Biology subjects

Parker, J. E.

Publications and source records attributed to Parker, J. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Arabidopsis cysteine protease RD19 limits RBOHD-generated ROS production in pattern triggered immunity

Plants perceive pathogenic threats through receptors localized at the plasma membrane and inside cells to initiate pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively. PTI and ETI pathways are interconnected and partially converge on the EDS1-PAD4-ADR1 branch which stimulates anti-pathogen defence. Besides these canonical immune pathways, proteolysis plays a pivotal role in immunity by regulating the abundance and activities of diverse components. We previously identified Arabidopsis papain-like cysteine protease RD19 as a PAD4 interactor and showed that RD19 promotes resistance to host-adapted pathogens. Here, we investigated the contribution of RD19 to bacterial flg22 and nlp20 elicited PTI responses which exhibit, respectively, partial and high PAD4 dependence. We show that although PAD4 and RD19 both promote PTI, they have separate functions. In resting (non-triggered) and nlp20-triggered tissues, RD19 limits RBOHD protein accumulation and consequently ROS production. Using N-terminomic enrichment and protease cleavage site identification methods we identify candidate RD19 substrates in resting and nlp20-responding tissues. Our analysis shows that two immune-related aspartyl proteases AED3 and AED2/ASPG1 are likely direct RD19 targets. This study reveals a role of RD19 in ROS regulation and advances our understanding of proteolysis and dynamic RD19 substrate targeting in plant immunity.

plant biology↗

bioRxiv2026

Conserved TIR-only proteins drive transcriptional defense and basal immunity in dicot and monocot plants

Toll/interleukin-1/resistance (TIR) domain NADase enzymes signal in plant immunity by producing ribosylated nucleotide second messengers which activate EDS1 dimer-helper NLR pathways to restrict pathogen growth. Members of a small, distinctive group of TIR-only proteins are conserved between dicots and monocots, yet their functions remain poorly understood. Here, we show that conserved TIR-only proteins in Arabidopsis and barley share a fundamental enzymatic role in promoting basal defense against virulent filamentous pathogens, independently of NLR mediated effector-triggered immunity. Metabolite analysis of transiently expressed Arabidopsis and barley TIR-only proteins revealed their capacity to produce ribosylated cyclic nucleotides in vivo. By comparing phenotypes of tir-only and eds1 pad4 CRISPR mutants in the two species, as well as adr1 mutants in barley, we established that the TIR-only proteins promote PAMP-triggered transcriptional defenses associated with pathogen restriction. Barley possesses just one essential TIR-only enzyme and mutations of the two conserved TIR-only members in Arabidopsis were not compensated for by numerous other TIR-domain genes in the basal immune response. These findings suggest that conserved TIR-only proteins make a crucial contribution to TIR basal defense signaling networks of Arabidopsis and barley. We propose that a shared function in transcriptional defense regulation could explain the evolutionary retention of this discrete TIR-only group across monocot and dicot lineages.

plant biology↗

bioRxiv2025

Small Molecule Binding to EDS1/PAD4 in LRR-RP-Mediated Pattern-Triggered Immunity

Pattern-triggered immunity (PTI) is a key defense mechanism initiated when pathogen-associated molecular patterns are recognized by receptors, including leucine-rich repeat receptor proteins (LRR-RPs)1,2. EDS1 and PAD4 are crucial for LRR-RP-mediated PTI activation3. Small molecule (SM) phosphoribosyl-AMP/ADP, generated by TIR-domain NADase activity, promote the recruitment of helper NLRs into EDS1-PAD4 complex4,5. Here, we show that BAK1 recruitment to LRR-RP complexes is unaffected in eds1-2 or pad4-1 mutants, but is abolished in the sobir1-12 mutant, highlighting the essential role of SOBIR1 in surface immune receptor complex formation. Furthermore, SM-binding to EDS1 and PAD4 is critical for LRR-RP-mediated PTI, as SM-binding-deficient mutants fail to restore immune responses. De novo SM synthesis is required for late PTI responses, including PR1 expression and bacterial resistance, but not for early responses such as ROS and ethylene production. The TNL SADR1 functions only in late PTI responses, suggesting distinct roles of multiple TIR-domain proteins in PTI signaling.

plant biology↗

bioRxiv2025

Reduced TRPC3 conductance underlies altered SNr activity under dopamine depletion: predictions from data-driven network models

