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Characterization of the starvation response in the Arabidopsis dcl1-9 mutant

ABSTRACT: The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to the well-established role of miRNAs as regulators of plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1 activation. To test this we have performed comparative analyses of the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE46713 | GEO | 2013/07/15

SECONDARY ACCESSION(S): PRJNA202068

REPOSITORIES: GEO

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Characterization of the starvation response in the Arabidopsis dcl1-9 mutant

Project description:The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to the well-established role of miRNAs as regulators of plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1 activation. To test this we have performed comparative analyses of the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis. To assess the impact of miRNA deficiency on the starvation response we performed transcriptomics analyses of WT and dcl1-9 plants by subjecting leaves to 6h of light (control) or darkness (starvation)

2013-07-15 | E-GEOD-46713 | biostudies-arrayexpress

A MULTI-DIMENSIONAL INTERACTOMICS VIEW ON THE PLANT SNRK1 KINASE COMPLEX REVEALS A KEY REGULATORY ROLE FOR THE CLASS II T6P SYNTHASE-LIKE PROTEINS – part1 AP-MS dataset

Project description:The plant SNF1-related kinase (SnRK1) plays a central role in energy and metabolic homeostasis. SnRK1 controls growth upon activation by energy-depleting stress conditions, while also monitoring key developmental transitions and nutrient allocation between source and sink tissues. To obtain deeper insight into the SnRK1 complex and its upstream regulatory mechanisms, we explored its protein interaction landscape in a multi-dimensional setting, combining affinity purification, proximity labeling and crosslinking mass spectrometry. Integration of these analyses not only offers a unique view on the composition, stoichiometry and structure of the core heterotrimeric SnRK1 complex but also reveals a myriad of novel robust SnRK1 interactors.

2022-08-30 | PXD029833 | Pride

A MULTI-DIMENSIONAL INTERACTOMICS VIEW ON THE PLANT SNRK1 KINASE COMPLEX REVEALS A KEY REGULATORY ROLE FOR THE CLASS II T6P SYNTHASE-LIKE PROTEINS – part2 TurboID-MS dataset

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Coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/ER stress and innate immunity pathways by inducible artificial microRNA silencing of the SNF4 activator subunit of Arabidopsis SnRK1

Project description:Arabidopsis SnRK1 is structurally and functionally related to the yeast Snf1 and mammalian AMP-activated kinases, which are activated in response to carbon/glucose limitation and stress conditions causing an imbalance of energy homeostasis increasing the AMP/ATP ratio. Mutations of the SNF4 activating subunit of trimeric Arabidopsis SnRK1 complexes are not transmitted through the male meiosis. Silencing of SNF4 by a β-estradiol-inducible artificial microRNA (amiR-SNF4) constructs was used to examine how inhibition of SnRK1 affects transcriptional regulation of different cellular pathways in dark and light grown seedlings. This study shows that amiR-SNF4 silencing of SnRK1 leads to coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/endoplasmic reticulum stress and pathogen defense responses by inducing simultaneous changes in numerous other essential hormonal and metabolic pathways in Arabidopsis. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and β-estradiol-induced amiR-SNF4 mutant seedlings 5 days after germination in the dark or light.

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Regulatory functions of cellular energy sensor SnRK1 for nitrate signaling through NLP7 repression

Project description:Coordinated metabolism of carbon and nitrogen is essential for optimal plant growth and development. Nitrate is an important molecular signal for plant adaptation to changing environmental conditions, but how nitrate regulates plant growth under carbon deficiency conditions remains unclear. Here, we show that the evolutionarily conserved energy sensor SnRK1 negatively regulates the nitrate signaling pathway. Nitrate promoted plant growth and downstream gene expression, but such effects were significantly repressed when plants were grown under carbon deficiency conditions. Mutation of KIN10, the α-catalytic subunit of SnRK1, partially suppressed the inhibitory effects of carbon deficiency on nitrate-mediated plant growth. KIN10 phosphorylated NLP7, the master regulator of nitrate signaling pathway, to promote its cytoplasmic localization and degradation. Furthermore, nitrate depletion induced KIN10 accumulation, whereas nitrate treatment promoted KIN10 degradation. Such KIN10-mediated NLP7 regulation allows carbon and nitrate availability to control the optimal nitrate signaling and ensures the coordination of carbon and nitrogen metabolism in plants.

2022-07-23 | GSE206841 | GEO

Quantitative proteomics Reveals Targets of Protein Kinase SnRK1 in Arabidopsis under Submergence

Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5�� h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.

