Biology subjects

Redkar, A.

Publications and source records attributed to Redkar, A..

10 recordsLinked to original sources

bioRxiv2025

Dissecting the root-fungal interface in 3D reveals spatially distinct signalling landscapes

Plant rhizospheric interactions represent intricate relationships that determine plant fitness and are crucial for interrogating host-pathogen dynamics, with significant fundamental and translational implications. Most fungal-plant interactions occur in soil - a disordered and granular 3D environment - and hence remain challenging to unravel due to complex regulatory networks. Our current body of evidence characterizing these molecular dialogues largely stems from experimental systems employing soil or in vitro 2D flat plates, hydroponics and gnotobiotic systems. Soil itself features widely varying visco-elasto-plastic material properties, and its inherent opacity precludes direct visualization of the infection progression in complex diseases such as wilts and root rots. Here, we introduce the first such optically transparent, 3D granular growth matrix to recapitulate complex properties of the soil microenvironment, which enables direct, cellular-level visualization of the plant-fungal interface. Our mechanically tunable 3D matrices support long-term co-culture of plants and fungi with compatibility to classical molecular and physiological assays for unravelling the early signalling events and inter-kingdom crosstalk. By leveraging the optical transparency of this matrix, we track fungal development in response to host signals ex-planta with 3D resolution, to report pioneering evidence of hyphal reprogramming preferentially towards the root tips during the early stages of infection. Crucially, we integrate spatiotemporal transcriptomic analyses and discover distinct pathogen-host ex- and in-planta modules during early signalling, which are likely associated with biomimetic soil-like environments. Together, our findings establish an integrable and versatile 3D platform offering an unprecedented view of the pathogen infection processes, which enables fundamental discoveries into the biological regulation of growth and infection. These insights hold immense potential for advancing our understanding of host immune responses and adaptation of filamentous pathogens, as well as open avenues to decipher drought and disease-resistance mechanisms with major agricultural benefits.

plant biology↗

bioRxiv2025

Cell-type-specific execution of effector-triggered immunity

Effector-triggered immunity (ETI) is a central component of host defense, but whether all cell types execute ETI similarly remains unknown. We combined chemically imposed immune activation with single-cell transcriptomics to profile ETI responses across all leaf cell types in Arabidopsis. Despite uniform ETI perception, we find striking divergence between transcriptional outputs: a core set of defense genes is broadly induced, while distinct cell types activate specialized immune modules. We infer that downstream immune execution is shaped not only by immune receptor activation, but also by cell identity and its associated transcriptional regulatory context, including local transcription factor availability and chromatin accessibility. We further demonstrate that transcriptional regulators preferentially induced in epidermal cells are required to restrict invasion by non-adapted pathogens. Their absence permits pathogen entry into deeper tissues despite intact recognition, revealing a spatial division of immune functions. Our findings uncover a layered immune architecture in plants, challenges the assumption of uniform immune execution, and provides a framework for exploring cell-type-specific resistance logic in multicellular hosts.

plant biology↗

bioRxiv2025

Transcriptional plasticity of fast core chromosomes governs establishment of a fungal pathogen on evolutionarily distant plant lineages

The Fusarium oxysporum (Fo) species complex encompasses a diverse range of filamentous plant pathogens, some of which provoke systemic infections in angiosperms, leading to vascular wilt disease. Current understanding of the Fo pathogenicity mechanisms is primarily centered on vascular plants, where individual isolates of Fo exhibit contrasting lifestyles across the endophyte-pathogen continuum on different host species. Although, Fo isolates were recently shown to cause disease on the non-vascular liverwort Marchantia polymorpha (Mp), the transcriptional control of Fo effectors during infection of this bryophytic host is largely unknown. Here, we took a comparative transcriptomic approach to ask how different Fo isolates with contrasting interaction outcomes on angiosperms (pathogenic versus endophytic) adapt to a distantly related plant lineage lacking xylem. We found that the core effector complement encoded on genomic regions shared across all Fo isolates are actively transcribed in Mp, whereas effectors encoded on lineage-specific (LS) genomic regions that contribute towards host-specific pathogenicity in angiosperms are not. Moreover, we observed enhanced transcriptional activation of effector clusters located on the three highly syntenic fast core chromosomes during growth on Mp, as well as divergent lineages and lifestyles, suggesting a conserved role in plant associations. Loss of a compatibility-associated effector encoded in a core effector cluster led to misregulation of other effectors in core clusters. Our findings reveal an unexpected role of fast core chromosomes in determining compatibility of Fo across a broad spectrum of plant lineages and establishes evolutionarily conserved gene networks essential for fungus-plant associations.

