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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

Identification of Arabidopsis NAI2 complex

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Transcription profiling of Arabidopis nai1-1, ER body deficient mutant, vs wild-type Col-0

Project description:ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1. Experiment Overall Design: Total RNA was purified from the roots of 20-day-old plants (3 plants were pooled for each genotype). Arabidopsis plants were grown under continuous light condition at 22ËC on MS medium paltes. The control plants and the nai1-1 mutant were cultivated in the same plate. This was done to avoid any difference in plant growth conditions between the mutants and the control plants.

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Suppression of oleosin in soybean cotyledon

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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]

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Oxidative burst causes loss of tapetal Ubisch body and male sterility in rice

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2024-06-30 | GSE250072 | GEO

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

nai1-1, ER body deficient mutant, vs wild-type Col-0

2007-06-04 | GSE6446 | 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.

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