Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of host benefits
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE222356 | GEO | 2023/06/07
REPOSITORIES: GEO
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Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Previous studies highlighted an important role of calcium Ca2+ signaling in the establishment of the plant–fungus interaction. We here report the comparative analysis of the effect of a mock- and S. indica-infection on both wild-type Arabidopsis plants (Col-3) and cbl7 knockout mutants. Our data provide evidence for the involement of the Ca2+ sensor CBL7 in the control of potassium distribution in the plant and in adjusting plant defense responses to allow the establishment of the plant–fungus symbiosis. The impairment of CBL7 was shown to translate into increased induction of plant defense-related genes.
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Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Co-cultivation of Arabidopsis thaliana seedlings with the fungus triggers a substantial induction of the growth of the root system. However, the molecular mechanisms by which the fungus promotes plant growth over an extended period of time is still unclear. We here report the comparative analysis of the effect of a mock- and S. indica-infection on wild-type Arabidopsis plants (Col-0) after 2 and 10 days of co-cultivation. Our data provide evidence for the induction of a number of genes that are consistingly induced during the plant–fungus interaction.
2023-09-04 | GSE241902 | GEO
Project description:High ambient temperature regulated the plant systemic response to the beneficial endophytic fungus Serendipita indica. Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild type plants.
2022-02-26 | GSE197325 | GEO
Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Moreover, previous studies highlighted an important impact of the fungus on auxin homeostasis during the infection of Arabidopsis thaliana plants. Auxin is a key determinant of plant growth, including the growth of the root system. Auxin overproducing mutants, like for instance YUC9oe (Hentrich et al., 2013 Plant J.), show a pronounced root phenotype that can be restored by the co-cultivation with S. indica. We here report the comparative analysis of the effect of a mock- and S. indica-infection on both wild-type Arabidopsis plants (Col-0) and YUC9 overexpressing mutants. Our data provide evidence for the induction of GRETCHEN HAGEN 3 (GH3) genes that are involved in conjugating active free indole-3-acetic acid with amino acids. The fungus triggered induction GH3s is suggested to be involved in affecting the cellular auxin homeostasis.
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Project description:The deep-sea tubeworm Riftia pachyptila is a model system for a mutualistic association: The adult worm has no digestive system, but completely relies on one phylotype of endosymbiotic chemosynthetic bacteria for nutrition. The bacteria, in turn, are provisioned by the host. Metabolism and physiology of this symbiosis, particularly of the uncultured symbiont, have been subject to various studies. Yet, how both partners interact on the molecular level remains largely unknown. To study these host-symbiont interactions in detail, we sequenced the R. pachyptila host transcriptome de novo, and conducted comprehensive metaproteomic comparisons of symbiont-containing and symbiont-free R. pachyptila tissues under energy-rich and energy-limiting conditions. Our results demonstrate that R. pachyptila invests a considerable part of its proteome to provision the symbionts with inorganic compounds. It acquires symbiont-derived biomass primarily by digesting parts of the symbiont population. The R. pachyptila immune system apparently not only protects the holobiont from pathogens, but is also involved in symbiont population control. The symbiont expresses a repertoire of proteins dedicated to communication with the host, including eukaryote-like proteins that may counteract phagocytosis. During energy limitation, i.e., when reduced sulfur compounds are lacking, the host apparently increases symbiont digestion. We show here an intricate network of interaction pathways that shapes the R. pachyptila holobiont. Together with the metabolic flexibility of the association under varying energy conditions, this probably forms the basis for the success of this tight association under the highly challenging deep-sea conditions.
2019-11-25 | PXD012439 | Pride
Project description:Bathymodiolus mussels inhabiting deep-sea hydrothermal vents harbor bacterial symbionts in their gills, which support the animals’ diet. While the basic mechanisms of energy generation and CO2 fixation that drive these symbioses are largely established, details of molecular interactions between the symbiotic partners and adaptations to their respective habitats remain unknown. In this study, we therefore comparatively examined the genomes and proteomes of two Bathymodiolus hosts and their respective symbionts from different geographical locations. Two mussel species were proteomically compared: i) B. thermophilus mussel containing sulfur-oxidizing symbiont from the east pacific rise. thermophilus and ii) B. azoricus containing thiotrophic and methanotrophic symbionts from the mid-atlantic ridge. Symbionts (for both species) and host components (for B. azoricus) were selectively enriched using a multi-step centrifugation procedure. Enriched host and symbiont fractions along with unenriched gill foot tissue were subject to in-depth semi-quantitative proteomic analyses using the orbitrap and velos mass spectrometers. Proteins were quantified based on their spectral counts using the normalized spectral abundance factor (NSAF) method. We identified common strategies of metabolic interactions that provide mutual nutritional support between host and symbionts, such as the detoxification of ambient sulfide by the Bathymodiolus host, which provides a stable thiosulfate reservoir for the thiotrophic symbionts, and a putative amino acid cycling mechanism that could supply the host with symbiont-derived amino acids. A suite of genes and proteins putatively related to virulence or defense functions was particularly abundant in the B. thermophilus symbiont, compared to its symbiont relatives, and may pose a host species-specific adaptation. Our results reveal both, a high degree of integration between the symbiotic partners, and great potential to adapt to the prevailing environment, which facilitate the holobiont’s survival in its hydrothermal vent habitat.
2019-11-08 | PXD011639 | Pride
Project description:We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). sRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (SE). Raw reads from sRNA sequencing were submitted to technical adapter trimming (Cutadapt) before upload.
2021-07-15 | E-MTAB-10650 | biostudies-arrayexpress
Project description:Bathymodiolus azoricus is a deep-sea mussel found in the hydrothermal vent fields of the Mid-Atlantic Ridge. It lives in symbiosis with sulfur- and methane-oxidizing γ-proteobacteria within its gills. In our study, we aimed to understand the metabolic and physiological interconnections between the symbiotic partners. For this purpose, symbionts and host were physically separated using density gradient centrifugation. This procedure yielded a symbiont-enriched gradient pellet fraction and a supernatant fraction enriched in host components. The cytosolic and membrane-associated proteome of both these fractions along with whole gill and foot tissue of the mussel were then investigated through 1D-PAGE LC-MS/MS. Proteins were quantified based on their spectral counts using the NSAF method. For efficient identification, sequences from evolutionarily related endosymbiotic and free-living bacteria and from bivalve host relatives were compiled into a comprehensive protein database. A total of 3178 host and symbiont proteins were identified from all samples.
2016-10-06 | PXD004061 | Pride
Project description:Background: The molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host Results: In the current study, we utilised dual RNA-seq approach to study both symbiont and coral transcriptomes during symbiosis establishment. The transcriptomic response of C. goreaui to the symbiotic state was complex, the most obvious feature of which was extensive and generalized downregulation of gene expression. Included in this “symbiosis-derived transcriptional repression” were a range of stress response and immune-related genes. In contrast, a range of genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of C. goreaui suggests that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship is established at the larval stage. The coral data imply the involvement of some SCRiP family members in the colonisation process and support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses. Conclusions: This study provides novel insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.
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