Biology subjects

Damm, A.

Publications and source records attributed to Damm, A..

12 recordsLinked to original sources

bioRxiv2026

3D printing and deep learning enable holistic and dynamic analyses of tens of thousands of parasites infecting hundreds of genotypes

Host-parasite interactions are dynamic systems, where parasites usually outnumber hosts by one or more orders of magnitude. However, our understanding is often limited by the assessment of parts of the host, at arbitrary time points, and/or aggregate parasite responses. Here we combined custom-built 3D-printed hardware and deep-learning-based algorithms to enable holistic (i.e. all infecting individuals on the whole plant), spatio-temporal, and parasite-centric analyses of plant-parasitism by nematodes from timelapse videos of infection over months. In so doing, we tracked the dynamic growth and development of all individual parasites, at the organismal level, for thousands of hosts across hundreds of genotypes of Arabidopsis thaliana. Categorising traits into the static (i.e. in an acquired image at a given time point) and dynamic (i.e. phenotypic changes over time), we revealed a greater extent of host-genetic control of parasite traits, and new physiological limits of the species under these conditions. Using this capability, we identify Quantitative Trait Loci (QTL) in the host plant associated with 18 phenotypic traits in the parasite as a resource for the community. Finally, we leverage the large and diverse dataset to understand fundamental features of the parasite, independent of host genotype, revealing aspects of the life cycle which are pseudo-deterministic as well as local, deleterious interactions between co-infecting parasites. Given that plant-parasitic nematodes cause an estimated $100 billion in agricultural damages per year, these insights are contextualised in a global challenge driven by plant-parasitic nematodes.

pathology↗

bioRxiv2026

A transcription factor-pair work in concert to regulate gene expression across the life cycle of the pinewood nematode, Bursaphelenchus xylophilus

The migratory endoparasitic pinewood nematode (PWN), Bursaphelenchus xylophilus, is the causal agent of pine wilt disease, causing significant economic and ecological losses in conifer forest ecosystems in Europe and Asia. Understanding the molecular mechanisms regulating PWN parasitism-related genes may lead to new sustainable solutions for control. Based on previous PWN transcriptomic datasets from the pre-parasitic and parasitic stages and from the pharyngeal gland cells (GC), an in silico analysis was performed to identify transcription factors (TF) highly expressed in the GC. Seven candidates TF genes were selected, and their spatial expression validated by in situ hybridisation. From those, two GC-expressed TFs, BXY_079 and BXY_022, each encoding zinc finger domains, were successfully knocked down by RNA interference. Transcriptomic data from silenced BXY_079 and BXY_022 TFs, analysed with existing life cycle specific transcriptomic data, showed that both TFs control genes expressed at similar times, by repressing male-related genes while activating genes expressed during the J3 and D3 stages, yet each represents the extreme of the others minor function. In addition to these common roles, BXY_079 also activates parasitism-related genes in the J2 stage. These BXY_079-activated parasitism-related genes predominantly encode proteins with lytic functions, including secreted peptidases and glycoside hydrolases. Consistent with their proposed role in parasitism, these genes are highly expressed during the parasitic juvenile stages and are likely involved in nematode feeding, tissue penetration, and migration within the host. In contrast, BXY_022 also represses the expression of several genes related to the reproduction system, such as major sperm proteins and cytosolic motility proteins, particularly in the adult male stage. Taken together, both dual-functional TFs work together, non-redundantly, to regulate gene expression across the life cycle, while each is additionally specialised to regulate diverse and distinct gene sets: ranging from genes implicated in lytic parasitic functions to sexual dimorphism.

pathology↗

bioRxiv2026

Antagonistic action of a nuclear hormone receptor pair coordinates a switch from lytic to biotrophic effector production in a plant-parasitic nematode

