Biology subjects

Peeters, N.

Publications and source records attributed to Peeters, N..

12 recordsLinked to original sources

bioRxiv2026

A conserved root-knot nematode effector targets plant kinesin light chain related proteins to promote parasitism

Root-knot nematodes (RKNs) are obligate plant parasites that establish biotrophic interactions with a wide range of host plants, causing major crop losses worldwide. During infection, RKNs secrete effector proteins from their esophageal glands into root tissues via a stylet. These effectors target specific subcellular compartments and manipulate host cell functions to induce the formation of hypertrophied and multinucleated giant cells, which serve as feeding sites essential for nematode development. Here we describe a new RKN-specific effector, EFFECTOR17 (EFF17), conserved in the five most damaging RKN species: Meloidogyne incognita, M. enterolobii, M. arenaria, M. javanica, and M. hapla. In situ hybridization showed that EFF17 genes are specifically expressed in the esophageal glands of various RKN species. Silencing EFF17 in M. incognita reduced its reproduction on Nicotiana benthamiana, demonstrating a key role in parasitism. Yeast two-hybrid and split luciferase assays revealed that tomato and Arabidopsis KINESIN LIGHT CHAIN RELATED (KLCR)/CELLULOSE-MICROUBULE UNCOUPLING (CMU) proteins are host targets of MiEFF17. Arabidopsis klcr mutants developed significantly fewer galls and egg masses. Our findings propose that EFF17 manipulates KLCR function to promote parasitism.

plant biology↗

bioRxiv2025

Time-resolved bottleneck analysis in bacterial infection dynamics

Within-host pathogen dynamics are shaped by successive host-imposed barriers that generate bottlenecks and ultimately determine infection outcome, yet these processes remain difficult to study in vivo. Here, we use neutral genetic barcoding to quantify the root-entry bottleneck during infection of tomato by the bacterial soil-borne phytopathogen Ralstonia pseudosolanacearum. We establish an updated theoretical framework showing that the temporal structure of pathogen entry, often overlooked, is a key determinant of root colonisation. We introduce the concept of time-resolved bottleneck, capturing infection scenarios in which entry occurs continuously while the pathogen population simultaneously expands within the host. We develop quantitative tools that exploit barcode dynamics to disentangle the respective roles of motility, growth, and spatial competition, enabling direct inference of in vivo pathogen fluxes and growth rates and linking host susceptibility to mechanistic features of colonisation. Extending beyond plants, reanalysis of two independent animal infection datasets reveals previously unrecognised within-host development patterns. Together, these results show that time-resolved bottleneck is a general principle of bacterial infection dynamics and propose a new standard for barcoding-based studies: a host- and pathogen-agnostic framework that is directly applicable to a majority of existing STAMP(-R)-style datasets, distributed as an open, annotated R/Python notebook to facilitate community reuse.

microbiology↗

bioRxiv2024

Realisation of a key step in the evolution of C4 photosynthesis in rice by genome editing.

C4 photosynthesis is a repeatedly evolved adaptation to photosynthesis that functions to reduce energy loss from photorespiration. The recurrent evolution of this adaptation is achieved through changes in the expression and localisation of several enzymes and transporters that are conventionally used in non-photosynthetic metabolism. These alterations result in the establishment of a biochemical CO2 pump that increases the concentration of CO2 around rubisco in a cellular environment where rubisco is protected from oxygen thus preventing the occurrence of photorespiration. A key step in the evolution of C4 photosynthesis is the change in subcellular localisation of carbonic anhydrase (CA) activity from the mesophyll cell chloroplast to the cytosol, where it catalyzes the first biochemical step of the C4 pathway. Here, we achieve this key step in C4 evolution in the C3 plant Oryza sativa (rice) using genome editing. We show that editing the chloroplast transit peptide of the primary CA isoform in the leaf results in relocalisation of leaf CA activity from the chloroplast to the cytosol. Through analysis of fluorescence induction kinetics in these CA relocalisation lines we uncover a role a new role for chloroplast CA in photosynthetic induction. We also reveal that relocalisation of CA activity to the cytosol causes no detectable perturbation to plant growth or leaf-level CO2 assimilation. Collectively, this work uncovers a novel role for chloroplast CA in C3 plants, and demonstrates that it is possible to achieve a key step in the evolution of C4 photosynthesis by genome editing. Significance statementC4 photosynthesis is a highly efficient adaptation to photosynthesis that fuels the worlds most productive crop plants. It evolved from conventional C3 photosynthesis through a series of changes in leaf biochemistry and anatomy. Here we achieve a key evolutionary step on the path to C4 photosynthesis in rice using genome editing. Specifically, we alter the primary location of carbonic anhydrase activity in the rice leaf from the chloroplast to the cytosol. In doing so, we uncover a novel role for carbonic anhydrase in facilitating the rapid induction kinetics of photosystem II, and initiate a new era of C4 engineering using precision breeding techniques.

