Biology subjects

Harms, A.

Publications and source records attributed to Harms, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular basis of the Druantia anti-phage defense system

Eukaryotes and prokaryotes have evolved diverse antiviral immune systems, many containing helicase modules central to defense. Druantia are widespread bacterial anti-phage defense systems, each built around a large helicase domain-containing protein, DruE, paired with variable subunits. Here, we investigate the molecular basis of a minimal two-protein module Druantia system, DruH-E. We demonstrate that DruH-E is sufficient to confer robust anti-phage defense. DruE exists in equilibrium between a monomer and an asymmetric dimer, with dimerization required for in vivo immunity. Cryo-EM structures define DruE asymmetric dimer assembly and its dsDNA unwinding mechanism, revealing a topologically closed architecture that is specifically activated by dsDNA substrates with a 3' overhang. We further identify DruH as an ssDNA-binding protein regulated by a metabolic switch, where its activity is inhibited by ATP at physiological concentrations through direct competition with ssDNA. Supported by mass spectrometry and single-cell microscopy data, we establish key determinants of the Druantia defense system and reveal how it mediates a direct antiviral immune mechanism.

microbiology↗

bioRxiv2026

Discovery of PilU as a second Type IV pilus retraction motor in Myxococcus xanthus

Type IV pili (T4P) drive social (S) motility in Myxococcus xanthus through cycles of extension and retraction powered by the ATPases PilB and PilT. Although the canonical retraction ATPase PilT is essential for force generation, M. xanthus encodes four PilT-like paralogs whose contributions to motility remain unclear. Here, we identify MXAN_1995 as the long-sought PilU protein that serves as a second T4P retraction motor. A frameshift mutation or deletion of pilU abolishes S-motility, while preserving pilus assembly and exopolysaccharide (EPS) production, phenocoping the pilT mutant. Single-cell analyses revealed that {Delta}pilU mutants exhibit rare, low-force movements, consistent with a role for PilU in force generation. Fluorescence microscopy showed PilU localizes predominantly to cell poles, similar to PilT; this localization is independent of PilT but partially dependent on core T4P assembly proteins. Notably, calcium differentially modulates motility, enhancing movement in wild-type cells while suppressing it in {Delta}pilU mutants, indicating a role for PilU under varying environmental conditions. Structural modeling, together with an intragenic suppressor, highlights a regulatory function for the intrinsically disordered C-terminal region of PilU. Together, our findings establish PilU as a secondary retraction ATPase and uncover a dual-motor retraction system that is environmentally responsive and mechanically tunable. ImportanceT4P are widespread motility and adhesion systems that enable bacteria to move, interact, and form multicellular communities. While the primary retraction ATPase PilT is well characterized, the function of additional PilT-like proteins remains unclear in many species. This work provides the first mechanistic characterization of PilU in Myxococcus xanthus, a model for multicellular behavior and T4P biology. We show that PilU is essential for productive T4P retraction, functioning as an accessory motor that enhances or stabilizes PilT-driven force generation. We further reveal that PilU activity is modulated by environmental calcium and depends on a flexible C-terminal region that influences motor complex dynamics. These findings uncover a dual-motor architecture that enables adaptive control of T4P retraction in response to environmental cues.

microbiology↗

bioRxiv2026

Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism

Successful viral infection requires efficient adsorption to the target cell, followed by membrane penetration for genome translocation into the host cytoplasm. Bacteriophage T4 initiates infection by binding to Escherichia coli receptors, triggering sequential conformational changes that culminate in genome delivery through viral channels spanning the host cell envelope. Here, we resolved structures of bacteriophage T4 at discrete stages. This revealed how long tail fiber extension affects the baseplate to initiate tail contraction, and the channel formation by the tape measure protein for genome translocation. We further demonstrate that the virus-encoded superinfection exclusion protein Imm binds to the tape measure protein to prevent secondary infections. Our findings offer insights into the coordinated process of genome delivery and phage-encoded superinfection exclusion proteins that prevent genome translocation.

