Ontology highlight
ABSTRACT:
PROVIDER: PRJNA623600 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11508649_1.fastq.gz | Fastqsanger.gz | |||
| SRR11508649_2.fastq.gz | Fastqsanger.gz | |||
| SRR11508650_1.fastq.gz | Fastqsanger.gz | |||
| SRR11508650_2.fastq.gz | Fastqsanger.gz | |||
| SRR11508651_1.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study was to identify fungal gene expression changes during early stages of symbiosis establishment with its Burkholderia endosymbionts. Results: Leveraging this RNA-seq dataset we identified fungal genes utilized for symbiosis establishment with bacteria.
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Project description:The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive CCaMK via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscules size. BCP1, SbtM1, and WRI5a, whose expression was correlated with NF-YC3 level, might be downstream of NF-YC3. NF-YC3 interacted with one of three NF-YBs, NF-YB3a, NF-YB5c, or NF-YB3b, in yeast and in planta, and interacted with NF-YA3a in yeast. Spatial expression of three NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Knockdown of three NF-YBs collectively, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be important downstream gene of common symbiosis signaling pathway.
2024-07-31 | GSE263861 | GEO
Project description: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 expression 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, indicating that nutrient exchange is not uniform but finely modulated across individual structures. Because arbuscules form and degenerate within only a few days, we further sought to capture translational regulation 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 for the first time in AM symbiosis. This revealed extensive spatiotemporal reprogramming of nutrient transport and signaling, with distinct sets of phosphate, nitrogen, and carbon transporters and regulators upregulated 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 upon collapse, defence markers were strongly upregulated, suggesting a host-driven shift towards symbiosis termination. Together, these findings highlight the nuanced and dynamic regulation of AM symbiosis at cellular resolution, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time, and providing a framework for further functional exploration.
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Project description: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 expression 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, indicating that nutrient exchange is not uniform but finely modulated across individual structures. Because arbuscules form and degenerate within only a few days, we further sought to capture translational regulation 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 for the first time in AM symbiosis. This revealed extensive spatiotemporal reprogramming of nutrient transport and signaling, with distinct sets of phosphate, nitrogen, and carbon transporters and regulators upregulated 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 upon collapse, defence markers were strongly upregulated, suggesting a host-driven shift towards symbiosis termination. Together, these findings highlight the nuanced and dynamic regulation of AM symbiosis at cellular resolution, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time, and providing a framework for further functional exploration.
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Project description:Rhizopus microsporus is one of the most common agents of mucormycosis, a severe and emerging infection caused by Mucorales fungi that poses a significant clinical challenge, particularly due to the growing population of immunocompromised individuals. An substantial proportion of clinical isolates harbor bacterial endosymbionts, which regulate key fungal functions, such asexual sporulation. The strict dependence on endosymbionts for spore formation has limited a comprehensive understanding of endosymbiosis in R. microsporus biology. Here, we demonstrate that sporulation in endosymbiont-cured strains of this fungus, which previously harbored Mycetohabitans bacteria, can be induced by light. Interestingly, both light and endosymbionts regulate sporulation through the same regulatory pathway, and a high proportion of the genes upregulated by these signals are known to be involved in asexual sporulation in other fungi, including Mucorales. Light-induced sporulation enabled comparative assays to assess the impact of symbiosis on fungal traits. In addition to previously known effects on fungal fitness, this study reveals that germination is independent of endosymbionts, although their presence accelerates the process. Furthermore, it shows that asexual spores lacking endosymbionts exhibit a reduced virulence in a mouse model of mucormycosis. The discovery of light-induced sporulation in endosymbiont-free strains of R. microsporus paves the way for future comparative studies using genetically identical backgrounds, advancing our understanding of fungal-bacterial symbiosis and its role in fungal biology and human pathogenesis.
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