Pathogens secrete overlapping and sequential waves of effectors to manipulate their host, and yet the regulators that conduct the ensemble are poorly understood. Here, we identify the Dorsal Gland Regulator DGR-1 in the beet cyst nematode Heterodera schachtii. DGR-1 controls the expression of 131 putative effectors, acting as a dual-functional switch that "switches off" early stage effectors involved in plant invasion, and "switches on" later stage effectors associated with biotrophic establishment in the host. Interestingly, DGR-1 works antagonistically with the only other known transcriptional regulator of effectors in plant-parasitic nematodes, the Subventral Gland Regulator-1 (SUGR-1), to coordinate this apparent switch from lytic to biotrophic effector production. Together, DGR-1 and SUGR-1 control the expression of nearly one half of all H. schachtii early-stage effectors, and over one fifth of effectors of any kind. The requirement to activate lytic effector functions in the cortex, and biotrophic effector functions in the vascular cylinder, suggests that this transcription factor pair must differentially respond to signals from the host. Consistent with this, we find that diffusates from the roots of A. thaliana Casparian strip mutant myb36/sgn3, which are enriched in molecules ordinarily restricted to the vascular cylinder, upregulate dgr-1, but not sugr-1, compared to Col-0. Taken together, these data indicate that H. schachtii responds to compartmentalised host-derived signals to appropriately regulate spatiotemporal effector expression during infection. Given that misregulating DGR-1 results in delayed development of parasitic nematodes in Arabidopsis and Mustard, strategies which impair effector regulation as a whole may hold promise for crop protection against these agriculturally important pathogens.

pathology↗

bioRxiv2026

Better late than never: the impact of hatching time on Heterodera schachtii parasitism

Plant-parasitic nematodes are a diverse, polyphyletic group of plant pathogens which can infect most plant tissues and all major crops. Amongst the most damaging clades are the cyst nematodes, which can remain dormant in the soil for decades as infection-competent, developmentally arrested, second-stage juveniles in eggs. Hatching is stimulated by a variety of factors. However, the impact of hatching factor responsiveness on nematode morphology, physiology, gene expression, and infection biology has not been explored. We examined the impact of hatching time on the beet cyst nematode, Heterodera schachtii. We found that late hatchers invaded host roots and established feeding sites in greater numbers than early hatchers. We demonstrate variation in baseline parasitism gene expression and in responsiveness of genes to effectostimulins, small, plant-derived molecules which upregulate parasitism genes. Three quarters of effectostimulin-induced transcriptional changes were also modulated, either positively or negatively, by hatching time. While there were no observable morphological differences between early and late hatching nematodes on the day of their emergence from the egg, the late hatchers displayed signs of faster utilisation of internal energy reserves after 7 days at 4{degrees}C, as evidenced by less body area attributed to fat, than early hatchers. Finally, we found no evidence of substantive genetic differences between early and late hatchers, they were representative of a single population, despite the observed differences in infection, gene expression, and physiology. Taken together, non-genetic differences likely drive late hatchers to more rapidly utilise their internal energy reserves, to be more responsive to host-derived signals, and to be ultimately more infective than their early hatching counterparts.

molecular biology↗

bioRxiv2026

Using a planted tree biodiversity experiment to evaluate imaging spectroscopy for species classification

Field-based monitoring of tree species in forests is often sparse due to logistical constraints. Remote sensing enables repeated, spatially contiguous collection of reflectance data across large areas. Tree species classification accuracy using such data is variable, likely because most studies use observational datasets where species occurrence correlates with environmental variation. We used two sites of a tree biodiversity experiment in Germany (BIOTREE: Kaltenborn and Bechstedt), where different species have been planted with high replication under controlled diversity levels, to assess how well tree species could be classified using reflectance data from airborne imaging spectroscopy and different classification methods (linear discriminant analysis, LDA, and a non-linear support vector machine, SVM). Reflectance data for 589 wavelengths between 400-2400nm were acquired at 1m spatial resolution during peak growing season. Reflectance spectra showed large and significant variation between taxonomic classes, orders, and species, and weak, but still significant, interactions between classes or orders and diversity levels. Classification accuracy reached 100% in training datasets, 77%-83% for the four species in Kaltenborn prediction datasets, and 31%-49% for the 16 species in Bechstedt prediction datasets. LDA provided more accurate predictions than SVM; and using similarly-spaced original wavelengths with LDA was as efficient as using principal components derived from the original data. While airborne imaging spectroscopy effectively distinguished up to four tree species in our datasets, classification accuracy was lower when 16 species had to be distinguished. In these cases, the methodology may be more useful for functional diversity monitoring than for tree species classification.

ecology↗

bioRxiv2026

Lipid Droplet Targeting Drives Substrate Access during Very Long Chain Fatty Acid Activation by Fat1

