Biology subjects

Herman, R.

Publications and source records attributed to Herman, R..

9 recordsLinked to original sources

bioRxiv2025

Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter

Pseudomonas aeruginosa PA01 is one of the major causes of disease persistence and mortality in patients with lung pathologies, relying on various host metabolites as carbon and energy sources for growth. The ict-ich-ccl operon (pa0878, pa0882, pa0883) in PAO1 is required for growth on the host molecule itaconate, a C5-dicarboxylate. However, it is not known how itaconate is taken up into P. aeruginosa. Here we demonstrate that a genetically linked tripartite ATP-independent periplasmic (TRAP) transporter (pa0884-pa0886), which is homologous to the known C4-dicarboxylate binding TRAP system, is essential for growth on itaconate, but not for the closely related C4-dicarboxylate succinate. Using tryptophan fluorescence spectroscopy we demonstrate that the substrate binding protein, IctP (PA0884), binds itaconate, but still retains higher affinity for the related C4-dicarboxylates. The structures of IctP bound to itaconate (1.80 [A]) and succinate (1.75 [A]), revealed an enclosed ligand binding pocket with ion pairing interactions with the ligand carboxylates. The C2 methylene group that is the distinguishing feature of itaconate compared to succinate is accommodated by a unique change in the IctP binding site from a Leu to Val, which distinguishes it from closely related C4-dicarboxylate binding SBPs. Together these data suggest that this transporter, which we name IctPQM, has duplicated from a canonical C4-dicarboxylate transporter and its evolution towards itaconate specificity enables this pathogen to now access a key metabolite for persistence in the host.

microbiology↗

bioRxiv2025

High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche

The skin microbiome is dominated by a few key genera, among which Staphylococcus is one of the most well-characterised. Recent studies have examined the roles of various Staphylococcus species such as S. epidermidis and S. hominis within broader skin microbial communities. However, these investigations often rely on isolates from multiple individuals and hence, limiting their ability to capture intra-community interactions. In this study, we focused on the axillary microbiome of a single healthy individual to characterise the genetic and functional diversity of resident Staphylococcus isolates. Using a low-cost, high-throughput DNA extraction and long-read whole genome sequencing pipeline, we generated complete genomes for 93 isolates spanning seven genetically distinct lineages across three major skin species. These comprised of one dominant with three additional lineages of S. epidermidis, two of S. hominis and one of S. capitis. Functional and metabolic analyses revealed species- and strain-specific features, suggesting potential metabolic cross-feeding and specialisation within this community, including within strains of S. epidermidis. These findings highlight the metabolic complexity and potential interdependence of staphylococci inhabiting a single skin site and the need for strain-level resolution of the community. The strains form part of the York Skin Microbiome (YSM) collection, a growing open biobank of genetically diverse skin isolates from matched individuals.

microbiology↗

bioRxiv2024

Revealing the diversity of commensal corynebacteria from a single human skin site

Our understanding of the skin microbiome has dramatically improved since the pioneering studies and the improvements in sequencing technologies. Species of the genus Corynebacterium are known to form a major part of the human skin microbiome but most detailed studies have focussed on other similarly prevalent genera like Staphylococcus and Cutibacteria. Prior to this study, there were few complete genomes for skin commensals of the genus Corynebacterium, with only 9 complete genomes available for the most commonly identified species C. tuberculostearicum. In this study we explored the genus Corynebacterium from a single body site by swabbing the axilla/underarm of 4 individuals and using a selective media to enrich for corynebacteria. We then generated whole genome sequencing data of these corynebacteria enriched isolates using long-read sequencing and subsequent bioinformatics analysis to reveal an unparalleled diversity of this genus from a single skin site. Through this approach, we obtained the closed genomes of 215 isolates, 154 derived from a single individual. With this genetic information, we were able to identify 7 different species including species previously not associated to the skin and two novel species provisionally named C. axilliensis and C. jamesii. We used pangenome analysis on 30 genetically distinct isolates spanning the 7 species to identify putative metabolic differences, antimicrobial resistance profiles, novel biosynthetic gene clusters (BGCs), prophages and phage defence systems. Our culture-based Nanopore sequencing approach has dramatically improved our overall knowledge of skin corynebacteria, and uniquely here also providing in-depth analysis from a single skin site, revealing a multitude of differences between the isolates. Here we not only improved our knowledge of axillary corynebacteria but also greatly expanded the publicly available number of cutaneous corynebacterial genomes complementing recent studies seeking to understand the diversity of skin corynebacteria.