microbiology↗

bioRxiv2026

DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity

Bacteria deploy diverse antiphage defense systems, including small bioactive molecules providing protection at the multicellular level. DNA-intercalating anthracyclines, such as daunorubicin, exhibit broad antiphage activity, but the underlying mechanism has remained elusive. Here, we systematically screened the Escherichia coli BASEL phage collection to elucidate the mode of action of DNA-intercalating antiphage molecules. We identified taxonomically distinct clusters of susceptible viral groups and show that, in T5-like phages (Markadamsvirinae), daunorubicin blocks infection after first-step transfer (FST). In the presence of daunorubicin, continued expression of pre-early genes leads to abortive infection via mutual destruction, where both phage and host succumb. Analogous abortive-infection phenotypes occur across taxonomically diverse phages exposed to chemically distinct DNA-intercalating molecules. Notably, we show that daunorubicin synergizes with downstream nucleic acid-targeting defenses underscoring context-dependent outcomes. Together, these findings reveal how chemical defense contributes to the multilayered antiviral immunity and highlight the intricate interplay between mechanistic inhibition and infection outcome.

microbiology↗

bioRxiv2025

Longitudinal Metabolomic Profiling of Biogenic Amines in Plasma and CSF, and Their Correlation, Reveals Sex-Specific and Age Changes in TgF344 Alzheimer's Disease Transgenic and Wildtype Rats

BackgroundAlterations in amine metabolism have been implicated Alzheimers disease (AD). Cerebrospinal fluid (CSF) and plasma are key biofluids in AD research. CSF is considered to better reflect brain metabolic alterations than plasma, while plasma can be obtained more easily. However, plasma-CSF relationships are unclear. AimTo investigate longitudinal changes of amines in plasma and CSF, and their correlation across the two, in male and female TgF344 AD transgenic versus wildtype (WT) rats. MethodLC-MS-based targeted metabolomics was used to analyze 60 and 55 amines in plasma and CSF, respectively, of male and female TgF344-AD and WT rats, at 12, 25, 50 and 85 weeks. Statistical analysis was performed using generalized logistic regressions, Pearson correlations, and differential correlations between groups and matrixes. ResultsCompared to WT controls, at 12 weeks, TgF344-AD rats showed an increase of 3-methylhistidine, anserine, cysteine, s-methylcysteine, while at 25 weeks, male TgF344-AD rats showed pronounced increases in CSF levels of alpha-aminobutyric acid, asparagine, glycylglycine, glycylproline, histidine, isoleucine, kynurenine, leucine, methionine, methionine sulfone, norepinephrine, phenylalanine, proline, tyrosine, and valine. At 50 weeks, female TgF344-AD rats exhibited reductions in CSF for DL-3-aminoisobutyric acid, gamma-aminobutyric acid, ornithine, and putrescine. Distinct plasma-CSF correlations were found for 1-methylhistidine, 2-aminoadipic acid, putrescine, kynurenine, N6,N6,N6-trimethyl-lysine, DL-3-aminoisobutyric acid, and taurine, particularly in TgF344-AD rats. ConclusionsBody fluid, age- and sex-dependent amine alterations in CSF and plasma of TgF344-AD rats compared to WT controls provide important insights into AD disease processes and may aid early diagnosis and therapeutic targeting.

systems biology↗

bioRxiv2025

Molecular insights into the dual activation of PomZ, a ParA/MinD P-loop ATPase, by the two ATPase activating proteins PomX and PomY

Positioning of the division site is precisely regulated. In Myxococcus xanthus, the PomX/Y/Z assembly associates with and translocates across the nucleoid in a PomZ ATPase-dependent manner to position the cytokinetic FtsZ-ring at midcell. Unlike other systems incorporating a ParA/MinD ATPase, the PomX/Y/Z system incorporates two ATPase Activating Proteins (AAPs), PomX and PomY, that stimulate PomZ activity. While PomX AAP activity, similarly to other characterized AAPs of ParA/MinD ATPases, resides in a short positively charged N-terminal peptide (PomXNPEP), the mechanism of PomY-mediated activation of PomZ remained unknown. We map PomY AAP activity to its C-terminal residues 496-682 (PomY496-682) and show that this activity is important for division site positioning and the initiation of cell division. Structural modeling suggests a bipartite PomY496-682 architecture, comprising a globular domain and an intrinsically disordered region containing the short 5 helix. However, modeling supported an interaction only between 5 and the PomZ dimer. The 5 binding site partially overlaps with that of the prototype AAP ParB on the ParA dimer but 5 lacks a positively charged residue critical for ParB AAP activity. Modeling supported that PomXNPEP binds the PomZ dimer at a site distinct from that of 5 and which overlaps with that of the prototype AAP MinE on the MinD dimer. These findings reveal a non-canonical AAP mechanism of PomY, while PomXNPEP likely functions analogously to MinE, indicating that PomX and PomY act in concert through distinct but complementary mechanisms to stimulate PomZ ATPase activity, thereby efficiently driving the positioning of the cytokinetic FtsZ-ring. ImportanceIn bacteria, the regulatory systems that position the division site often incorporate a ParA/MinD ATPase. These ATPases also function in the positioning of numerous other macromolecular complexes in bacteria. Characteristically, these ATPases depend on stimulation of their ATPase activity by a single cognate ATPase activating protein (AAP). However, the Myxococcus xanthus cell division regulatory system PomX/Y/Z system stands out by incorporating two AAPs, PomX and PomY, that activate the PomZ ATPase. Similar to other AAPs, PomX uses a short, positively charged N-terminal peptide (PomXNPEP) to stimulate PomZ activity. We map PomY AAP activity to a C-terminal region spanning residues 496-682 (PomY496-682). Structural modeling using AlphaFold 3 supports that the AAP activity of PomY496-682 and PomXNPEP involves two distinct, non-overlapping binding sites at the dimer interface of ATP-bound PomZ. Altogether, these results provide insights into the molecular mechanism of the activation by two AAPs of a ParA/MinD ATPase.