Fatty acids, the most abundant building blocks for lipid synthesis, require conjugation with Coenzyme A (CoA) for their incorporation into membrane lipids. Of those, very long chain fatty acids (VLCFAs), the precursors of yeast ceramides, are particularly hydrophobic. Yet it remains unresolved where and how the sole VLCFA-CoA synthetase Fat1 activates them. Here we show that lipid droplets (LDs) are both the site of free VLCFAs storage, as well as their place of activation. Free VLCFAs preferentially partition into LDs in molecular simulations and in vitro reconstitutions, whereas Fat1 targets the LD surface in cells via a N-terminal amphipathic helix. Structural predictions identify an essential hydrophobic cavity in Fat1 that connects the active site to the membrane, suggesting that VLCFAs directly shuttle from the LD core into the enzymatic pocket. Our model explains how the organelle targeting of a fatty acid activator evolved to match the biophysical properties and consequently the subcellular localization of its highly hydrophobic substrate.

biochemistry↗

bioRxiv2024

Steric Repulsion Counteracts ER-to-Lipid Droplet Protein Movement

Lipid droplets (LDs) are uniquely shaped organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer, continuous with the cytosolic leaflet of the endoplasmic reticulum (ER). The dynamics and function of LDs are closely tied to their proteome composition, which is subject to dynamic remodeling. Key proteins essential for LD biology relocate from the ER to LDs, yet the mechanisms governing their movement and accumulation in LDs remain poorly understood. Here, we developed an innovative ex vivo tool to quantify and classify ER proteins based on their affinity for LDs. We found a broad spectrum of ER-to-LD partitioning affinities. We identified steric hindrance as a key factor in regulating ER-to-LD protein transfer, where proteins with only slightly higher LD affinity can effectively displace those with lower affinity from the LD surface. Consistent with this model, we observed that differentiation of 3T3 pre-adipocytes into adipocytes involves extensive remodeling of ER proteins targeting LDs, with Plin1--a high-affinity LD protein--becoming predominantly recruited and excluding other ER proteins. These findings highlight lateral protein-protein exclusion as a fundamental mechanism in shaping the LD proteome, providing new insights into LD biogenesis and function.

biophysics↗

bioRxiv2024

Mechanosensitivity of an ABC Membrane Transporter Revealed by Single Molecule FRET and Activity Measurement

While mechanosensitive ion channels gating has been well documented, the effect of membrane mechanics, in particular membrane curvature, on the function of transporters remains elusive. Since conical shape transmembrane proteins locally deform membranes, conversely membrane bending could impact their conformations and their function. We tested this hypothesis using BmrA, a bacterial ABC exporter that exhibits large conformational changes upon ATP hydrolysis, switching between open and closed states with opposite V-shapes. After reconstitution in liposomes of different curvatures, and at two different temperatures, we showed that BmrA ATPase activity decreases by 2.9-fold when their diameter decreases from 125 to 29 nm. Moreover, using single-molecule FRET, we observed that the fraction of closed conformations is reduced in highly curved vesicles when adding ATP or non-hydrolysable AMP-PNP. Our results are well explained by a theoretical 2-states model including the effect of membrane mechanics on protein shape transition. Our work reveals that the functional cycle of conical transporters is curvature sensitive, to an extent depending on protein geometry. Significance StatementBiological membranes actively regulate protein function. While some ion channels are known to sense membrane tension, whether transporters also respond to mechanical cues was unknown. We show that the conical-shaped bacterial exporter BmrA is sensitive to membrane curvature, with both its activity and conformation landscape determined by the surrounding lipid bilayer. This reveals a previously unrecognized mechanism of mechanosensitivity, suggesting that membrane geometry and transporter shape are intrinsically coupled, providing a general principle of regulation across biological systems.

biophysics↗

bioRxiv2024

The SUbventral-Gland master Regulator (SUGR) of nematode virulence

All pathogens must tailor their gene expression to their environment. Therefore, targeting host:parasite biology that regulates these changes in gene expression could open up routes to pathogen control. Here, we show that in the plant-parasitic nematode Heterodera schachtii, host signals (termed effectostimulins) within plant roots activate the master regulator sugr1. SUGR1, then, directly binds effector promoters, and orchestrates their production. Effector production, in turn, facilitates host entry, releasing more effectostimulins. These data show that gene expression during the very earliest stages of parasitism is defined by a feed forward loop for host entry. Importantly, we demonstrate that blocking SUGR1 blocks parasitism, underlining the SUGR1 signalling cascade as a valuable target for crop protection. Given that nematodes also parasitise humans and other animals, the potential impact is broad: disrupting effector production could, in principle, be applied to any pathogen that secrets effectors. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/576598v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@cebedaorg.highwire.dtl.DTLVardef@153fe87org.highwire.dtl.DTLVardef@16b6957org.highwire.dtl.DTLVardef@d0e920_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2024