plant biology↗

bioRxiv2021

Krüppel-like factor 4 is required for development and regeneration of germline and yolk cells from somatic stem cells in planarians

Sexually reproducing animals segregate their germline from their soma. In addition to gamete-producing gonads, planarian and parasitic flatworm reproduction relies on yolk-cell-generating accessory reproductive organs (vitellaria) supporting development of yolkless oocytes. Despite the importance of vitellaria for flatworm reproduction (and parasite transmission), little is known about this unique evolutionary innovation. Here we examine reproductive system development in the planarian Schmidtea mediterranea, in which pluripotent stem cells generate both somatic and germ cell lineages. We show that a homolog of the pluripotency factor Klf4 is expressed in primordial germ cells, presumptive germline stem cells, and yolk-cell progenitors. klf4 knockdown animals fail to specify or maintain germ cells; surprisingly, they also fail to maintain yolk cells. We find that yolk cells display germ-cell-like attributes and that vitellaria are structurally analogous to gonads. In addition to identifying a new proliferative cell population in planarians (yolk cell progenitors) and defining its niche, our work provides evidence supporting the hypothesis that flatworm germ cells and yolk cells share a common evolutionary origin.

developmental biology↗

bioRxiv2021

Conserved secreted effectors determine endophytic growth and multi-host plant compatibility in a vascular wilt fungus

Fungal interactions with plant roots, either beneficial or detrimental, have a major impact on agriculture and ecosystems. The soil inhabiting ascomycete Fusarium oxysporum (Fo) constitutes a species complex of worldwide distribution causing vascular wilt in more than a hundred different crops. Individual isolates of the fungus exhibit host-specific pathogenicity, determined by proteinaceous effectors termed secreted in xylem (SIX). However, such isolates can also colonize roots of non-host plants asymptomatically as endophytes, or even protect them against pathogenic isolates. The molecular determinants of multi-host plant colonization are currently unknown. Here, we identified a set of fungal effectors termed ERCs (Early Root Compatibility effectors), which are secreted during early biotrophic growth of Fo on both host and non-host plants. In contrast to the strain-specific SIX effectors, which are encoded on accessory genomic regions, ERCs are encoded on core regions and are found across the entire Fo species complex as well as in other phytopathogens, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence on the host plant and rapid activation of plant immune responses, while in a non-pathogenic isolate it led to impaired root colonization and loss of biocontrol ability. Strikingly, some ERCs also contribute to Fo infection on the non-vascular land plant Marchantia polymorpha. Our results reveal an evolutionarily conserved mechanism for multi-host colonization by root infecting fungi.

plant biology↗

bioRxiv2021

The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors

The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their specificity for infecting different host species. The White Rust Resistance 4 (WRR4) locus in Col-0 accession of Arabidopsis thaliana contains three genes that encode TIR-NLR resistance proteins. The Col-0 alleles of WRR4A and WRR4B confer resistance to at least four A. candida races (2, 7 and 9 from B. juncea, B. rapa and B. oleracea, respectively, and Race 4 from Capsella bursa-pastoris). Resistance mediated by both paralogs can be overcome by Col-0-virulent isolates of Race 4. After comparing repertoires of candidate effectors in resisted and resistance-breaking strains, we used transient co-expression in tobacco or Arabidopsis to identify effectors recognized by WRR4A and WRR4B. A library of CCG effectors from four A. candida races was screened for WRR4A- or WRR4B- dependent elicitation of hypersensitive response (HR). These CCG genes were validated for WRR-dependent HR by bombardment assays in wild type Col-0, wrr4A or wrr4B mutants. Our analysis revealed eight WRR4A-recognized CCGs and four WRR4B-recognized CCGs. Remarkably, the N-terminal region of 100 amino acids after the secretion signal is sufficient for WRR4A recognition of these eight recognized effectors. This multiple recognition capacity potentially explains the broad-spectrum resistance to many A. candida races conferred by WRR4 paralogs.

plant biology↗

bioRxiv2021

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We re-sequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared to a previous version. Our annotation of the new assembly, aided by RNASeq information, revealed a dramatic 250% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and particularly the role of CCG effectors in virulence and avirulence on different hosts.