Sufficient loss of dopamine within the basal ganglia (BG) leads to neuronal activity changes, including altered firing rates and firing patterns, thought to underlie parkinsonian motor symptoms. Yet, within BG neuronal populations, baseline activity and responses to inputs are highly variable, complicating efforts to identify key factors associated with pathological changes. We introduce a novel approach to constructing a computational neuron population model that, when applied to the mouse substantia nigra pars reticulata (SNr), captures the firing heterogeneity observed across slice and in vivo recordings. This model reproduces the diversity of SNr neuron responses to stimulation of GABAergic input terminals, yielding new insights into the mechanisms underlying this variability. Moreover, our modeling pinpoints significant decreases in TRPC3 conductance in SNr dendrites as a key determinant of altered SNr activity in the dopamine depleted state, with important implications for efforts to restore functional SNr activity in this condition. TeaserIn silico model capturing heterogeneity suggests factors behind SNr altered activity in dopamine depletion and responses to input

neuroscience↗

bioRxiv2025

Cooperation between a root fungal endophyte and host-derived coumarin scopoletin mediates Arabidopsis iron nutrition

O_LIIron acquisition is a critical challenge for plants, especially in iron-deficient soils. Recent research underscores the importance of root-exuded coumarins in modulating the root microbiome community structure and facilitating iron uptake. However, interactions between root-associated fungi and coumarins in plant iron nutrition remain unknown. We investigated the mechanism by which a fungal endophyte, Macrophomina phaseolina (F80), enhances Arabidopsis iron nutrition. C_LIO_LIFungal-coumarin interactions were assessed by profiling metabolites and measuring iron mobilisation in F80 cultures supplemented with specific coumarins, alongside quantifying growth performance and iron content in Arabidopsis coumarin-biosynthesis mutants inoculated with F80. C_LIO_LIOur findings reveal that an interaction between the coumarin scopoletin and F80 in the rhizosphere rescues plant growth under iron-limiting conditions by resolving the iron mobility bottleneck. F80 exhibits a capacity to modify scopoletin into iron-chelating catechol coumarin esculetin, thereby releasing available iron. C_LIO_LIWe conclude that Arabidopsis-produced scopoletin functions as a precursor for fungal conversion into iron-chelating coumarins. By extending the role of coumarins from bacterial to fungal members of the root microbiota, this study places coumarins at the centre of commensal-mediated enhancement of plant iron nutrition across microbial kingdoms. C_LI

plant biology↗

bioRxiv2025

GH25 lysozyme mediates tripartite interkingdom interactions and microbial competition on the plant leaf surface

Microbial communities inhabiting plants have emerged as crucial factors in regulating plant health and defense against disease-causing pathogens. The basidiomycete yeast Moesziomyces bullatus ex. Albugo on Arabidopsis (MbA) releases Glycoside Hydrolase 25 (GH25) protein which regulates the leaf microbiome by antagonizing an oomycete A. laibachii biotrophic pathogen MbA. Application of both MbA and GH25 protein rescued fresh shoot weight of A. thaliana upon A. laibachii infection, showing its potential in plant protection. Tripartite interaction assays did not reveal antagonistic activity of GH25 towards other plant pathogenic oomycetes or fungi besides A. laibachii. We identified a core set of bacteria are closely associated with A. laibachii and established that GH25 inhibits members of this core group. Among A. laibachii-associated bacteria that were inhibited by GH25, Curtobacterium sp. could override the inhibition of A. laibachii by MbA. We describe a tripartite antagonistic interaction in which bacterium and oomycete protect each other from growth inhibition by MbA. Curtobacterium sp., in turn, exhibits specific inhibition of A. laibachii-associated bacteria that are not targeted by MbA but themselves antagonize A. laibachii. Our study reveals an inter-kingdom interaction network in which a GH25 lysozyme shapes the antagonistic relationship between yeast, a pathogenic oomycete and an oomycete-associated bacterium.

microbiology↗

bioRxiv2024

Stimulation of the Medial SNr Promotes Sustained Motor Recovery and Counteracts Parkinsonian Pathophysiology in Dopamine Depleted Mice