The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 659 effector gene loci: 293 "known" high-confidence homologs of plant-parasitic nematode effectors, and 366 "novel" effectors with high gland cell expression. In doing so we define a comprehensive "effectorome" of a plant-parasitic nematode. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

plant biology↗

bioRxiv2023

The α/β hydrolase domain-containing protein 1 (ABHD1) acts as a lysolipid lipase and is involved in lipid droplet formation

Lipid droplets (LDs) are the major sites of lipid and energy homeostasis. However, few LD biogenesis proteins have been identified. Here, using Chlamydomonas as a model, we show that ABHD1, a member of the /{beta} hydrolase domain-containing protein family, is a novel type of LD-associated protein which stimulates LD formation through two distinct actions on the LD surface, one enzymatic and the other structural. ABHD1 was localized to LD surface in Chlamydomonas cells. The knockout mutants contained similar amounts of triacylglycerols (TAG) but their LDs showed an increased content in lyso- derivatives of the betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine (DGTS). Over-expression of ABHD1 in Chlamydomonas induced LD formation and boosted TAG content, suggesting a key role in LD biogenesis. The purified recombinant ABHD1 protein hydrolyzed lyso-DGTS, producing a free fatty acid and a glyceryltrimethylhomoserine moiety. In vitro experiments using droplet- embedded vesicles showed that ABHD1 promoted LD emergence. Taken together, these results identify ABHD1 as a new player in LD formation by its lipase activity on lyso-DGTS and by its distinct biophysical property. This study further suggests that lipases targeted to LDs and able to act on their polar lipid coat may be interesting tools to promote LD assembly in eukaryotic cells. Significant statementLipid droplets are subcellular organelles specialized for triacylglycerol storage. Their dynamic turnover is key to managing energy homeostasis in response to cell cycle states and environmental cues. To gain insights into LD biogenesis, we characterized a putative /{beta}- hydrolase (ABHD1) in the model algae Chlamydomonas reinhardtii and show it is located at the LD surface. We found that ABHD1 overexpression promotes LD formation and acts as a lipase mainly on lyso derivatives of the betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), the major lipid constituent of the LD hemi-membrane. We also show that ABHD1 has a remarkable biophysical property favoring LD budding. This work thus identifies a novel type of lipase acting on betaine lipid and provides a first example of a protein with a dual function nvolved in LD formation.

biochemistry↗

bioRxiv2021

Glutathione contributes to plant defense against parasitic cyst nematodes

Cyst nematodes (CNs) are an important group of root-infecting sedentary endoparasites that severely damage many crop plants worldwide. An infective CN juvenile enters the hosts roots and migrates towards the vascular cylinder, where it induces the formation of syncytial feeding cells, which nourish the CN throughout its parasitic stages. Here, we examined the role of glutathione (L-{gamma}-glutamyl-L-cysteinylglycine, GSH) in Arabidopsis thaliana upon infection with the CN Heterodera schachtii. Arabidopsis lines with mutations pad2, cad2, or zir1 in the glutamate-cysteine ligase (GSH1) gene, which encodes the first enzyme in the glutathione biosynthetic pathway, displayed enhanced CN susceptibility, but susceptibility was reduced for rax1, another GSH1 allele. Biochemical analysis revealed differentially altered thiol levels in these mutants that was independent of nematode infection. All GSH-deficient mutants exhibited impaired activation of defense marker genes as well as genes for biosynthesis of the antimicrobial compound camalexin early in infection. Further analysis revealed a link between glutathione-mediated plant susceptibility to CN infection and the production of camalexin upon nematode infection. These results suggest that GSH levels affects plant susceptibility to CN by fine-tuning the balance between the cellular redox environment and the production of compounds related to defense against infection.

plant biology↗