Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA318469 | ENA |
REPOSITORIES: ENA
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Project description:The N-end rule pathway is a highly conserved constituent of the ubiquitin proteasome system, though little information exists regarding biological roles. Here we show that the cysteine (Cys-) and glutamine (Gln)-specific amino-terminal (Nt)-amidase NTAQ1 branches are both components of the plant immune system, through the E3 ligase PROTEOLYSIS (PRT)6. Both ntaq1 and prt6 mutants of Arabidopsis thaliana showed enhanced basal resistance to the hemibiotroph pathogen Pseudomonas syringae, associated with constitutive expression of defence-response genes and activation of synthesis pathway of the phytoalexin camalexin. We observed a role in stomatal defence for the Nt-Cys substrates ETHYLENE RESPONSE FACTOR VII transcription factors. Transgenic barley lines with reduced HvPRT6 expression showed enhanced resistance against Ps japonica and Blumeria graminis f. sp. Hordei, indicating a conserved role of the pathway in immunity. These data demonstrate that different branches of the N-end rule pathway act at distinct levels of the plant immune response.
2018-11-06 | PXD008520 | Pride
Project description:Targeted proteomics has become increasingly popular recently because of its ability to precisely quantify selected proteins in complex cellular backgrounds. We demonstrate the utility of an LTQ-Orbitrap Velos Pro mass spectrometer in targeted parallel reaction monitoring (PRM) despite its unconventional dual ion trap configuration. We evaluated absolute specificity (>99%) and sensitivity (100 amol on column in 1µg total cellular extract) using full and mass range scans as survey scans together with data dependent (DDA) and targeted MS/MS acquisition. The instrument duty cycle was a critical parameter limiting sensitivity necessitating peptide retention time scheduling. We assessed synthetic peptide and recombinant peptide standards to predict or experimentally determine target peptide retention times. We applied optimized PRM to protein degradation in signaling regulation, an area that is receiving increased attention in plant physiology. We quantified relative abundance of selected proteins in plants mutant for enzymatic components of the N-end rule degradation (NERD) pathway such as the two tRNA-arginyl-transferases ATE1 and ATE2 and the two E3 ubiquitin ligases PROTEOLYSIS1 and 6 searching for upregulated proteins. We also targeted FLAGELLIN SENSITIVE2 (FLS2), a pattern recognition receptors responsible pathogen sensing, in ubiquitin ligase mutants to assay the attenuation of plant immunity by degradation of the receptor.
2015-12-09 | PXD001119 | Pride
Project description:In Arabidopsis thaliana the evolutionary conserved N-terminal acetyltransferase (Nat) complexes NatA and NatB co-translationally acetylate 60% of the proteome. Both have recently been implicated in the regulation of plant stress responses. While NatA mediates drought tolerance, NatB is required for pathogen resistance and the adaptation to high salinity and high osmolarity. Salt and osmotic stress impair protein folding and result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER). The ER-membrane resident E3 ubiquitin ligase DOA10 targets misfolded proteins for degradation during ER stress and is conserved among eukaryotes. In yeast, DOA10 recognizes conditional degradation signals (Ac/N-degrons) created by NatA and NatB. Assuming that this mechanism is preserved in plants, the lack of Ac/N-degrons required for efficient removal of misfolded proteins might explain the sensitivity of NatB mutants to protein harming conditions. In this study, we investigate the response of NatB mutants to dithiothreitol (DTT) and tunicamycin (TM) induced ER stress. We report that NatB mutants are hypersensitive to DTT but not TM, suggesting that the DTT hypersensitivity is caused by an over-reduction of the cytosol rather than an accumulation of unfolded proteins in the ER. In line with this hypothesis, the cytosol of NatB depleted plants is constitutively over-reduced and a global transcriptome analysis reveals that their reductive stress response is permanently activated. Moreover, we demonstrate that doa10 mutants are susceptible to neither DTT nor TM, ruling out a substantial role of DOA10 in ER-associated protein degradation (ERAD) in plants. Contrary to previous findings in yeast, our data indicates that N-terminal acetylation (NTA) does not inhibit ER targeting of a substantial amount of proteins in plants. In summary, we provide further evidence that NatB-mediated imprinting of the proteome is vital for the response to protein-harming stress and rule out DOA10 as the sole recognin for substrates in the plant ERAD pathway.
2021-11-29 | GSE186324 | GEO
Project description:Intron-containing gene expression in eukaryotes proceeds through the process of RNA splicing to generate protein-coding messenger RNAs (mRNAs). Herein a large and dynamic ribonucleoprotein complex — the spliceosome — removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must also ensure accurate and timely removal of diverse and highly prevalent introns. Here we show that Sde2 is a conserved splicing regulator, contains a ubiquitin fold, and supports splicing of a subset of pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Its orthologs in S. pombe and humans are synthesized as precursors harboring a ubiquitin fold, followed by an invariant GGKGG motif and an uncharacterized C-terminal domain (referred to as Sde2-C). The precursor must be cleaved at GG^K by the ubiquitin specific proteases Ubp5 and Ubp15 to produce the Sde2-C protein containing a lysine residue at its C-terminus, and is a substrate of the N-end rule pathway of proteasomal degradation. The truncated Sde2-C functions as a component of the spliceosome, and loss of Sde2-C results in inefficient splicing of selected introns from target genes having functions in DNA replication, transcription and telomeric silencing. Thus, the ubiquitin-like processing of Sde2 — associated with its regulation by the N-end rule pathway — contributes to genomic stability in S. pombe through specific pre-mRNA splicing events.