microbiology↗

bioRxiv2025

Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ

The constant arms race of bacteriophages and their bacterial hosts has inspired major breakthroughs in biotechnology and shaped phages as fierce predators with great clinical potential to fight multidrug-resistant bacterial pathogens. However, the vast amount of genomic "dark matter" composed of genes of unknown function in phage genomes remains a major obstacle for the molecular understanding of phage-host interactions. Here we present HIDEN-SEQ, a transposon-insertion sequencing method for phages that systematically links viral genes to selectable phenotypes. Using model phage T4, we show that HIDEN-SEQ readily reproduces the gene essentiality map established over decades of research. Subsequently, we show that our method is easily portable to different phages far beyond classical laboratory models. Across a panel of bacterial hosts and growth conditions, HIDEN-SEQ reveals many conditionally essential phage genes, including previously unknown viral anti-defense factors that we could match to specific antiviral defenses of the respective hosts. Compared to analogous techniques, HIDEN-SEQ provides unprecedented depth and near base-pair resolution as well as great ease of use and portability. We therefore anticipate that HIDEN-SEQ will accelerate discoveries in phage biology by uncovering functions of viral dark matter with direct relevance for microbial ecology, biotechnology, and improvements of phage therapy.

microbiology↗

bioRxiv2025

Automated Bacteriophage Evolution Studies with the Aionostat

Bacteriophages, the viruses that infect bacteria, are the most abundant and diverse biological entities on our planet. They play a critical role in shaping ecosystems and are increasingly recognized for their potential in treating bacterial infections. Yet, our comprehension of their biology and evolutionary dynamics is limited, largely because research has concentrated on a select few well-characterized phages or relies on broad metagenomic studies with limited follow-up analysis of individual phages. This knowledge gap hinders our capacity to exploit their therapeutic and ecological possibilities - and while some studies have attempted to bridge it, such efforts typically require a lot of manual labor, highlighting the need for high-throughput, reproducible methods for in-depth study of phage evolution. To address this gap, we introduce the Aionostat, a novel automated continuous culture device designed to facilitate bacteriophage directed evolution experiments at scale. The Aionostats potential is showcased through two example experiments. In the first, phages from the BASEL collection rapidly adapted to a challenging E. coli strain, acquiring mutations and deletions that improved their infectivity. In the second experiment, we evolved a mixture of these phages on the same E.coli strain, leading to the emergence of recombinant phages with increased fitness. By automating these experiments, the Aionostat enables faster, more reproducible studies of phage evolution that would be impractical to perform by hand, thereby opening new avenues for investigating viral dynamics, engineering phage therapies, and studying evolutionary principles in broader biological contexts.

evolutionary biology↗

bioRxiv2024

Unlocking hidden phage diversity to complete the BASEL collection for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory) which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity had remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. These results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

