Biology subjects

Paszkowski, U.

Publications and source records attributed to Paszkowski, U..

9 recordsLinked to original sources

bioRxiv2026

Gain-of-function CCaMK in rice overrides genetic and anatomical barriers to arbuscular mycorrhizal colonisation

Arbuscular mycorrhizal (AM) symbiosis is conserved across land plants and is the default nutrient uptake strategy in nature. Within roots, AM colonisation is tightly patterned and dynamically tuned by nutritional cues. Multiple genetic modules contribute to this regulation, including the phosphate starvation response, DWARF14-LIKE (D14L) karrikin signalling, and the common symbiosis signalling pathway (CSSP). Transcriptional overlap among these has led to the hypothesis that phosphate starvation and D14L signalling act upstream of the CSSP. Here, we examined the epistatic relationship between D14L and CSSP in rice. Overexpression of an autoactive gain-of-function CCaMK (gofCCaMKox) restored AM colonisation and symbiosis marker gene expression in d14l mutants to wild-type levels or above, whereas overexpression of wild-type CCaMK did not, confirming that CSSP operates downstream of D14L signalling. However, gofCCaMKox did not rescue the d14l mesocotyl elongation phenotype, supporting a bifurcation of D14L into developmental and symbiotic outputs. Unexpectedly, gofCCaMKox also expanded fungal access to normally restrictive tissue domains (the meristematic zone and endodermis) assigning a role for CCaMK activation in defining root zone and cell-type competence for AM colonisation. Despite restored colonisation, introduction of gofCCaMKox into d14l produced arbuscules, which however were less developed and had increased hyphal septation, revealing a CCaMK-independent role for D14L in intraradical colonisation and arbuscule development. Transcriptome profiling resolved AM-relevant genes into modules controlled by CCaMK activation alone, in combination with D14L, or requiring additional colonisation-associated cues, and further suggested CCaMK primarily acts through AP2 transcription factors. Together, these findings reinforce CCaMK as a master regulator of AM symbiosis at the genetic, transcriptomic and anatomical levels while uncovering CCaMK-independent functions of D14L in arbuscule development.

plant biology↗

bioRxiv2025

Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution

Arbuscular mycorrhizal (AM) symbiosis develops through successive colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, tree-like intracellular structures that are transient yet essential sites of nutrient exchange. To dissect the cellular and structural complexity of AM establishment in rice roots colonized by Rhizophagus irregularis, we applied dual-species spatial transcriptomics to simultaneously monitor plant and fungal gene transcripts at single-cell resolution. This approach revealed surprising differences in transcriptional activity between fungal structures and showed that morphologically similar arbuscules can be transcriptionally distinct. These findings suggest hidden functional diversity among arbuscules at single-cell resolution. Because arbuscules form and degenerate within only a few days, we further sought to capture translational activities across their life span. We pioneered AM-inducible TRAP-seq (Translating Ribosome Affinity Purification followed by RNA-seq) using stage-specific promoters, enabling cell-type- and stage-resolved profiling in AM symbiosis. This revealed extensive spatiotemporal reprogramming of nutrient transport and signalling, with distinct sets of phosphate, nitrogen, and carbon transporters and regulators induced or repressed at different stages of arbuscule development, suggesting that nutrient exchange is dynamically regulated across the arbuscule life cycle. More broadly, cell wall biosynthesis genes and key defence markers were suppressed during arbuscule formation, whereas at a later stage, defence markers were strongly upregulated, suggesting a host-driven shift towards arbuscule termination. Together, these findings highlight the nuanced and dynamic regulation of AM symbiosis at the cellular level, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time.

plant biology↗

bioRxiv2025

Defining the pre-symbiotic transcriptional landscape of rice roots

Plants interact with a plethora of organisms in the rhizosphere, with outcomes that range from detrimental to beneficial. Arbuscular mycorrhizal (AM) symbiosis is the most ubiquitous beneficial plant interaction in terrestrial ecosystems and involves soil borne fungi of the Glomeromycotina. It is believed that plants detect diagnostic signals for the discrimination between beneficial arbuscular mycorrhizal (AM) fungi and parasitic fungi during the pre-symbiotic molecular crosstalk. Here, we investigated the transcriptome of rice roots upon exposure to the complete cocktail of fungal exudates from either beneficial Rhizophagus irregularis or pathogenic Magnaporthe oryzae. We report that regardless of the exudate donor species, the transcriptional response lacked diagnostic differences. Instead, the profiles were marked by the common suppression of symbiosis signalling components, accompanied by the induction of a generic stress response (GSR) and defense-related signature, which was retained in a suite of symbiosis signalling mutants impaired at different stages of symbiosis development. However, upon permitting physical engagement with AM fungi, a striking reversion in the transcriptional responses occurred marked by the simultaneous relaxation of symbiosis signalling suppression and down-regulation of defense-related and GSR markers, overall comparable between wild-type and mutants. Our data therefore reveal that rather than specific recognition in the rhizosphere, a sequence of signals orchestrates stress, immunity and symbiosis, pivoting towards symbiosis potentially at the stage of plant-fungal contact formation. Significance StatementMost plant roots engage in symbiosis with beneficial mycorrhizal fungi. Before physical contact, early signal exchanges involve diffusible molecules. The bouquet of chemicals released by beneficial versus detrimental fungi has been proposed to convey specificity for signal transduction, transcriptional output and responses. Here we characterised the transcriptomes of rice roots to exudates from beneficial and pathogenic fungi, and found that they lack specific signatures but elicit a generic stress and immune response and suppression of symbiosis signalling. This profile was reversed, along with activation of symbiotic transcriptional responses, only when AM fungi were allowed to establish physical contact. This reveals the need for additional, unknown, layers of signal exchanges for plants to commit to symbiosis.

