Biology subjects

Wall, D.

Publications and source records attributed to Wall, D..

11 recordsLinked to original sources

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

C. elegans models of Alternating Hemiplegia of Childhood have dominant neuromuscular junction defects

Dominant missense mutations in ATP1A3, encoding a Na+, K+ ATPase -3 subunit, can cause Alternating Hemiplegia of Childhood (AHC), but how these mutations lead to AHC remains unclear. Here, we establish the first C. elegans AHC models by introducing AHC-causing ATP1A3 patient mutations (D801N, E815K, L839P, and G947R) into the orthologous gene, eat-6, using CRISPR/Cas9. Homozygous C. elegans AHC model animals have recessive developmental defects. Heterozygous AHC model animals have dominant defects in neuromuscular junction (NMJ) function that are inconsistent with haploinsufficiency and dominant sleep or arousal defects. Previous work in a Drosophila G755S AHC model found that loss of a K-dependent, Na/Ca{superscript 2} exchanger exacerbated neuronal defects. We introduced a loss-of-function allele of the orthologous C. elegans gene, ncx-4, into C. elegans AHC models; loss of ncx-4 function did not consistently alter C. elegans AHC model defects across alleles. Our results establish novel C. elegans models of AHC with robust phenotypes, demonstrate that AHC mutations disrupt NMJ function, and provide proof-of-concept for discovering cross-species modifiers of AHC-related phenotypes. Summary StatementWe report the first C. elegans models of Alternating Hemiplegia of Childhood. D801N, E815K, L839P, and G947R AHC model animals have recessive development defects and dominant neuromuscular defects.

neuroscience↗

bioRxiv2026

Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities

Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.

microbiology↗

bioRxiv2025

Experimental evolution of promiscuous kin recognition from a homotypic specific cell surface receptor

Recognizing the difference between self and nonself is a crucial step in the development of multicellularity. Myxococcus xanthus is a model organism for studying these processes during the transition from single cell to multicellular life. The polymorphic cell surface receptor TraA helps to mediate these transitions by directing cooperative behavior toward kin or clonemates. TraA is a highly specific receptor, capable of recognizing other TraA proteins with identical or nearly identical sequences by homotypic binding, but the molecular basis of recognition is poorly understood. In this study, we designed a targeted TraA library, consisting of thousands of variants, which changed 10 predicted specificity residues. By screening this library, we identified TraA variants with different combinations of substitutions that resulted in altered recognition, often leading to promiscuous TraA-TraA binding. Additionally, we identified key residues that dictate specificity between distant TraA groups and showed that changing these residues altered the recognition specificity. Furthermore, we propose a model to explain how TraA recognition specificity evolved through the generation of intermediate promiscuous variants driven by reward/punishment interactions. Our results highlight the malleable nature of the TraA variable domain involved in specificity, shedding light on the molecular and evolutionary basis of social recognition in M. xanthus.

microbiology↗

bioRxiv2025

Acquired CRISPR spacers and rhamnose-glucose polysaccharide defects confer resistance to Streptococcus mutans phage ΦAPCM01

Streptococcus mutans is a major cause of dental caries worldwide. Targeted therapeutic strategies to eradicate S. mutans include oral phage rinses. In this study, we investigated how phage resistance develops in S. mutans. As a model phage, we used {phi}APCM01, which is known to infect a serotype e strain. We isolated and sequenced the genomes of 15 spontaneous resistant mutants and found that 10 had acquired novel CRISPR spacers targeting the phage, with a total of 18 new spacers identified. Additionally, eight strains contained mutations in rhamnose-glucose polysaccharide (RGP) biosynthetic genes, three of which also acquired spacers. Only the rgp mutants exhibited defects in phage absorption, supporting the role of these cell surface glycans as the phage receptor. Mutations in rgpF and the newly identified gene rgpX led to severe cell division defects and impaired biofilm formation, the latter of which shared by the rgpD mutant. Thus, rgp mutations confer phage resistance but impose severe fitness costs, limiting pathogenic potential. Surprisingly, we found that {phi}APCM01 was capable of binding to and injecting its genome into UA159, a model serotype c strain. However, UA159 was resistant to infection due to an unknown post-entry defense mechanism. Consequently, {phi}APCM01 has the potential to infect both major serotypes associated with dental caries. RepositoriesThe genome sequence of Streptococcus mutans DPC6143 was deposited at NCBI with the accession number NZ_CP172847.1.