Dopamine loss alters the activity of neural circuits in the basal ganglia, contributing to motor symptoms of Parkinsons disease and catalepsy. Treatments that reduce basal ganglia pathophysiology alleviate motor symptoms but require maintenance. Cell-type specific interventions can reduce pathophysiology and provide sustained therapeutic benefits, but a lack of understanding of pathways involved limits translation. Here, we establish patterns of neuromodulation and electrophysiological biomarkers at the level of basal ganglia output that predict the duration of therapeutic effects. Focal activation of neurons in the ventromedial substantia nigra reticulata (SNr) engaged a gradual recovery of movement that persisted for hours after treatment, accompanied by a persistent reduction in parkinsonian pathophysiology. Global SNr inhibition, as prescribed by the classic rate model, provided only transient effects on movement and did not reverse network pathophysiology. These findings represent important steps towards developing therapeutic strategies that aim to repair, rather than simply mask, circuit dysfunction in disease.

neuroscience↗

bioRxiv2024

Immune regulators EDS1 and PAD4 constrain ADR1-dependent disease resistance in rice

Withdrawal StatementThe authors have withdrawn this manuscript owing to finding inconsistencies in genotyping of kitaake rice eds1 pad4 double mutant lines and to establishing that combined loss of EDS1 and PAD4 does not underlie the stunted autoimmune-like phenotype reported in this preprint. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors: Jane Parker, Thomas Kroj and Haitao Cui (co-corresponding)

plant biology↗

bioRxiv2022

Oligomerisation of a plant helper NLR requires cell-surface and intracellular immune receptor activation

Plant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signalling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and their activation of defense also requires the lipase-domain proteins EDS1, SAG101 and PAD4. We investigated how the helper NLR NRG1 supports TNL-initiated immunity with EDS1 and SAG101. We find that NRG1 associates with EDS1 and SAG101 at the plasma membrane and in the nucleus, but only self-associates at the plasma membrane. Activation of TNLs is sufficient to trigger NRG1-EDS1-SAG101 interaction, but cell-surface receptor-initiated defense is also required to form an oligomeric Resistosome. The data point to formation of NRG1-EDS1-SAG101 heterotrimers in the nucleus upon intracellular receptor activation alone and indicate formation of NRG1-EDS1-SAG101 Resistosomes at the plasma membrane upon co-activation of intracellular and cell surface-receptor pathways.

plant biology↗

bioRxiv2022

TIR-catalyzed ADP-ribosylation reactions produce signaling molecules for plant immunity

Plant pathogen-activated immune signaling by nucleotide-binding leucine-rich repeat (NLR) receptors with an N-terminal Toll/Interleukin-1 receptor (TIR) domain converges on Enhanced Disease Susceptibility 1 (EDS1) and its direct partners Phytoalexin Deficient 4 (PAD4) or Senescence-Associated Gene 101 (SAG101). TIR-encoded NADases produce signaling molecules to promote exclusive EDS1-PAD4 and EDS1-SAG101 interactions with helper NLR sub-classes. Here we show that TIR-containing proteins catalyze adenosine diphosphate (ADP)-ribosylation of adenosine triphosphate (ATP) and ADP ribose (ADPR) via ADPR polymerase-like and NADase activity, forming ADP-ribosylated ATP (ADPr-ATP) and ADPr-ADPR (di-ADPR), respectively. Specific binding of di-ADPR or ADPr-ATP allosterically promotes EDS1-SAG101 interaction with helper NLR N requirement gene 1A (NRG1A) in vitro and in planta. Our data reveal an enzymatic activity of TIRs that enables specific activation of the EDS1-SAG101-NRG1 immunity branch.

plant biology↗

bioRxiv2022

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity

Plant nucleotide-binding leucine-rich-repeat receptors (NLRs) with an N-terminal toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded NADase activity for immune signaling. TIR-NLR (TNL) signaling requires conserved helper NLRs NRG1 and ADR1 and the lipase-like protein EDS1 that functions as a heterodimer with each of its paralogs PAD4 and SAG101. We show that TIR-containing proteins catalyze production of 2-(5-phosphoribosyl)-5-adenosine mono-/di-phosphate (pRib-AMP/ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP/ADP. pRib-ADP binding triggers a conformational change in the PAD4 C-terminal domain to allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP/ADP as a missing link in TIR signaling via EDS1-PAD4 and as likely second messengers for plant immunity.