plant biology↗

bioRxiv2023

The association between Dioscorea sansibarensis and Orrella dioscoreae as a model for hereditary leaf symbiosis

Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host.

plant biology↗

bioRxiv2022

Arabidopsis thaliana rosette growth habit is a photomorphogenic trait controlled by the TALE homeodomain protein ATH1 and involves TOR kinase

Here, we demonstrate that Arabidopsis rosette habit is a bona fide photomorphogenic trait controlled by the homeodomain protein ATH1. In light, ATH1 expression at the SAM is induced by broad wavelengths, mediated through multiple photoreceptors, and requires inactivation of COP1 and PIF photomorphogenesis inhibitors. Such induced ATH1 prevents elongation of rosette internodes by maintaining the rib zone area of the SAM in an inactive state. In the absence of light, Arabidopsis plants cannot complete seedling establishment after germination due to inactivity of the shoot apical meristem (SAM). Light requirement for SAM activation can be overcome by availability to the meristem of metabolizable sugars, such as sucrose. However, under these conditions plants fail to establish a typical compact rosette and display a caulescent growth habit. We show that this is due to insufficient expression of ATH1 at the SAM. ATH1 induction restores rosette habit in dark-grown plants through inhibition of PIF gene expression. Together, this suggests that a SAM-specific, double-negative ATH1-PIF feedback loop is at the basis of Arabidopsis rosette habit. Induction of ATH1 expression and restoration of rosette habit in darkness also occurs at increased levels of sucrose. Both sugar and light signals that induce ATH1 are mediated by TOR kinase. Overall, these results support a fundamental role for ATH1 in Arabidopsis rosette habit and further strengthen a role for TOR kinase as a central hub for integration of energy and light signals controlling organogenesis at the SAM.

plant biology↗

bioRxiv2021

An NLR Integrated Decoy toolkit to identify plant pathogen effector targets

Plant resistance genes (or NLR "Nod-like Receptors") are known to contain atypical domains procuring them with a decoy capacity. Some of these integrated domains (or ID) allow the plant to lure the virulence determinants ("effectors") of pathogens and triggering a specific NLR immune reaction. In this work, our goal was to generate a library of known IDs that could be screened with plant pathogen effectors in order to identify putative new effector virulence targets and NLR-effector pairs. We curated the IDs contained in NLRs from seven model and crop plant species. We cloned 52 IDs representing 31 distinct Pfam domains. This library was screened for interaction by yeast-two-hybrid with a set of 31 conserved Ralstonia solanacearum type III effectors. This screening and the further in planta interaction assay allowed us to identify three interactions, involving different IDs (kinase, DUF3542, WRKY) and two type III effectors (RipAE and PopP2). PopP2 was found to physically interact with ID#85, an atypical WRKY domain integrated in the GmNLR-ID85 NLR protein from Soybean. Using a imaging method in living plant cells, we showed that PopP2 associates with ID#85 in the nucleus. But unlike the known WRKY-containing Arabidopsis RRS1-R NLR receptor, this newly identified soybean WRKY domain could not be acetylated by PopP2 and its atypical sequence (WRKYGKR) also probably renders it inefficient in plant immunity triggering. This ID toolkit is available for screening with other plant pathogen effectors and should prove useful to discover new effectors targets and potentially engineer new plant resistance genes.