microbiology↗

bioRxiv2025

Mechanism of bacterial outer membrane exchange revealed by quantitative microscopy

Kin recognition, the ability to distinguish self from nonself at the cellular level is critical to multicellular life. Myxococcus xanthus is a multicellular bacterium that cooperates among genetically-related cells and reduces exploitation by nonkin through outer membrane exchange (OME) of common goods and toxins. The polymorphic cell surface receptor called TraA and its partner protein TraB mediate kin recognition by OME, but its molecular mechanism remains unknown. Here we show that TraAB induce OME by overcoming the repulsive interaction between cells. Using quantitative microscopy techniques, we determined that TraA and TraB form complexes at a 1:1 ratio and that as few as one intercellular TraAB-TraAB dimer is sufficient to induce OME. We visualized the OME of single protein particles between cells and revealed that OME depends on the free diffusion of outer membrane (OM) contents. Our findings suggest a mechanism that shows analogies to the eukaryotic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), which mediate plasma membrane fusion. M. xanthus OME provides a novel pathway that leads to an underlying conserved mechanism for membrane fusion that is a foundation process for multicellularity.

microbiology↗

bioRxiv2024

Chimeric aggregative multicellularity in absence of kin discrimination

Aggregative multicellularity is a cooperative strategy employed by some microorganisms. Unlike clonal expansion within protected environments during multicellular eukaryotic development, an aggregation strategy introduces the potential for genetic conflicts and exploitation by cheaters, threatening the stability of the social system. Myxococcus xanthus, a soil-dwelling bacterium, employs aggregative multicellularity to form multicellular fruiting bodies that produce spores in response to starvation. Studies of natural fruiting bodies show that this process is restricted to close kin or clonemates. Here, we investigate the mechanisms underlying kin recognition during development in M. xanthus. By co-culturing two distantly related M. xanthus strains under vegetative and starvation conditions, we observed that the strains segregate in both contexts. During vegetative growth, one strain antagonized the other using the type VI secretion system (T6SS). T6SS-mediated antagonism was also observed during development, resulting in monoclonal fruiting bodies when WT strains were mixed. In contrast, mixtures of T6SS knockout strains formed chimeric fruiting bodies, that produced viable spores from both strains. These findings suggest that T6SS is the primary mechanism of kin discrimination in distantly related M. xanthus strains, and its use ensures the development of monoclonal fruiting bodies and social integrity.

microbiology↗

bioRxiv2023

Community structure of known and previously unknown endobacteria associated with spores of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant root symbionts which can house two endobacteria: Ca. Moeniiplasma glomeromycotorum (CaMg) and Ca. Glomeribacter gigasporarum (CaGg). However, little is known about their distribution and population structure in natural AMF populations and whether AMF can harbour other endobacteria. We isolated AMF from two environments and surveyed the surface-sterilized spores for endobacteria. We found that CaMg and CaGg differed significantly in distribution whereby CaMg were extremely abundant (80%) and CaGg were extremely rare (2%) in both environments. Unexpectedly, we discovered an additional and previously unknown level of bacterial diversity within AMF spores which extended beyond the known endosymbionts, with as many as 277 other bacterial taxa detected in individual spores. Detailed analysis of endobacterial communities inside AMF spores revealed that: (i)CaGg were not limited in distribution to the Gigasporacea family of AMF, as previously thought, (ii) CaMg community structure was driven by AMF host genotype, (iii) a significant inverse correlation existed between the diversity of CaMg and diversity of all other endobacteria. The latter suggests the existence of competition dynamics between different bacterial populations inside AMF spores and provides a basis for generation of testable hypotheses regarding the function of CaMg in AMF biology.

