The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya.
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ABSTRACT:
SUBMITTER: Chaturvedi A
PROVIDER: S-EPMC8298701 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate fungal spore germination and hyphal branching, and promote the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We detected the presence of a cytokinin (isopentenyl adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellin A4) in spore extracts. We also used gas chromatography to show that R. irregularis produces ethylene from methionine and the α-keto γ-methylthio butyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.
| S-EPMC7567356 | biostudies-literature
Project description:Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if the AMF life cycle involves a sexual or parasexual stage. We used publicly available genome sequences to test if Rhizophagus irregularis dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display exclusively signatures of parasexual reproduction involving gene conversion. We used short-read and long-read sequence data to identify nucleus-specific alleles within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types as the dikaryon. We observed that the two nucleus-specific alleles of the dikaryon A5 are more related to the homolog sequences of monokaryon isolates displaying the same putative MAT-type than between each other. We also observed that these nucleus-specific alleles displayed reciprocal recombination signatures. These results confirm that dikaryon and monokaryon isolates displaying the same putative MAT-type are related in their life-cycle. These results suggest that a genetic exchange mechanism, involving reciprocal recombination in dikaryon genomes, allows AMF to generate genetic diversity.
| S-EPMC9249182 | biostudies-literature
Project description:Arbuscular mycorrhizal fungi arguably form the most successful and wide-spread endosymbiosis with plants. In general terms there is very little host-specificity in this interaction, indicating an extremely broad compatibility. However, host preferences as well as varying symbiotic efficiencies have been observed, the molecular basis of which is still largely unknown. Secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host-range. We investigated the expression of SP encoding genes of R. irregularis DAOM197198 in three evolutionary distantly related plant species, Medicago truncatula (Medicago), Nicotiana benthamiana (Nicotiana) and Allium schoenoprasum (Chives). In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the symbiotic interaction in Medicago. Our data indicate that the vast majority of 288 expressed SPs show equal expression levels in the interaction with all three host plants. In addition, a subset (~15%) of the SPs show significant differential expression depending on the host plant and/or environmental condition. This host-dependent expression appears to be controlled locally in the hyphal network in response to host metabolic cues. Overall, this study offers a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.
2018-03-27 | GSE99655 | GEO
Project description:Arbuscular mycorrhizal fungi (AMF), which form an ancient and widespread mutualistic symbiosis with plants, are a crucial but still enigmatic component of the plant micro biome. Nutrient exchange has probably been at the heart of the success of this plant-fungus interaction since the earliest days of plants on land. To characterize genes from the fungal partner involved in nutrient exchange, and presumably important for the functioning of the AM symbiosis, genome-wide transcriptomic data obtained from the AMF Rhizophagus irregularis were exploited. A gene sequence, showing amino acid sequence and transmembrane domains profile similar to members of the PTR2 family of fungal oligopeptide transporters, was identified and called RiPTR2. The functional properties of RiPTR2 were investigated by means of heterologous expression in Saccharomyces cerevisiae mutants defective in either one or both of its di/tripeptide transporter genes PTR2 and DAL5. These assays showed that RiPTR2 can transport dipeptides such as Ala-Leu, Ala-Tyr or Tyr-Ala. From the gene expression analyses it seems that RiPTR2 responds to different environmental clues when the fungus grows inside the root and in the extraradical phase.
| S-EPMC4153046 | biostudies-literature
Project description:Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.
| S-EPMC5982333 | biostudies-literature
Project description:Arbuscular mycorrhizal fungi (AMF) are plant symbionts that have a pivotal role in maintaining soil fertility and nutrient cycling. However, these microsymbionts may be exposed to organic pollutants like pesticides or veterinary drugs known to occur in agricultural soils. Anthelminthics are veterinary drugs that reach soils through the application of contaminated manures in agricultural settings. Their presence might threaten the function of AMF, considered as sensitive indicators of the toxicity of agrochemicals to the soil microbiota. We determined the impact of the anthelminthic compounds albendazole and ivermectin on the establishment and functionality of the symbiosis between the model-legume Lotus japonicus and the AMF Rhizophagus irregularis. Our analyses revealed negative effects of albendazole on the development and functionality of arbuscules, the symbiotic organelle of AMF, at a concentration of 0.75 μg g-1. The impairment of the symbiotic function was verified by the reduced expression of genes SbtM1, PT4 and AMT2;2 involved in arbuscules formation, P and N uptake, and the lower phosphorus shoot content detected in the albendazole-treated plants. Our results provide first evidence for the toxicity of albendazole on the colonization capacity and function of R. irregularis at concentrations that may occur in agricultural soils systematically amended with drug-containing manures.
| S-EPMC10696295 | biostudies-literature
Project description:The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AMfungi, and 108 genes were only expressed in non- mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AMcolonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AMfungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for under- standing the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.
2019-03-30 | GSE129059 | GEO
Project description:Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that have the potential to improve crop yield. These multinucleate organisms are either "homokaryotic" or "dikaryotic". In AMF dikaryons, thousands of nuclei originating from two parental strains coexist in the same cytoplasm. In other fungi, homokaryotic and dikaryotic strains show distinct life history traits (LHTs), such as variation in growth rates and fitness. However, how such traits compare between dikaryons and homokaryons of AMF is unknown. To address this, we measured 20 LHT of four dikaryons and five homokaryons of the model fungus Rhizophagus irregularis across root organ cultures of three host plants (carrot, chicory, and tobacco). Our analyses show that dikaryons have clearly distinct life history strategies (LHSs) compared to homokaryons. In particular, spores of homokaryons germinate faster and to a higher proportion than dikaryons, whereas dikaryons grow significantly faster and create a more complex hyphal network irrespective of host plant species. Our study links AMF nuclear status with key LHT with possible implications for mycorrhizal symbiotic functioning.
| S-EPMC8374082 | biostudies-literature
Project description:Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant-microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.
| S-EPMC6131194 | biostudies-literature
Project description:Nutrient acquisition and transfer are essential steps in the arbuscular mycorrhizal (AM) symbiosis, which is formed by the majority of land plants. Mineral nutrients are taken up by AM fungi from the soil and transferred to the plant partner. Within the cortical plant root cells the fungal hyphae form tree-like structures (arbuscules) where the nutrients are released to the plant-fungal interface, i.e., to the periarbuscular space, before being taken up by the plant. In exchange, the AM fungi receive carbohydrates from the plant host. Besides the well-studied uptake of phosphorus (P), the uptake and transfer of nitrogen (N) plays a crucial role in this mutualistic interaction. In the AM fungus Rhizophagus irregularis (formerly called Glomus intraradices), two ammonium transporters (AMT) were previously described, namely GintAMT1 and GintAMT2. Here, we report the identification and characterization of a newly identified R. irregularis AMT, GintAMT3. Phylogenetic analyses revealed high sequence similarity to previously identified AM fungal AMTs and a clear separation from other fungal AMTs. Topological analysis indicated GintAMT3 to be a membrane bound pore forming protein, and GFP tagging showed it to be highly expressed in the intraradical mycelium of a fully established AM symbiosis. Expression of GintAMT3 in yeast successfully complemented the yeast AMT triple deletion mutant (MATa ura3 mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2). GintAMT3 is characterized as a low affinity transport system with an apparent Km of 1.8 mM and a V max of 240 nmol(-1) min(-1) 10(8) cells(-1), which is regulated by substrate concentration and carbon supply.
| S-EPMC4879785 | biostudies-literature