plant biology↗

bioRxiv2019

EffectorK, a comprehensive resource to mine for pathogen effector targets in the Arabidopsis proteome

Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogens own benefit. However, effectors can also be recognized by host immune proteins leading to the activation of defense responses. Effectors are thus essential components in determining the outcome of plant-pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large-scale yeast two-hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal and animal pathogens. This network contains our experimental data and protein-protein interactions from 2,035 peer-reviewed publications (48,200 Arabidopsis-Arabidopsis and 1,300 Arabidopsis-effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis targets suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector targets, particularly effector hubs and bacterial core effector targets, occupy important positions for network organization as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph-oriented knowledge database that allows users to navigate the network, search for homology or find possible paths between host and/or effector proteins. EffectorK is available at www.effectork.org and allows users to submit their own interactomic data. Author summaryPlant pests and diseases caused by bacteria, oomycetes, fungi or animals are threatening food security worldwide. Understanding how these pathogens infect and manipulate the host is key to develop sustainable crop resistance in the long term. Effector proteins are secreted by pathogens to subvert the host immune responses. The roles of several effector proteins have been described; however, it is yet poorly understood how effectors interact with host proteins at a global level. To address this issue, we have generated EffectorK, an interactive database focused on the model plant species Arabidopsis thaliana. This database contains manually curated Arabidopsis-effector protein interactions from the available literature on a wide variety of pathogens. It also contains new experimental data on effectors from two vascular pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. This work integrates all the gathered knowledge over the last decades and allows to identify general patterns of how effectors interact with the host proteome. This knowledge is easily accessible and searchable at www.effectork.org.

plant biology↗

bioRxiv2019

Experimental system and image analysis software for high throughput phenotyping of mycorrhizal growth response in Brachypodium distachyon

O_LIPlant growth response to Arbuscular Mycorrhizal (AM) fungi is variable and depends on genetic and environment factors that still remain largely unknown. Identification of these factors can be envisaged using high-throughput and accurate plant phenotyping.\nC_LIO_LIWe setup experimental conditions based on a two-compartment system allowing to measure Brachypodium distachyon mycorhizal growth response (MGR) in an automated phenotyping greenhouse. We developed a new image analysis software \"IPSO Phen\" to estimate of B. distachyon aboveground biomass.\nC_LIO_LIWe found a positive MGR in the B. distachyon Bd3-1 genotype inoculated with the AM fungi Rhizophagus irregularis only if nitrogen and phosphorus were added together in the compartment restricted to AM fungi. Using this condition, we found genetic diversity in B. distachyon for MGR ranging from positive to negative MGR depending on the plant genotype tested.\nC_LIO_LIOur result on the interaction between nitrogen and phosphorus for MGR in B. distachyon opens new perspectives about AM functioning. In addition, our open-source software allowing to test and run image analysis parameters on large amount of images generated by automated plant phenotyping facilities, will help to screen large panels of genotypes and environmental conditions to identify the factors controlling the MGR.\nC_LI

plant biology↗

bioRxiv2019

Common neural and transcriptional correlates of inhibitory control across emotion, memory, and response inhibition

Inhibitory control is crucial for regulating emotions, and it may also enable memory control. However, evidence for their shared neurobiological correlates is limited. Here, we report meta-analyses of neuroimaging studies on emotion regulation, or memory control, and link neural commonalities to transcriptional commonalities using the Allen Human Brain Atlas (AHBA). Based on 95 fMRI studies, we reveal a role of the right inferior parietal lobule embedded in a frontal-parietal-insular network during emotion and memory control, which is similarly recruited during response inhibition. These co-activation patterns also overlap with the networks associated with "inhibition", "cognitive control", and "working memory" when consulting the Neurosynth. Using the AHBA, we demonstrate that emotion and memory control-related brain activity patterns are associated with transcriptional profiles of a specific set of "inhibition-related" genes. Gene ontology enrichment analysis of these "inhibition-related" genes reveal associations with the neuronal transmission and risk for major psychiatric disorders as well as seizures and alcoholic dependence. In summary, this study identified a neural network and a set of genes associated with inhibitory control across emotion regulation, memory control. These findings facilitate our understanding of the neurobiological correlates of inhibitory control and may contribute to the development of novel brain stimulation and pharmacological interventions.