microbiology↗

bioRxiv2024

Structural unification of diverse membrane-boundacyltransferases reveals a conserved fold that defines the Transmembrane Acyl Transferase (TmAT) superfamily

The movement of acyl groups across biological membranes is essential for many cellular processes. One major family of proteins catalysing this reaction are the acyl transferase family 3 (AT3) proteins, which form a pore to allow acyl-CoA to penetrate the membrane for transfer onto an extracytosolic acceptor molecule. Recent structures of the sequence-unrelated human heparan--glucosaminide N-acetyltransferase (HGSNAT) support a similar transmembrane acyl-group transfer mechanism. Here we demonstrate that both protein families contain a conserved 10-transmembrane helical fold with high structural and detectable sequence conservation around the acyl-CoA pore, supporting the previously proposed Transmembrane Acyl Transferase (TmAT) protein superfamily. In addition, we identify TmAT proteins, including the human Golgi sialate-O-acetyltransferase (CASD1), the human/fungal PIG-W/GWT1 enzymes and the bacterial vancomycin resistance protein VanTG, where the TmAT domains function has been largely unrecognised. We conclude that the TmAT fold represents an ancient architecture for transmembrane acyl-group transfer with important roles in the dynamic modification of glycans in diverse processes across the three domains of life.

biochemistry↗

bioRxiv2023

Interrogation of RNA-protein interaction dynamics in bacterial growth

Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.

microbiology↗

bioRxiv2022

Structure and function of BcpE2, the most promiscuous GH3-family beta-glucosidase for scavenging glucose from heterosides

Cellulose being the most abundant polysaccharide on earth, beta-glucosidases hydrolyzing cello-oligosaccharides are key enzymes to fuel glycolysis in microorganisms developing on plant material. In Streptomyces scabiei, the causative agent of common scab in root and tuber crops, a genetic compensation phenomenon safeguards the loss of the gene encoding the cello-oligosaccharide hydrolase BglC by awakening the expression of alternative beta-glucosidases. Here we reveal that the BglC compensating enzyme BcpE2 is the GH3-family beta-glucosidase that displays the highest reported substrate promiscuity able to release the glucose moiety of all tested types of plant-derived heterosides (aryl {beta}-glucosides, monolignol glucosides, cyanogenic glucosides, anthocyanosides, and coumarin heterosides). BcpE2 structure analysis highlighted a large cavity in the PA14 domain that covers the active site, and the high flexibility of this domain would allow proper adjustment of this cavity for disparate heterosides. The exceptional substrate promiscuity of BcpE2 provides microorganisms a versatile tool for scavenging glucose from plant-derived nutrients that widely vary in size and structure. Importantly, scopolin is the only substrate commonly hydrolyzed by both BglC and BcpE2 thereby generating the potent virulence inhibitor scopoletin. Next to fueling glycolysis, both enzymes thus also interfere with the plant defense mechanisms to fine-tune the strength of virulence.