microbiology↗

bioRxiv2022

Global monitoring of soil animal communities using a common methodology

Here we introduce the Soil BON Foodweb Team, a cross-continental collaborative network that aims to monitor soil animal communities and food webs using consistent methodology at a global scale. Soil animals support vital soil processes via soil structure modification, direct consumption of dead organic matter, and interactions with microbial and plant communities. Soil animal effects on ecosystem functions have been demonstrated by correlative analyses as well as in laboratory and field experiments, but these studies typically focus on selected animal groups or species at one or few sites with limited variation in environmental conditions. The lack of comprehensive harmonised large-scale soil animal community data including microfauna, mesofauna, and macrofauna, in conjunction with related soil functions, limits our understanding of biological interactions in soil communities and how these interactions affect ecosystem functioning. To provide such data, the Soil BON Foodweb Team invites researchers worldwide to use a common methodology to address six long-term goals: (1) to collect globally representative harmonised data on soil micro-, meso-, and macrofauna communities; (2) to describe key environmental drivers of soil animal communities and food webs; (3) to assess the efficiency of conservation approaches for the protection of soil animal communities; (4) to describe soil food webs and their association with soil functioning globally; (5) to establish a global research network for soil biodiversity monitoring and collaborative projects in related topics; (6) to reinforce local collaboration networks and expertise and support capacity building for soil animal research around the world. In this paper, we describe the vision of the global research network and the common sampling protocol to assess soil animal communities and advocate for the use of standard methodologies across observational and experimental soil animal studies. We will use this protocol to conduct soil animal assessments and reconstruct soil food webs on the sites included in the global soil biodiversity monitoring network, Soil BON, allowing us to assess linkages among soil biodiversity, vegetation, soil physico-chemical properties, and ecosystem functions. In the present paper, we call for researchers especially from countries and ecoregions that remain underrepresented in the majority of soil biodiversity assessments to join us. Together we will be able to provide science-based evidence to support soil biodiversity conservation and functioning of terrestrial ecosystems.

ecology↗

bioRxiv2021

Emergent myxobacterial behaviors arise from reversal suppression induced by kin contacts

A wide range of biological systems - from microbial swarms to bird flocks, display emergent behaviors driven by coordinated movement of individuals. To this end, individual organisms interact by recognizing their kin and adjusting their motility based on others around them. However, even in the best-studied systems, the mechanistic basis of the interplay between kin recognition and motility coordination is not understood. Here, using a combination of experiments and mathematical modeling, we uncover the mechanism of an emergent social behavior in Myxococcus xanthus. By overexpressing cell surface adhesins, TraA and TraB, involved in kin recognition, large numbers of cells adhere to one another and form organized macroscopic circular aggregates that spin clockwise or counterclockwise. Mechanistically, TraAB adhesion results in sustained cell-cell contacts that trigger cells to suppress cell reversals, and circular aggregates form as the result of cells ability to follow their own cellular slime trails. Furthermore, our in-silico simulations demonstrate a remarkable ability to predict self-organization patterns when phenotypically distinct strains are mixed. For example, defying naive expectations, both models and experiments found that strains engineered to overexpress different and incompatible traAB allelles nevertheless form mixed circular aggregates. Therefore, this work provides key mechanistic insights into M. xanthus social interactions and demonstrates how local cell contacts induce emergent collective behaviors by millions of cells. ImportanceIn many species, large populations exhibit emergent behaviors whereby all related individuals move in unison. For example, fish in schools can all dart in one direction simultaneously to avoid a predator. Currently, it is impossible to explain how such animals recognize kin through brain cognition and elicit such behaviors at a molecular level. However, microbes also recognize kin and exhibit emergent collective behaviors that are experimentally tractable. Here, using a model social bacterium, we engineer dispersed individuals to organize into synchronized collectives that create emergent patterns. With experimental and mathematical approaches we explain how this occurs at both molecular and population levels. The results demonstrate how the combination of local physical interactions triggers intracellular signaling, which in turn leads to emergent behavior on a population scale.

biophysics↗

bioRxiv2019

Global distribution of earthworm diversity

Soil organisms provide crucial ecosystem services that support human life. However, little is known about their diversity, distribution, and the threats affecting them. Here, we compiled a global dataset of sampled earthworm communities from over 7000 sites in 56 countries to predict patterns in earthworm diversity, abundance, and biomass. We identify the environmental drivers shaping these patterns. Local species richness and abundance typically peaked at higher latitudes, while biomass peaked in the tropics, patterns opposite to those observed in aboveground organisms. Similar to many aboveground taxa, climate variables were more important in shaping earthworm communities than soil properties or habitat cover. These findings highlight that, while the environmental drivers are similar, conservation strategies to conserve aboveground biodiversity might not be appropriate for earthworm diversity, especially in a changing climate.\n\nOne sentence summaryGlobal patterns of earthworm diversity, abundance and biomass are driven by climate but patterns differ from many aboveground taxa.

ecology↗