neuroscience↗

bioRxiv2019

The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN

Race 1 strains of Pseudomonas syringae pv. tomato, which causes bacterial speck disease of tomato, are becoming increasingly common and no simply-inherited genetic resistance to such strains is known. We discovered that a locus in Solanum lycopersicoides, termed Pseudomonas tomato race 1 (Ptr1), confers resistance to race 1 Pst strains by recognizing the type III effector AvrRpt2. In Arabidopsis, AvrRpt2 degrades the RIN4 protein thereby activating RPS2-mediated immunity. Ptr1 also recognized homologs of AvrRpt2 from diverse bacteria including one in Ralstonia pseudosolanacearum and this correlated with the ability of AvrRpt2 to degrade RIN4. Using site-directed mutagenesis of AvrRpt2 we found that Ptr1 and RPS2 recognize identical features of AvrRpt2. However, the genome sequence of S. lycopersicoides revealed no RPS2 homolog in the Ptr1 region. Ptr1 could play an important role in controlling bacterial speck disease and its future cloning may shed light on an example of convergent evolution for recognition of a widespread type III effector.

plant biology↗

bioRxiv2018

NRG1-mediated recognition of HopQ1 reveals a link between PAMP and Effector-triggered Immunity.

O_LIMembers of the hopQ1/XopQ family of effectors are conserved amongst pathogenic bacteria suggesting an important function in virulence. Therefore, the identification of R proteins recognising members of this family is potentially of high value to achieve broad-spectrum resistance in crops.\nC_LIO_LIRecent studies demonstrated that HopQ1/XopQ recognition is EDS1-dependant and is mediated by the TIR-NB-LRR protein Roq1. Using our recently described R gene RNAi library, we have investigated the mechanism of HopQ1 recognition and the other components of its signalling network.\nC_LIO_LIWe show that silencing of the CCR-NB-LRR helper protein N Requirement Gene 1 (NRG1) prevents HopQ1 recognition in N. benthamiana and that NRG1 expression confers recognition of HopQ1 and restricts Pto DC3000 proliferation in the otherwise susceptible host Arabidopsis. Moreover NRG1 expression is briefly but strongly induced at a very early stage of the plant innate response, establishing a strong dependency link between PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI).\nC_LIO_LIOverall we demonstrate that in addition to Roq1, HopQ1 recognition in N. benthamiana requires the CCR-NB-LRR protein NRG1 and propose a model based on the dual requirement of a CCR-NB-LRR and a TIR-NB-LRR that could extend beyond HopQ1 detection and possibly be used to recognize other pathogen effectors.\nC_LI

plant biology↗

bioRxiv2017

Heterologous expression of the immune receptor EFR in Medicago truncatula reduces pathogenic infection, but not rhizobial symbiosis

Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad-spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen-associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae-specific PRR ELONGATION FACTOR-THERMO UNSTABLE RECEPTOR (EFR) from Arabidopsis thaliana to the legume Medicago truncatula, conferring recognition of the bacterial EF-Tu protein. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF-Tu-derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR-Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling.\n\nSignificance StatementCrop engineering helps reducing the economic and environmental costs of plant disease. The genetic transfer of immune receptors across plant species is a promising biotechnological approach to increase disease resistance. Surface-localized pattern-recognition receptors (PRRs), which detect conserved characteristic microbial features, are functional in heterologous taxonomically-diverse plant species, and confer broad-spectrum disease resistance. It was unclear whether PRR transfer negatively impacts the association of the recipient plants with symbiotic microbes. Here, we show that a legume engineered with a novel PRR recognizing a conserved bacterial protein becomes more resistant to an important bacterial pathogen without significant impact on nitrogen-fixing symbiosis with rhizobia. This finding is of particular relevance as attempts to transfer this important symbiosis into non-legume plants are ongoing.

plant biology↗