microbiology↗

bioRxiv2024

Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems

Toxin-antitoxins (TAs) are prokaryotic two-gene systems comprised of a toxin neutralised by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilises the antitoxin by recognising its chaperone addiction (ChAD) element. TACs have been shown to mediate antiphage defence, but the mechanisms of viral sensing and restriction are unexplored. We identify and characterise two Escherichia coli antiphage TAC systems containing HigBA and CmdTA TA units, HigBAC and CmdTAC. The HigBAC is triggered through recognition of the gpV major tail protein of phage {lambda}. Both the ChAD and gpV are recognised by the HigC chaperone through analogous aromatic molecular patterns, explaining the mechanism of activation. We show that the CmdT ADP-ribosyltransferase toxin modifies mRNA to shut down protein synthesis. We establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with the HigC chaperone phage sensor. HighlightsE. coli HigBAC and CmdTAC are translation-targeting phage immunity TAC systems HigC chaperone recognises phage {lambda} major tail protein to trigger HigBAC toxicity CmdT ADP-ribosyltransferase toxin abrogates translation through modification of mRNA HigC combined with CmdTA yields hybrid broad-spectrum antiphage defence system

microbiology↗

bioRxiv2024

A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis

Phenotypic heterogeneity in bacteria results from stochastic processes or deterministic genetic programs. These deterministic programs often incorporate the versatile second messenger c-di-GMP, and by deploying c-di-GMP metabolizing enzyme(s) asymmetrically during cell division give rise to daughter cells with different c-di-GMP levels. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent genetic program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity switched on during cytokinesis, resulting in a dramatic but transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating mirror-symmetric, phenotypically similar daughters with correct motility behaviours. These findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations ensure the formation of dissimilar or similar daughter cells.

microbiology↗

bioRxiv2023

Phenotypic heterogeneity drives phage-bacteria coevolution in the intestinal tract

Phenotypic heterogeneity in bacteria can generate reversible resistance against various stressors, including predation by phages. This allows mixed populations of phenotypically resistant and sensitive bacteria to coexist with virulent phages. However, it remains unclear if these dynamics prevent the evolution of genetic resistance in bacteria and how they affect the evolution of phages. In this work, we focus on bistable alterations of the O-antigen (known as phase variation) in Salmonella Typhimurium (S.Tm) to study how heterogeneous phenotypic resistance affects phage-bacteria coevolution. Our findings reveal that phase variation allows a stable coexistence of S.Tm with a virulent T5-like phage in vitro. This coexistence is nevertheless short-lived when S.Tm and the phage interact within the intestinal tract of mice. In this context, the phage evolves to also infect phenotypically resistant S.Tm cells, incidentally altering infectivity on other Salmonella serovars. In return, the broader host range of the evolved phages drives the evolution of genetic resistance in S.Tm, which results in phage extinction. This work demonstrates that phenotypic heterogeneity profoundly influences the antagonistic coevolution of phages and bacteria, with outcomes intricately tied to the ecological context.

microbiology↗

bioRxiv2022

A phase-separated biomolecular condensate nucleates polymerization of the tubulin homolog FtsZ to spatiotemporally regulate bacterial cell division

Cell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social, predatory bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single large megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we studied the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization, suggesting a novel cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. PomY-nucleated FtsZ polymerization shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanisms ancient origin.

cell biology↗

bioRxiv2022

Phage Paride hijacks bacterial stress responses to kill dormant, antibiotic-tolerant cells

Bacteriophages are fierce viral predators with no regard for pathogenicity or antibiotic resistance of their bacterial hosts1,2. Despite early recognition of their therapeutic potential and the current escalation of bacterial multidrug resistance, phages have so far failed to become a regular treatment option in clinical practice3-5. One reason is the occasional discrepancy between poor performance of selected phages in vivo despite high potency in vitro3,4,6,7. Similar resilience of supposedly drug-sensitive bacterial infections to antibiotic treatment has been linked to persistence of dormant cells inside patients8,9. Given the abundance of non-growing bacteria also in the environment10,11, we wondered whether some phages can infect and kill these antibiotic-tolerant cells. As shown previously12-16, most phages failed to replicate on dormant hosts and instead entered a state of hibernation or pseudolysogeny. However, we isolated a new Pseudomonas aeruginosa phage named Paride with the exciting ability to directly kill dormant, antibiotic-tolerant hosts by lytic replication, causing sterilization of deep-dormant cultures in synergy with the {beta}-lactam meropenem. Intriguingly, efficient replication of Paride on dormant hosts depends on the same bacterial stress responses that also drive antibiotic tolerance. We therefore suggest that Paride hijacks weak spots in the dormant physiology of antibiotic-tolerant bacteria that could be exploited as Achilles heels for the development of new treatments targeting resilient bacterial infections.