plant biology↗

bioRxiv2021

Differential requirement for the EDS1 catalytic triad in A. thaliana and N. benthamiana

O_LIHeterodimeric complexes incorporating the lipase-like proteins EDS1 with PAD4 or SAG101 are central hubs in plant innate immunity. EDS1 functions encompass signal relay from TIR domain-containing intracellular NLR-type immune receptors (TNLs) towards RPW8-type helper NLRs (RNLs) and, in A. thaliana, bolstering of signaling and resistance mediated by cell-surface pattern recognition receptors (PRRs). Biochemical activities underlying these mechanistic frameworks remain unknown. C_LIO_LIWe used CRISPR/Cas-generated mutant lines and agroinfiltration-based complementation assays to interrogate functions of EDS1 complexes in N. benthamiana. C_LIO_LIWe do not detect impaired PRR signaling in N. benthamiana lines deficient in EDS1 complexes or RNLs. Intriguingly, mutations within the catalytic triad of Solanaceae EDS1 can abolish or enhance TNL immunity in N. benthamiana. Furthermore, nuclear EDS1 accumulation is sufficient for N. benthamiana TNL (Roq1) immunity. C_LIO_LIReinforcing PRR signaling in Arabidopsis might be a derived function of the TNL/EDS1 immune sector. Dependency of Solanaceae but not A. thaliana EDS1 on catalytic triad residues raises the possibility that a TNL-derived small molecule binds to the Solanaceae EDS1 lipase-like domain, and that EDS1 lipase-like domain pocket contributions to TNL immune responses vary between lineages. Whether and how nuclear EDS1 activity connects to membrane pore-forming RNLs remains unknown. C_LI

plant biology↗

bioRxiv2021

XopQ induced stromule formation in Nicotiana benthamiana is causally linked to ETI signaling and depends on ADR1 and NRG1

In Nicotiana benthamiana, expression of the Xanthomonas effector XopQ triggers ROQ1-dependent ETI responses and in parallel accumulation of plastids around the nucleus and the formation of stromules. Both processes were proposed to contribute to ETI-related hypersensitive cell death and thereby to plant immunity. Whether these reactions are directly connected to ETI signaling events has not been tested. Here we utilized transient expression experiments to determine whether XopQ-mediated plastid reactions are a result of XopQ perception by ROQ1 or a consequence of XopQ virulence activity. We find that N. benthamiana mutants lacking ROQ1, both RNLs (NRG1 and ADR1) or EDS1, fail to elicit XopQ-dependent host cell death and stromule formation. Mutants lacking only NRG1 lost XopQ-dependent cell death but retained some stromule induction that was abolished in the RNL double mutant. This analysis aligns XopQ-induced stromules with the ETI signaling cascade but not to host programmed cell death. Furthermore, data reveal that XopQ-triggered plastid clustering is not strictly linked to stromule formation during ETI. Our data suggest that stromule formation, in contrast to chloroplast peri-nuclear dynamics, is an integral part of the N. benthamiana ETI response and that both RNL sub-types play a role in this ETI response. One sentence summaryGenetic analysis aligns effector triggered immunity (ETI) induced stromule formation with the ETI signaling cascade but not programmed cell death and questions stromule guided peri-nuclear plastid clustering.

plant biology↗

bioRxiv2021

Differential EDS1 requirement for cell death activities of plant TIR-domain proteins

Toll/interleukin-1 Receptor (TIR) domains are integral to immune systems across all domains of life. TIRs exist as single-domain and as larger receptor or adaptor proteins. In plants, TIRs constitute N-terminal domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors. Although TIR-NLR and TIR signaling requires the Enhanced disease susceptibility 1 (EDS1) protein family, TIR domains persist in species that have incomplete or no EDS1 members. To assess whether particular TIR groups appear with EDS1, we searched for TIR-EDS1 co-occurrence patterns. Using a large-scale phylogenetic analysis of TIR domains from 39 algae and land plant species, we identify four conserved TIR groups, two of which are TIR-NLRs present in eudicots and two are more widespread. Presence of one TIR-only protein group is highly correlated with EDS1 and members of this group elicit EDS1-dependent cell death. By contrast, a more widely represented TIR group of TIR-NB-WD40/TPR (TNP) proteins (formerly called XTNX) has at least one member which can induce EDS1-independent cell death. Our data provide a new phylogeny-based plant TIR classification and identify TIR groups that appear to have evolved with and are dependent on EDS1, while others have EDS1-independent activity. One sentence summaryLand plants have evolved four conserved TIR groups

