Biology subjects

Wahl, M.

Publications and source records attributed to Wahl, M..

10 recordsLinked to original sources

bioRxiv2026

Primordial endocrine cells uncouple sexual differentiation from sex-chromosomes

Sexuality among the animal kingdom is remarkably plastic, spanning from gonochorism to sequential or simultaneous hermaphroditism. Over 70 years ago, Charniaux-Cotton hypothesized that sexual plasticity in crustaceans is mediated by primordial cells present in both sexes, which differentiate into an androgenic gland (AG) only in males. Although AG engraftments can masculinize genetic females, it remained unclear whether this reflects long-term integration of donor cells within the host or activation of host primordial AG progenitors. Using the freshwater prawn as an exceptional case of sexual plasticity, where AG-cell transfer yields functional neo-males bearing only female sex-chromosomes, we show, through cellular-resolution approaches, that the AG arises from primordial cells present in every individual, indicating autosomal machinery of sexual differentiation completely independent from the sex-chromosomes.

developmental biology↗

bioRxiv2026

Regulatory landscapes and structural choreography of transcription initiation in spirochetes

Spirochaetota is a deeply rooted bacterial phylum of evolutionary and medical importance. We show that the spirochetal RNA polymerase (RNAP) has a diminished ability to melt promoters compared to its Escherichia coli counterpart. This deficiency is compensated by CarD and is not linked to the phylums natural resistance to the antibiotic rifampicin. CryoEM analysis revealed that the spirochetal RNAP disengages the -35 element during promoter unwinding, which contrasts with other bacterial RNAPs that release this element later during the initial transcription. Our research also details the unusually tight, non-sequence-specific binding of the spirochetal RNAP holoenzyme to DNA, which may be linked to the highly extended structure of the spirochetal nucleoid. We support these observations with a structural analysis of the dimeric holoenzyme non-specifically bound to DNA. Our results highlight the functional diversity of bacterial transcription systems and lay the foundation for understanding transcription regulation in pathogenic spirochetes.

molecular biology↗

bioRxiv2025

The co-localizing Zorya II, Druantia III, and ARMADA II defense systems on O-island 172 confer synergistic anti-phage defense in enterohemorrhagic Escherichia coli

In this study, we show that the enterohemorrhagic Escherichia coli (EHEC) strain EDL933 {Delta}stx1/2 is highly resistant to phages. The genes encoding the three phage defense systems Zorya II, Druantia III, and ARMADA II were found to co-localize on O-island 172 (OI-172) in EDL933. The three phage defense systems co-occur in 426 E. coli strains comprising 66 distinct serotypes, including 277 O157:H7 isolates and 117 diverse non-pathogenic strains. Efficiency of plating (EOP) assays were used to explore the phage spectrum and synergy of the three defense systems and their contribution to the phage resistance of strain EDL933 {Delta}stx1/2. Using {Delta}zorABE, {Delta}druHE, and {Delta}armABCD single system deletion mutants in EDL933 {Delta}stx1/2, we showed that Druantia III and ARMADA II protect to different extents against a broad spectrum of phages, including the Drexlerviridae, Siphoviridae, Demerecviridae, Vequintavirinae and Autographiviridae, but not against hypermodified Tevenvirinae. Additionally, Zorya II caused strong protection only against Autographiviridae. Furthermore, EOP assays of combined system mutants revealed strong synergistic interactions of Druantia III and ARMADA II to provide more robust immunity against a similar phage spectrum than the additive protection of the individual systems. In contrast, Druantia III and Zorya II act only weakly synergistically against a few phages. Altogether, our results revealed that Druantia III and ARMADA II are responsible for most of the phage resistance of EDL933 {Delta}stx1/2, whereas Zorya II provides additional immunity against podoviruses. Future studies are underway to elucidate the molecular basis of the synergistic interactions between the Druantia III and ARMADA II defense systems. IMPORTANCEShiga toxin-producing E. coli (STEC) O157:H7 strains cause life-threatening diseases, such as hemorrhagic colitis and the hemolytic uremic syndrome. Currently, EHEC infections can be only treated symptomatically, since antibiotics are not recommended due to induction of the Shiga toxin. While phage therapy could offer a treatment option, we show that the EHEC strain EDL933 {Delta}stx1/2 is highly resistant to many phages. EOP assays of defense mutants in the host strain revealed that the co-occurring defense systems Zorya II, Druantia III, and ARMADA II on OI-172 confer most of the phage resistance in EHEC. Moreover, our data uncovered that Druantia III and ARMADA II act synergistically in the anti-phage defense in EDL933 {Delta}stx1/2, explaining the robust immunity against a broad spectrum of phages. These results support the idea that the design of novel inhibitors against the Druantia III and ARMADA II systems could be combined with phage therapies to efficiently eradicate EHEC.