plant biology↗

bioRxiv2025

Reductive evolution of the DNA replication machinery in endosymbiotic fungi

The molecular machinery for replicating and repairing DNA accurately is critically important for life and highly conserved across the Tree of Life. Here we show that two major lineages of fungi, Glomeromycotina and Microsporidia, lost DNA polymerase complexes involved in replication and translesion synthesis. Catalytic and non-catalytic subunits of DNA polymerases are co-eliminated, consistent with their physical and functional interactions described in other eukaryotes. We detect lineage-specific variation in genome-wide mutation rates, showing that DNA polymerase gene losses correlate with increased genetic variation. We find that the Glomeraceae family of arbuscular mycorrhizal (AM) fungi has lived for [~]360 My without a leading strand replisome, raising the question of how these fungi can replicate DNA. We provide evidence that the cell cycle of Rhizophagus irregularis is active when in symbiosis with a host, but not without. This indicates a higher level of integration between AM fungi and plants than previously appreciated, and suggests the existence of a regulatory or functional contribution provided by a host to the fungal cell cycle. We propose that alternative modes of DNA replication and cell cycle provide mutational opportunities for fungal adaptation, and play roles in the evolution of endosymbioses.

evolutionary biology↗

bioRxiv2025

Drought drives reversible disengagement of root-mycorrhizal symbiosis

The increasing frequency and severity of droughts pose a major threat to agriculture, food security and ecosystems. Plants respond to water deficit by adjusting growth and metabolism to enhance survival; these adjustments impact the soil microorganisms interacting with plant roots. Plants establish symbiotic relationships with arbuscular mycorrhizal fungi which supply soil nutrients in exchange for carbon metabolites via an intricate dual-species interface within roots. These fungi are dependent upon host-derived photosynthates and are thus potentially vulnerable to plant perturbations during drought. Here, we demonstrate that the plant-mycorrhizal relationship is dynamic when water becomes limiting. During water deficit, rice de-prioritizes nutrient acquisition gene regulatory networks, including its AM symbiotic program, in a strategy conserved with tomato. The fungal symbiont correspondingly represses its growth, undergoing metabolic quiescence, coupled with decommissioning of hyphae within the hosts root. Following re-watering, the host re-engages with its partner fungus, re-invigorating fungal growth and arbuscule establishment. This coordinate, reversible and enduring inter-organismal association may aid host survival under transient stress, but suggests that mutualisms in native and crop plants are potentially fragile in increasingly erratic climates.

plant biology↗

bioRxiv2022

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

The root systems of most plant species are aided by the soil foraging capacities of symbiotic Arbuscular Mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here are the most contiguous and highest-quality nuclear and mitochondrial genome assemblies of an arbuscular mycorrhizal fungus to date, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of Rhizophagus irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalogue of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While symbiotic nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle. HighlightsO_LIAssembly of 32 highly contiguous chromosomal scaffolds for R. irregularis, with 23 complete and gapless C_LIO_LIGene annotation based on short- and long-read RNA-Seq data from different developmental stages C_LIO_LIComplete annotation set including mitochondrial genes, DNA methylome, small RNAome, repetitive/transposable elements, functional annotation C_LIO_LIIdentification of a burst of lineage-restricted genetic innovation in the Glomeromycotina subphylum C_LI

genomics↗

bioRxiv2021

Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species and have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Characterising the epigenomic status of R. irregularis provides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.

genomics↗

bioRxiv2020

Transcriptional responses to arbuscular mycorrhizal symbiosis development are conserved in the early divergent Marchantia paleacea

Arbuscular mycorrhizal symbiosis (AMS) arose in land plants more than 400 million years ago, perhaps acting as a major contributor to plant terrestrialization. The ability to engage in AMS is evolutionarily conserved across most clades of extant land plants, including early diverging bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components that underpin AMS in early diverging land plants as the mechanisms regulating the symbiosis were primarily characterized in angiosperms. Several AMS associated genes were recently shown to be conserved in liverworts and hornworts, but evidence of them being associated with symbiosis in bryophytes is scarce. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across progressive stages of symbiosis development. Gene orthology inference and comparative analysis of the M. paleacea transcriptional profile with a well characterised legume model -Medicago truncatula - revealed a deep conservation of transcriptional responses to AMS across distantly related species. We identified evolutionarily conserved patterns of expression of genes required for pre-symbiotic signalling, intracellular colonization and symbiotic nutrient exchange. Our study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across distantly related land plants. If bryophytes are confirmed to be monophyletic, our analysis provides novel insights on the first molecular pathways associated with symbiosis at the dawn of plant colonization of land. Significance StatementArbuscular mycorrhizal symbiosis (AMS) between plants and soil fungi was proposed as one of the key adaptations enabling land colonization by plants. The symbiosis is widespread across most extant plant clades, including early-diverging bryophytes, suggesting that it evolved before the last common ancestor of land plants. Recent phylogenetic analyses uncovered that genes regulating AMS in angiosperms are present in the genomes of bryophytes. Our work shows that a set of these genes are transcriptionally induced during AMS in liverworts. Based on the conservation of their transcriptional profiles across land plants, we propose that these genes acquired an AMS-associated function before the last common ancestor of land plants.

plant biology↗

bioRxiv2017

Coordinated Changes In The Accumulation Of Metal Ions In Maize (Zea mays ssp. mays L.) In Response To Inoculation With The Arbuscular Mycorrhizal Fungus Funneliformis mosseae

Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of nineteen elements was determined in the roots and leaves of a panel of thirty maize varieties, grown under phosphorus limiting conditions, with, or without, inoculation with the fungus Funneliformis mosseae. Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a coordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants.\n\nAbbreviations

plant biology↗