2017-09-22 | GSE97097 | GEO
Project description:The polycomb repressive complex 2 (PRC2) regulates epigenetic gene repression in eukaryotes. Mechanisms controlling its developmental specificity and signal-responsiveness are poorly understood. Here, we identify an oxygen-sensitive N-terminal (N-) degron in the plant PRC2 subunit VERNALIZATION(VRN)2, a homolog of animal Su(z)12, that promotes its degradation via the N-end rule pathway. We provide evidence that this N-degron arose early during angiosperm evolution via gene duplication and N-terminal truncation, facilitating expansion of PRC2 function in flowering plants. We show that proteolysis via the N-end rule pathway prevents ectopic VRN2 accumulation, and that hypoxia and long-term cold exposure lead to increased VRN2 abundance, which we propose may be due to inhibition of VRN2 turnover via its N-degron. Furthermore, we identify an overlap in the transcriptional responses to hypoxia and prolonged cold, and show that VRN2 promotes tolerance to hypoxia. Our work reveals a mechanism for post-translational regulation of VRN2 stability that could potentially link environmental inputs to the epigenetic control of plant development.
2018-12-07 | GSE123459 | GEO
Project description:With frequent fluctuations in global climate, plants often experience co-occurring dry-wet cycles and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed or drought recovered plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis plants were exposed to individual drought stress (soil drying at 40% FC, D), Pseudomonas syringae pv tomato DC3000 (PStDC3000), infection and their combination. Plants recovered from drought stress were also exposed to PStDC3000. Beside we have also infiltrated P. syringae pv tabaci (PSta, non-host pathogen) individually or in combination with drought stress. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of plants leaves under individual drought stress and pathogen infection was compared with their combination. Results implicate that plants exposed to combined drought and pathogen stress experience a new state of stress where each combination of stressor and their timing defines the plant responses and thus should be studied explicitly. Global transcriptional analysis in Arabidopsis leaves exposed to individual and combined drought and pathogen stress.
2017-02-11 | GSE79681 | GEO
Project description:The plant innate immunity consists of the two interconnected mechanisms, pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Although much is known about how plants trigger immune responses upon pathogen recognition, the genetic program by which plants avoid an overshoot in pathogen-triggered immune responses remains largely unknown. Here, we discovered a trihelix transcription factor, GT-3a, as an immune-inducible negative regulator of bacterial resistance in Arabidopsis thaliana. Analysis of public RNA-seq data revealed that GT-3a is specifically induced by ETI activation not by PTI activation. Overexpression of GT-3a suppressed resistance against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) and Pto-elicited expression of salicylic acid (SA)-responsive genes. Our results suggest that transcriptional induction of GT-3a circumvents the overshooting of SA-mediated defense responses during ETI.
2024-02-18 | GSE248054 | GEO
Project description:Plant microRNAs (miRNAs) have been implicated in plant immunity. These mainly focusing Arabidopsis thaliana threatened by (hemi-)biotrophic pathogens such as the bacterial pathogen Pseudomonas syringae. Here, we show that the Arabidopsis miRNA pathway is important for defense responses against the necrotrophic fungus Alternaria brassicicola. The miRNA pathway mutant ago1 exhibits an exaggerated response when treated with A. brassicicola, proposing that AGO1 is positive regulator. We found a subset of Arabidopsis miRNAs that quickly change their expression and their abundance in AGO1 complexes in plants exposed to A. brassicicola. The miRNAs responding to pathogen treatment are mainly targeting genes encoding metabolic enzymes, proteins involved protein degradation or transposons. In case of miR163, A. brassicicola infection results in increased levels of miRNA precursors and preferential accumulation of an unspliced form of pri-miR163, suggesting that A. brassicicola infection changes the transcriptional and post-regulation of pri-miRNAs. miR163 acts as a negative regulator of plant defense because mir163 mutants are more resistant when treated with A. brassicicola. Taken together, our results reveal the existence of positively and negatively acting Arabidopsis miRNA modulating the defense responses against A. brassicicola and highlight the importance of host miRNAs in the interaction between plants and necrotrophic pathogens.
2019-06-17 | GSE83487 | GEO
Project description:Plant microRNAs (miRNAs) have been implicated in plant immunity. These mainly focusing Arabidopsis thaliana threatened by (hemi-)biotrophic pathogens such as the bacterial pathogen Pseudomonas syringae. Here, we show that the Arabidopsis miRNA pathway is important for defense responses against the necrotrophic fungus Alternaria brassicicola. The miRNA pathway mutant ago1 exhibits an exaggerated response when treated with A. brassicicola, proposing that AGO1 is positive regulator. We found a subset of Arabidopsis miRNAs that quickly change their expression and their abundance in AGO1 complexes in plants exposed to A. brassicicola. The miRNAs responding to pathogen treatment are mainly targeting genes encoding metabolic enzymes, proteins involved protein degradation or transposons. In case of miR163, A. brassicicola infection results in increased levels of miRNA precursors and preferential accumulation of an unspliced form of pri-miR163, suggesting that A. brassicicola infection changes the transcriptional and post-regulation of pri-miRNAs. miR163 acts as a negative regulator of plant defense because mir163 mutants are more resistant when treated with A. brassicicola. Taken together, our results reveal the existence of positively and negatively acting Arabidopsis miRNA modulating the defense responses against A. brassicicola and highlight the importance of host miRNAs in the interaction between plants and necrotrophic pathogens.
2019-06-17 | GSE83478 | GEO
Project description:The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic protein
2017-03-29 | MSV000080791 | MassIVE