biochemistry↗

bioRxiv2021

Predicting Bird Distributions Under Global Change

An introduction to predictive distribution modelling for conservation to encourage novel perspectives. The rapid pace and potentially irreversible consequences of global change create an urgent need to predict the spatial responses of biota for conservation to better inform the prioritization and management of terrestrial habitats and prevent future extinctions. Here, we provide an accessible entry point to the field to guide near-future work building predictive species distribution models (SDMs) by synthesizing a technical framework for the proactive conservation of avian biodiversity. Our framework offers a useful approach to navigate the challenges surrounding the large spatio-temporal resolution of datasets and datasets that favor hypothesis testing at broad spatio-temporal scales and coarse resolutions, which can affect our ability to assess the validity of current predicted distributions. We explain how to improve the accuracy of predictive models by determining the extent to which: 1) dispersal limitation impacts the rate of range shifts, 2) taxa are rare at their range limits, and 3) land use and climate change interact. Finally, we offer approaches to filling knowledge gaps by creatively leveraging existing methods and data sources. RESUMENUna introduccion a la modelizacion predictiva de la distribucion para la conservacion con el fin de fomentar nuevas perspectivas. El rapido ritmo y las consecuencias potencialmente irreversibles del cambio global crean una necesidad urgente de predecir las respuestas espaciales de la biota para la conservacion, con el fin de informar mejor la priorizacion y gestion de los habitats terrestres y prevenir futuras extinciones. Aqui proporcionamos un punto de entrada accesible al campo para guiar el trabajo del futuro proximo en la construccion de modelos predictivos de distribucion de especies (SDM), sintetizando un marco tecnico para la conservacion proactiva de la biodiversidad aviar. Nuestro marco ofrece un enfoque util para navegar por los retos que rodean a la gran resolucion espacio-temporal de los conjuntos de datos y a los conjuntos de datos que favorecen la comprobacion de hipotesis a escalas espacio-temporales amplias y resoluciones gruesas, lo que puede afectar a nuestra capacidad para evaluar la validez de las distribuciones predichas actuales. Explicamos como mejorar la precision de los modelos predictivos determinando hasta que punto 1) la limitacion de la dispersion influye en el ritmo de los cambios de area de distribucion, 2) los taxones son raros en los limites de su area de distribucion, y 3) el uso del suelo y el cambio climatico interactuan. Por ultimo, proponemos enfoques para colmar las lagunas de conocimiento aprovechando de forma creativa los metodos y fuentes de datos existentes.

ecology↗

bioRxiv2021

Exposure to fruit-flavoring during adolescence increases nicotine consumption and promotes dose escalation

The rise of e-cigarette popularity has sparked interest in the role of palatable flavors on nicotine use. Despite growing evidence that sweet flavorants enhance nicotine reward, their influence on nicotine consumption has not been studied extensively. In addition, the impact that flavored nicotine use in adolescence could have on nicotine reward and dependence in adulthood remains unclear. This study examined the role of flavored nicotine access on nicotine preference and consumption longitudinally, from adolescence to adulthood. Male and female adolescent mice preferred a fruit-flavored nicotine solution. However, only adolescent female mice with access to flavored nicotine consumed higher doses. Furthermore, while adolescent male mice escalated consumption of both flavored and unflavored nicotine, female mice only escalated when given access to flavored nicotine. As mice matured into adulthood, there was no evidence that a history of flavored-nicotine access altered preference for unflavored nicotine. However, when the nicotine concentration was reduced, mice that had consumed strawberry-flavored nicotine in adolescence maintained baseline nicotine consumption levels longer than mice that initiated nicotine use without flavor in adolescence. Finally, addition of fruit-flavorants into the nicotine solution during adulthood led to increased levels of nicotine consumption, regardless of previous flavored-nicotine access or of familiarity with the selected flavorant. These results indicate that flavorants increase nicotine consumption independent of life stage, possibly posing a disproportionate risk to adolescent females. Our results also point to an effect of adolescent flavored-nicotine use on nicotine dose maintenance in adulthood, which could have implications for the success of future quit attempts.

pharmacology and toxicology↗

bioRxiv2020

Biochemical and structural insights into the activation of PBP1b by the essential domain of FtsN

Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division PG synthesis localizes at mid-cell under the control of a multiprotein complex, the divisome. In Escherichia coli, septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. The region L75 to Q93 of FtsN (EFtsN) was shown to be essential and sufficient for its functioning in vivo but the specific target and the molecular mechanism remained unknown. Here, we show that EFtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its GTase activity. We also report the crystal structure of PBP1b in complex with EFtsN which provides structural insights into the mode of binding of EFtsN at the junction between the GTase and UB2H domains of PBP1b. Interestingly, the mutations R141A/R397A of PBP1b, within the EFtsN binding pocket, reduce the activation of PBP1b by FtsN. This mutant was unable to rescue {Delta}ponB-ponAts strain at nonpermissive temperature and induced a mild cell chaining phenotype and cell lysis. Altogether, the results show that PBP1b is a target of EFtsN and suggest that binding of FtsN to PBP1b contributes to trigger septal PG synthesis and cell constriction.

microbiology↗