2016-04-07 | PXD002353 | Pride

Quantitative Phosphoproteomics Reveals Targets of Protein Kinase SnRK1 in Arabidopsis under Submergence

Project description:SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed as a central integrator of regulatory pathways in plant stress and energy starvation signaling. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. To gain further insight into submergence signaling mechanisms, we determined the temporal response to energy starvation through AMP/ATP quantification and used quantitative phosphoproteomics to compare the global changes in phosphopeptides in Col-0 and SnRK1.1K48M. We found that the phosphorylation levels of 59 peptides increased and the levels of 96 peptides decreased in Col-0 within 0.5–3 h of submergence. Among the 59 peptides with increased phosphorylation in Col-0, 49 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved in sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. In particular, the phosphorylation of MAPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MAPK6 activity that directly dephosphorylates MAPK6, was also regulated by SnRK1.1. These results reveal insights into the function of SnRK1 and the downstream signaling factors of submergence.

2016-04-07 | PXD001815 | Pride

Impact of the SnRK1 protein kinase on sucrose homeostasis and the transcriptome during the diel cycle

Project description:Sucrose Non-Fermenting1-Related Kinase1 (SnRK1) is an evolutionarily conserved protein kinase with key functions in energy management during stress responses in plants. To address a potential role of SnRK1 under non-stress conditions, we performed a metabolomic and transcriptomic characterization of 20 d-old rosettes of Arabidopsis SnRK1 gain- and loss-of-function mutants during the diurnal cycle. SnRK1 manipulation altered the slope of the correlation between sucrose and trehalose 6-phosphate (Tre6P). It also modulated the flux of carbon to the tricarboxylic acid cycle downstream of Tre6P-signalling. SnRK1 depletion modified expression of SnRK1-induced genes least at the end of the day (when Tre6P levels peak) and most at the end of the night (when Tre6P levels are lowest). Expression of a subset of these genes was attenuated by inducible Tre6P accumulation in a time-of-day dependent manner. Finally, transcriptional profiling uncovered a wide impact of SnRK1 on gene expression in non-stress conditions, establishing a clear connection with iron and sulfur metabolism. In conclusion, SnRK1 plays central functions in metabolic and transcriptional regulation in the absence of stress. SnRK1 is further involved in the reciprocal control of sucrose-driven Tre6P production and/or degradation and its activity is modulated by daily fluctuations in Tre6P levels.

2021-06-01 | GSE168382 | GEO

Transcription profiling of pea seed development

Project description:SnRK1 (sucrose-non-fermenting-1-related) protein kinases are involved in the regulation of plant metabolism controlling both gene expression and phosphorylation. The aim of the study was to investigate the role of SnRK1 in pea seed development. To study the effect of SnRK1 deficiency, transgenic pea plants were generated carrying a gene for VfSnRK1 in antisense orientation under control of seed specific vicilin promoter. Selected transgenic lines were characterized with decreased levels of PsSnRK1 mRNA and reduced up to 71% phosphorylation activity. Antisense inhibition of SnRK1 resulted in reduced seeds fresh weight, defect of pollen development. To dissect the SnRK1-antisense phenotype at the molecular level, a search for genes with differential expression patterns in transgenic plant versus wild type seeds has been performed using cDNA macroarray analysis. Radioactive labeled cDNA probes were prepared from RNA isolated from embryo of developing seeds of wild type (11, 13, 15, 17, 19, and 21 DAP) and transgenic SnRK1-antisense plant (13, 15, 17 and 19 DAP), which correspond to the transition phase of seed development, and hybridized to cDNA macroarrays.

2013-01-30 | E-IPKG-1 | biostudies-arrayexpress

Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK

Project description:Chronologically aging yeast cells are prone to adaptive regrowth, whereby mutants with a survival advantage spontaneously appear and re-enter the cell cycle in stationary phase cultures. Adaptive regrowth is especially noticeable with short-lived strains, including those defective for SNF1, the homolog of mammalian AMP-activated protein kinase (AMPK). SNF1 becomes active in response to multiple environmental stresses that occur in chronologically aging cells, including glucose depletion and oxidative stress. SNF1 is also required for the extension of chronological lifespan (CLS) by caloric restriction (CR) as defined as limiting glucose at the time of culture inoculation. To identify specific downstream SNF1 targets responsible for CLS extension during CR, we screened for adaptive regrowth mutants that restore chronological longevity to a short-lived snf1∆ parental strain. Whole genome sequencing of the adapted mutants revealed missense mutations in TPR motifs 9 and 10 of the transcriptional co-repressor Cyc8 that specifically mediate repression through the transcriptional repressor Mig1. Another mutation occurred in MIG1 itself, thus implicating the activation of Mig1-repressed genes as a key function of SNF1 in maintaining CLS. Consistent with this conclusion, the cyc8 TPR mutations partially restored growth on alternative carbon sources and significantly extended CLS compared to the snf1∆ parent. Furthermore, cyc8 TPR mutations reactivated multiple Mig1-repressed genes, including the transcription factor gene CAT8, which is responsible for activating genes of the glyoxylate and gluconeogenesis pathways. Deleting CAT8 completely blocked CLS extension by the cyc8 TPR mutations on CLS, identifying these pathways as key Snf1-regulated CLS determinants.

2018-03-28 | GSE110409 | GEO

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