plant biology↗

bioRxiv2021

In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris

Candida auris has emerged as a healthcare-associated and multidrug-resistant fungal pathogen of great clinical concern. While as much as 50% of C. auris clinical isolates are reported to be resistant to amphotericin B, to date, no mechanisms contributing to this resistance have been identified. We report here mutations in the C. auris sterol-methyltransferase gene, ERG6, as the first identified mechanism of amphotericin B resistance in this emerging pathogen and describe the clinical case in which this high-level amphotericin B resistance was acquired in vivo during therapy. Whole genome sequencing revealed the four C. auris isolates obtained from this single patient case to be genetically related and identified a mutation in ERG6 as being associated with amphotericin B resistance. Cas9-mediated genetic manipulations confirmed this mutation alone to confer a >32-fold increase in amphotericin B resistance, and comprehensive sterol profiling revealed an abrogation of ergosterol biosynthesis and a corresponding accumulation of cholesta-type sterols in isolates and strains harboring the clinically derived ERG6 mutation. Together these findings represent the first significant step forward in the understanding of clinical amphotericin B resistance in C. auris.

microbiology↗

bioRxiv2021

Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity

Transcriptional corepressors of the Topless family are important regulators of plant hormone and immunity signaling. The lack of a genome-wide profile of their chromatin associations limits understanding of transcriptional regulation in plant immune responses. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed on GFP-tagged Topless-related 1 (TPR1) expressed in Arabidopsis thaliana lines with and without constitutive immunity dependent on Enhanced Disease Susceptibility 1 (EDS1). RNA-seq profiling of pathogen-infected tpl/tpr mutants and assessments of growth and physiological parameters were employed to determine TPL/TPR roles in transcriptional immunity and defense homeostasis. TPR1 bound to promoter regions of ~1,400 genes and ~10% of the detected binding required EDS1 immunity signaling. A tpr1 tpl tpr4 (t3) mutant displayed mildly enhanced defense-related transcriptional reprogramming upon bacterial infection but not increased bacterial resistance. Bacteria or pep1 phytocytokine-challenged t3 plants exhibited, respectively, photosystem II dysfunction and exacerbated root growth inhibition. Transgenic expression of TPR1 restored the t3 physiological defects. We propose that TPR1 and TPL-family proteins function in Arabidopsis to reduce detrimental effects associated with activated transcriptional immunity.

plant biology↗

bioRxiv2021

The receptor kinase SRF3 coordinates iron-level and flagellin dependent defense and growth responses in plants

Iron is critical for host-pathogen interactions. While pathogens seek to scavenge iron to spread, the host aims at decreasing iron availability to reduce pathogen virulence. Thus, iron sensing and homeostasis are of particular importance to prevent host infection and part of nutritional immunity. While the link between iron homeostasis and immunity pathways is well established in plants, how iron levels are sensed and integrated with immune response pathways remain unknown. We identified a receptor kinase, SRF3 coordinating root growth, iron homeostasis and immunity pathways via regulation of callose synthase activity. These processes are modulated by iron levels and rely on SRF3 extracellular and kinase domain which tune its accumulation and partitioning at the cell surface. Mimicking bacterial elicitation with the flagellin peptide flg22 phenocopies SRF3 regulation upon low iron levels and subsequent SRF3-dependent responses. We propose that SRF3 is part of nutritional immunity responses involved in sensing external iron levels.

plant biology↗

bioRxiv2021

The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley

Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally show early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. HighlightsO_LIThe root endophytic fungus Serendipita vermifera can functionally replace core bacterial microbiota members in mitigating pathogen infection and disease symptoms. C_LIO_LIS. vermifera additionally stabilizes and potentiates the protective activities of root-associated bacteria and mitigates the negative effects of a non-native bacterial community in A. thaliana. C_LIO_LIInter-kingdom synergistic beneficial effects do not require extensive host transcriptional reprogramming nor high levels of S. vermifera colonisation. C_LIO_LIInter-kingdom protective benefits are largely independent of the host while synergism leading to early inter-kingdom growth promotion is driven by host species and microbiota composition. C_LI

plant biology↗