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MetaboLights MTBLS1383 - GNPS Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants

ABSTRACT: Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body ?-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the ?-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system.

INSTRUMENT(S): LTQ Orbitrap|1000449

ORGANISM(S): Arabidopsis Thaliana|3702

SUBMITTER: Kenji Yamada

PROVIDER: MSV000085767 | GNPS | Thu Jul 16 13:34:00 BST 2020

REPOSITORIES: GNPS

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Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants

Project description:Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system.

2020-02-04 | MTBLS1383 | MetaboLights

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [DNA methylation]

Project description:Background: Plants memorize previous pathogen attacks and are ‘primed’ to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear. Results: Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss of function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1. Conclusions: Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.

2023-04-14 | GSE98162 | GEO

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [expression]

2023-04-14 | GSE59914 | GEO

Glycolytic Enzyme Coalesce in G bodies Under Hypoxic Stress

Project description:Glycolysis is upregulated in cells under specific conditions, such as hypoxia and high energy demand, to achieve the metabolic requirements for continued cell proliferation. However, the mechanism of this increased glycolytic rate remains poorly understood. In the budding yeast Saccharomyces cerevisiae, we discovered that hypoxia induces concentration of many glycolytic enzymes, including the Pfk2p subunit of the ratelimiting enzyme, phosphofructokinase, into a single, non-membrane-bound granule that we define as the "glycolytic body" or "G body". Pfk2p localization to G bodies depends on its N-terminal, intrinsically disordered region. In order to identify factors important for G body formation, we conducted a yeast kinome screen and identified the AMP kinase ortholog, Snf1p, to be required for the localization of multiple glycolytic enzymes to G bodies. Further, proteomic analyses of purified G bodies identified a core set of resident factors, many of which are essential for G body integrity. Cells incapable of forming G bodies in hypoxic conditions display abnormal cell division and produce inviable daughter cells. Conversely, cells that form G bodies show increased glucose consumption and decreased levels of glycolytic intermediates. Importantly, G bodies also form in human, hepatocarcinoma cells upon hypoxic stress. Together, our results suggest that G body formation is a conserved, adaptive response to increase glycolytic output during hypoxia or tumorigenesis.

2017-07-24 | PXD006686 | Pride

HITS-CLIP analysis of Yb binding sites in Drosophila ovary cell line

Project description:piRNAs direct Piwi to repress transposons to maintain genome integrity in Drosophila ovarian somatic cells. piRNA maturation and association with Piwi occur at perinuclear Yb bodies, the centers of piRNA biogenesis. Here, we show that piRNA intermediates arising from the piRNA cluster flamenco (flam) concentrate into perinuclear foci adjacent to Yb bodies, termed Flam bodies. Although flam expression is not required for Yb body formation, Yb, the core component of Yb bodies, is required for Flam body formation. Abolishment of the RNA-binding activity of Yb disrupts both Yb bodies and Flam bodies. Loss of Zucchini, an endoribonuclease necessary for piRNA maturation, enlarges Flam bodies, which now superimpose with Yb bodies. Yb directly binds flam, but not neighboring protein-coding gene, transcripts. Thus, Yb integrates piRNA processing factors and piRNA intermediates into Yb bodies and Flam bodies, respectively, through direct binding to enhance piRNA biogenesis and formation of piRNA-inducing silencing complexes. HITS-CLIP was performed using OSC (Ovarian Somatic Cells). The antibody for Drosophila Yb, which was generated in this study, was used. Obtained CLIP tags were analyzed using illumina HiSeq200.

2014-06-24 | E-GEOD-54875 | biostudies-arrayexpress

Identification of Arabidopsis NAI2 complex

Project description:ER bodies are ~10-µm-long, spindle-shaped structures that occur in Brassicaceae plants. They are distributed throughout the epidermal cells of cotyledons and hypocotyls, but subsequently disappear with seedling growth, while they constitutively develop in the epidermal cells of roots. NAI2 is an ER body protein responsible for ER body formation. To understand molecular mechanism of ER body formation by NAI2, we generated transgenic plants that expressed NAI2-GFP under control of the native NAI2 promoter, and conducted immunoprecipitation with anti-GFP antibodies and detected with mass

2020-01-17 | PXD016606 | Pride

HITS-CLIP analysis of Yb binding sites in Drosophila ovary cell line

2014-06-24 | GSE54875 | GEO

MNase-seq analysis of Col-0 and chr11-1 chr17-1

Project description:Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. Here we use the Micrococcal Nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in plants and the role of the Arabidopsis thaliana Imitation Switch (AtISWI) subfamily remodelers in the pattern formation. Our data revealed three patterns in wild-type plants: 1) Promoters have a relative low nucleosome density compared with gene bodies; 2) Nucleosome density is negatively associated with gene expression levels; 3) The evenly and periodically spaced nucleosomes in gene bodies are positively associated with gene expression levels. Double mutations in the AtISWI genes CHROMATIN REMODELING 11 (CHR11) and CHR17 resulted in loss of the evenly-spaced-nucleosome pattern in gene bodies, but did not affect nucleosome density, suggesting that the primary role of AtISWI is to slide nucleosomes in gene bodies for promotion of transcription.

2014-03-30 | GSE50242 | GEO

Suppression of oleosin in soybean cotyledon

Project description:3 samples, 2 reps each. comparison of wildtype cotyledon to RNAioleosin transgenic Using RNAi, the seed oil body protein 24-kDa oleosin has been suppressed in transgenic soybeans. The endoplasmic reticulum (ER) forms micro-oil bodies about 50 nm in diameter that coalesce with adjacent oil bodies forming a hierarchy of oil body sizes. The oil bodies in the oleosin knockdown form large oil body-ER complexes with the interior dominated by micro-oil bodies and intermediate-sized oil bodies, while the peripheral areas of the complex are dominated by large oil bodies. The complex merges to form giant oil bodies with onset of seed dormancy that disrupts cell structure. The transcriptome of the oleosin knockdown shows few changes compared to wild-type. Proteomic analysis of the isolated oil bodies of the 24-kDa oleosin knockdown shows the absence of the 24-kDa oleosin and the presence of abundant caleosin and lipoxygenase. The formation of the micro-oil bodies in the oleosin knockdown is interpreted to indicate a function of the oleosin as a surfactant.

2008-08-15 | GSE12300 | GEO

Chromatin Immunoprecipitation sequencing of heterochromation associated proteins in Tetrahymena

Project description:In the ciliated protozoan Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. We previously reported that dephosphorylation of the HP1-like protein Pdd1p is required for the formation of heterochromatin bodies during the process of programmed DNA elimination in the ciliated protozoan Tetrahymena. Here, we show that the heterochromatin body component Jub4p is required for Pdd1p phosphorylation, heterochromatin body formation and DNA elimination. Moreover, our analyses of unphosphorylatable Pdd1p mutants demonstrate that Pdd1p phosphorylation is required for heterochromatin body formation and DNA elimination, while it is dispensable for local heterochromatin assembly. Therefore, both phosphorylation and the following dephosphorylation of Pdd1p are necessary to facilitate the formation of heterochromatin bodies. We suggest that Jub4p-mediated phosphorylation of Pdd1p creates a chromatin environment that is a prerequisite for subsequent heterochromatin body assembly and DNA elimination. New macronuclei (MACs) of exconjugants were isolated from wild-type and various mutant cells at 12 hpm (hours post-mixing), sheared chromatin was immunoprecipitated andprecipitated DNA was analyzed by high-throughput sequencing

2016-07-15 | E-GEOD-83249 | biostudies-arrayexpress

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