microbiology↗

bioRxiv2024

Identification and characterization of a synaptic active zone assembly protein

At presynaptic active zones (AZs), scaffold proteins play a crucial role in coordinating synaptic vesicle (SV) release and forming intricate nanoarchitectures essential for synaptic function. Despite their suspected importance, factors governing the assembly of nanoscale AZ scaffolds have remained elusive. Here, we identify "Blobby" as a novel regulator of AZ nanopatterning, localized within the AZ scaffold. Genetic loss of the extended Blobby protein led to aberrant accumulation of AZ scaffold proteins ("blobs") and disrupted the nanoscale architecture of the AZ scaffold, resulting in a significant reduction in the packing density of voltage-gated Ca2+ channels at AZs, as observed through intravital single-molecule imaging. This disruption correlated with decreased evoked synaptic currents and SV release probability. Our findings suggest that Blobby plays a crucial role in switching the AZ scaffold into a state which allows to fine-tune the dynamic nanopatterning of Ca2+ channels to maintain proper release.

neuroscience↗

bioRxiv2023

Concerted transformation of a hyper-paused transcription complex and its reinforcing protein

RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an -helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a {beta}-barrel, which binds the ribosome. Our structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life. HIGHLIGHTS- The nontemplate DNA strand of an ops-paused transcription complex forms a hairpin - Autoinhibited RfaH binds and twists the ops hairpin to expand the RNA:DNA hybrid - RfaH-hairpin contacts are solely responsible for triggering RfaH activation - Upon recruitment, RfaH hyper-stabilizes the pause and promotes RNAP backtracking

biochemistry↗

bioRxiv2023

Widespread gene regulator Psu inhibits transcription termination factor rho by forced hyper-oligomerization

Many bacteriophages modulate the host transcription machinery for efficient expression of their own genomes. Phage P4 polarity suppression protein, Psu, is a building block of the viral capsid and inhibits the hexameric transcription termination factor, {rho}, by presently unknown mechanisms. We elucidated cryogenic electron microscopy structures of {rho}-Psu complexes, showing that Psu dimers laterally clamp two inactive, open {rho} rings and promote their expansion to higher-oligomeric states. Systematic ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders {rho} ring closure and traps nucleotides in their binding pockets on {rho}. Structure-guided mutagenesis in combination with growth, pull-down and termination assays further delineated the functional {rho}-Psu interfaces. Bioinformatic analyses suggested that, in addition to guarding its own genome against {rho}, Psu enables expression of diverse phage-defense systems commonly found in P4-like mobile genetic elements across bacteria. Thus, Psu is a widespread gene regulator that inhibits {rho} via forced hyper-oligomerization.

molecular biology↗

bioRxiv2022

Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

Regulation and functionality of species-specific alternative splicing has remained enigmatic to the present date. Calcium/calmodulin-dependent protein kinase II{beta} (CaMKII{beta}) is expressed in several splice variants and plays a key role in learning and memory. Here, we identify and characterize several primate-specific CAMK2B splice isoforms, which show altered kinetic properties and changes in substrate specificity. Furthermore, we demonstrate that primate-specific Camk2{beta} alternative splicing is achieved through branch point weakening during evolution. We show that reducing branch point and splice site strengths during evolution globally renders constitutive exons alternative, thus providing a paradigm for cis-directed species-specific alternative splicing regulation. Using CRISPR/Cas9 we introduced a weaker human branch point into the mouse genome, resulting in human-like CAMK2B splicing in the brain of mutant mice. We observe a strong impairment of long-term potentiation in CA3-CA1 synapses of mutant mice, thus connecting branch point-controlled, species-specific alternative splicing with a fundamental function in learning and memory.

molecular biology↗

bioRxiv2022

CaMKII activity spreads by inter-holoenzyme phosphorylation

The dodecameric protein kinase CaMKII is expressed throughout the body. The alpha isoform is responsible for synaptic plasticity and participates in memory through its phosphorylation of synaptic proteins. Its elaborate subunit organization and propensity for autophosphorylation allow it to preserve neuronal plasticity across space and time. The prevailing hypothesis for the spread of CaMKII activity, involving shuffling of subunits between activated and naive holoenzymes, is broadly termed subunit exchange. In contrast to the expectations of previous work, we found little evidence for subunit exchange upon activation, and no effect of restraining subunits to their parent holoenzymes. Rather, mass photometry, crosslinking mass spectrometry, single molecule TIRF microscopy and biochemical assays identify inter-holoenzyme phosphorylation (IHP) as the mechanism for spreading phosphorylation. The transient, activity-dependent formation of groups of holoenzymes is well suited to the speed of neuronal activity. Our results place fundamental limits on the activation mechanism of this kinase.

biophysics↗

bioRxiv2021

Molecular Basis of Antibiotic Self-Resistance in a Bee Larvae Pathogen

Paenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays high antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for the N-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor in P. larvae by deactivation of paenilamicin. Using tandem MS, NMR spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as the N-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a new ribosome inhibitor. Here, we further elucidated the crystal structure of PamZ:acetyl-CoA complex at 1.34 [A] resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity of P. larvae to fight American Foulbrood.

biochemistry↗

bioRxiv2017

Quantitative analysis of population-scale family trees using millions of relatives

Family trees have vast applications in multiple fields from genetics to anthropology and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. Here, we collected 86 million profiles from publicly-available online data from genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of longevity by inspecting millions of relative pairs and to provide insights to population genetics theories on the dispersion of families. We also report a simple digital procedure to overlay other datasets with our resource in order to empower studies with population-scale genealogical data.\n\nOne Sentence SummaryUsing massive crowd-sourced genealogy data, we created a population-scale family tree resource for scientific studies.

genomics↗