microbiology↗

bioRxiv2021

Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity

Nucleotide-based signaling molecules (NSMs) are widespread in bacteria and eukaryotes, where they control important physiological and behavioral processes. In bacteria, NSM-based regulatory networks are highly complex, entailing large numbers of enzymes involved in the synthesis and degradation of active signaling molecules. How the converging input from multiple enzymes is transformed into robust and unambiguous cellular responses has remained unclear. Here we show that Escherichia coli converts dynamic changes of c-di-GMP into discrete binary signaling states, thereby generating heterogeneous populations with either high or low c-di-GMP. This is mediated by an ultrasensitive switch protein, PdeL, which senses the prevailing cellular concentration of the signaling molecule and couples this information to c-di-GMP degradation and transcription feedback boosting its own expression. We demonstrate that PdeL acts as a digital filter that facilitates precise developmental transitions, confers cellular memory, and generates functional heterogeneity in bacterial populations to evade phage predation. Based on our findings, we propose that bacteria apply ultrasensitive regulatory switches to convert dynamic changes of NSMs into binary signaling modes to allow robust decision-making and bet-hedging for improved overall population fitness.

microbiology↗

bioRxiv2021

A new sugar for an old phage: A c-di-GMP dependent polysaccharide pathway sensitizes E. coli for bacteriophage infection

Bacteriophages are ubiquitous parasites of bacteria and major drivers of bacterial ecology and evolution. Despite an ever-growing interest in their biotechnological and therapeutic applications, detailed knowledge of the molecular mechanisms underlying phage-host interactions remains scarce. Here, we show that bacteriophage N4 exploits a novel surface glycan, NGR, as a receptor to infect its host Escherichia coli. We demonstrate that this process is regulated by the second messenger c-di-GMP and that N4 infection is specifically stimulated by the diguanylate cyclase DgcJ while the phosphodiesterase PdeL effectively protects E. coli from N4-mediated killing. PdeL-mediated protection requires its catalytic activity to reduce c-di-GMP and includes a secondary role as a transcriptional repressor. We demonstrate that PdeL binds to and represses the promoter of the wec operon, which encodes components of the ECA exopolysaccharide pathway. However, only the acetylglucosamine epimerase WecB but none of the other ECA components is required for N4 infection. Based on this, we postulate that NGR is an N-acetylmannosamine-based carbohydrate polymer that is produced and exported to the cell surface of E. coli in a c-di-GMP dependent manner where it serves as a receptor for N4. This novel carbohydrate pathway is conserved in E. coli and other bacterial pathogens, serves as the primary receptor for a range of N4-like bacteriophages, and is induced at elevated temperature and by specific amino acid-based nutrients. These studies provide an entry point into understanding how bacteria use specific regulatory mechanisms to balance costs and benefits of highly conserved surface structures. ImportanceBecause bacterial surface glycans are in direct contact with the environment they can provide essential protective functions during infections or against competing bacteria. But such structures are also Achilles heels as they can serve as primary receptors for bacteriophages. Bacteria thus need to carefully control the exposure of conserved surface glycans to balance costs and benefits. Here, we identify a novel exopolysaccharide that is widely conserved in E. coli and is used by N4 and related bacteriophages as primary receptor. We demonstrate that the synthesis of NGR (N4 glycan receptor) is tightly controlled by the second messenger c-di-GMP in a highly specific manner and by a single diguanylate cyclase. These studies provide an example of how bacteria can alleviate the strong selective pressure imposed on them by bacteriophages entering through conserved surface structures by carefully regulating their synthesis and secretion.

microbiology↗

bioRxiv2021

Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism

Starting with a comprehensive generic reconstruction of human metabolism, we generated high-quality, constraint-based, genome-scale, cell-type and condition specific models of metabolism in human dopaminergic neurons, the cell type most vulnerable to degeneration in Parkinsons disease. They are a synthesis of extensive manual curation of the biochemical literature on neuronal metabolism, together with novel, quantitative, transcriptomic and targeted exometabolomic data from human stem cell-derived, midbrainspecific, dopaminergic neurons in vitro. Thermodynamic constraint-based modelling enabled qualitatively accurate and moderately quantitatively accurate prediction of dopaminergic neuronal metabolite exchange fluxes, including predicting the consequences of metabolic perturbations in a manner also consistent with literature on monogenic mitochondrial Parkinsons disease. These dopaminergic neurons models provide a foundation for a quantitative systems biochemistry approach to metabolic dysfunction in Parkinsons disease. Moreover, the plethora of novel mathematical and computational approaches required to develop them are generalisable to study any other disease associated with metabolic dysfunction.

systems biology↗

bioRxiv2021

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

microbiology↗