration and foraging. These dynamic responses allow colonies to balance competition, cooperation, and reproduction in fluctuating environments. Our insights highlight the ecological and evolutionary significance of plasticity in shaping Streptomyces biology, with implications for natural product discovery and understanding microbial community dynamics.

Antimicrobial resistance poses a major global health threat, often driven by empirical antibiotic use due to the relatively slow (24-72 h) diagnostic pathway for urinary tract infections (UTIs). Due to their low cost and ease of multiplexing, electrochemical biosensors offer a promising alternative. Herein, we report on the Microplate Dx RapidPlate platform, a rapid electrochemical impedance spectroscopy (EIS)-based approach for accelerated antibiotic susceptibility testing (AST) directly from urine samples, without pre-treatment. This report charts the evolution of the core EIS-based AST measurement from a laboratory prototype into a fully realized Alpha prototype platform with an accompanying 32-channel electrochemical cartridge designed specifically for interrogation of urine samples. A total of 89 clinically derived urine samples were evaluated at three clinical sites (U.K. and India), with results compared against standard methods (VITEK 2 and disk diffusion). The impedance-based RapidPlate system detected bacterial growth within 50 min and provided susceptibility profiles by 85 min, with 95% concordance to reference tests. Consistent performance was demonstrated across diverse clinical settings and organisms, including Escherichia coli and Klebsiella pneumoniae. The RapidPlate AST system has demonstrated great potential as a cost-effective, point-of-care tool for rapid AST, supporting and improving UTI management and antimicrobial stewardship.

Severe sepsis presents a critical healthcare challenge where rapid pathogen identification is vital for timely intervention.