plant biology↗

bioRxiv2021

Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida recognition specificities

The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR)-genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Col-0 provides resistance to many but not all white rust races, and encodes a nucleotide-binding (NB), leucine-rich repeat (LRR) (NLR) immune receptor protein. Col-0 WRR4A resistance is broken by a Col-0-virulent isolate of A. candida race 4 (AcEx1). We identified an allele of WRR4A in Arabidopsis accession Oy-0 and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed as a transgene in the oilseed crop Camelina sativa. SignificanceA C-terminal extension in an allele of the Arabidopsis resistance-protein WRR4A changes effector recognition specificity, enabling the WRR4AOy-0 allele to confer immunity to Albugo candida races that overcome the WRR4ACol-0 allele. This resistance can be transferred to the oil-producing crop Camelina sativa. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/437434v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a68de6org.highwire.dtl.DTLVardef@ae0addorg.highwire.dtl.DTLVardef@4b3384org.highwire.dtl.DTLVardef@12330b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2021

Marchantia polymorpha model reveals conserved infection mechanisms in the vascular wilt fungal pathogen Fusarium oxysporum

The non-vascular plant Marchantia polymorpha has emerged as a valuable model for studying evolutionarily conserved microbial infection strategies and plant immune responses. However, only a handful of fungal pathogens of Marchantia have been described so far. Here we establish a new pathosystem using the root-infecting vascular wilt fungus Fusarium oxysporum. On angiosperms, this fungus exhibits exquisite adaptation to the plant vascular niche and host-specific pathogenicity, both of which are conferred by lineage-specific effectors secreted during growth in the xylem. We show that F. oxysporum isolates with different lifestyles - pathogenic or endophytic - are able to infect this non-vascular liverwort causing tissue maceration and plant cell killing. Similar to bacterial pathogens, F. oxysporum induces a PAMP-triggered immune response in M. polymorpha. Analysis of isogenic fungal mutants established that infection of Marchantia requires conserved fungal pathogenicity mechanisms such as mitogen activated protein kinases, transcriptional regulators and cell wall remodeling enzymes. Remarkably, lineage-specific virulence effectors are dispensable for infection, most likely due to the absence of xylem tissue in this non-vascular plant. The F. oxysporum - M. polymorpha system provides new insights into the mechanism and evolution of pathogenic and endophytic fungus-plant interactions. Significance statementRoot-infecting vascular fungi cause wilt diseases and provoke devastating losses in hundreds of crops. It is currently unknown how these pathogens evolved and whether they infect non-vascular plants, which diverged from vascular plants over 450 million years ago. Here we show that two strains of the fungus Fusarium oxysporum with opposed lifestyles, causing either wilting and death or beneficial protection on tomato, produce similar disease symptoms on the non-vascular plant Marchantia polymorpha. We define a set of core fungal pathogenicity factors required on both vascular and non-vascular plants and show that host-specific effectors contributing to disease on tomato are dispensable on Marchantia. These findings suggest that systemic wilt disease evolved in fungal pathogens after the emergence of vascular land plants.

plant biology↗

bioRxiv2019

Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity

Plant nucleotide-binding domain, leucine-rich repeat receptor (NLR) proteins play important roles in recognition of pathogen-derived effectors. However, the mechanism by which plant NLRs activate immunity is still largely unknown. The paired Arabidopsis NLRs RRS1-R and RPS4, that confer recognition of bacterial effectors AvrRps4 and PopP2, are well studied, but how the RRS1/RPS4 complex activates early immediate downstream responses upon effector detection is still poorly understood. To study RRS1/RPS4 responses without the influence of cell-surface receptor immune pathways, we generated an Arabidopsis line with inducible expression of effector AvrRps4. Induction does not lead to hypersensitive cell death response (HR) but can induce electrolyte leakage, which often correlates with plant cell death. Activation of RRS1 and RPS4 without pathogens cannot activate mitogen-associated protein kinase cascades, but still activates upregulation of defense genes, and therefore resistance against bacteria.\n\nHighlightInducible expression of AvrRps4 activates RRS1/RPS4-mediated effector-triggered immunity without the presence of pathogens, allowing us to characterise downstream immune responses triggered by TIR-NLRs without cell-surface receptor-mediated immunity.

plant biology↗