Impact of the SnRK1 protein kinase on sucrose homeostasis and the transcriptome during the diel cycle
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ABSTRACT:
PROVIDER: PRJNA707060 | ENA |
REPOSITORIES: ENA
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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
Project description: Not available
| S-EPMC8566312 | biostudies-literature
Project description:Metabolism, cell cycle stages, and related transcriptomes in eukaryotic algae change with the diel cycle of light availability. In the unicellular red alga Cyanidioschyzon merolae, the S and M phases occur at night. To examine how diel transcriptomic changes in metabolic pathways are related to the cell cycle and to identify all genes, for which mRNA levels change depending on the cell cycle, we examined diel transcriptomic changes in C. merolae. In addition, we compared transcriptomic changes between the wild type and transgenic lines, in which the cell cycle was uncoupled from the diel cycle by the depletion of either cyclin-dependent kinase A (CDKA) or retinoblastoma-related (RBR) protein. Of 4,775 nucleus-encoded genes, the mRNA levels of 1,979 genes exhibited diel transcriptomic changes in the wild type. Of these, the periodic expression patterns of 454 genes were abolished in the transgenic lines, suggesting that the expression of these genes is dependent on cell cycle progression. The periodic expression patterns of most metabolic genes, except those involved in starch degradation and de novo dNTP synthesis, were not affected in the transgenic lines, indicating that the cell cycle and transcriptomic changes in most metabolic pathways are independent of the diel cycle. Approximately 40% of the cell–cycle–dependent genes were of unknown function, and approximately 19% of these genes of unknown function are shared with the green alga Chlamydomonas reinhardtii. The dataset presented in this study will facilitate further studies on the cell cycle and its relationship with metabolism in eukaryotic algae.
2019-11-26 | GSE131944 | GEO
Project description:Iron (Fe) is an important growth limiting factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of the water. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day:night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe’) concentrations of 1160, 233, 58 and 12 pM. We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe’ concentration and CO2 availability, respectively. At the highest Fe’ (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe’ (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel transcriptional patterns for genes in most central metabolism pathways, the diel periodicity of light- signaling molecules and glycolytic genes, was relatively robust in response to reduced Fe’. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel pattern at low Fe’, while transcripts that encoded the non-active enzyme lost the diel pattern. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.
2019-09-12 | GSE131042 | GEO
Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h).
2013-06-28 | GSE48181 | GEO
Project description:Investigation of whole genome gene expression level changes in Trichodesmium erythraeum IMS101 during a 24-hr light and dark cycle. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2019. The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). mBio 10:e02495-18. https://doi.org/10.1128/mBio.02495-18.
2017-06-11 | GSE99896 | GEO
Project description:Insufficient leaf photosynthesis promotes sheath NSC transport to the panicle during grain filling. SnRK1 regulates assimilate distribution between plant tissues and organs. However, the mechanism by which SnRK1 regulates sheath NSC transport to the panicle and its response to limited leaf assimilation remain unclear. Here, we performed leaf cutting (LC) at anthesis to simulate insufficient leaf assimilation and set no treatment as a CK. In response to LC, SnRK1 activity increased rapidly, and NSC transport was advanced. Sheath NSCs were not transported in a snrk1a mutant with deficient SnRK1 activity. These results indicated that SnRK1 activity is important for sheath NSC transport. The high correlation of T6P and sucrose and the inhibition of SnRK1 by T6P in sheaths in vitro implied that T6P slightly inhibits SnRK1 activity in rice sheaths in response to sucrose availability. The increase in SnRK1 activity was accompanied by an increase in OsSnRK1a expression and a low sucrose content. Low sucrose signaling increases SnRK1 transcription. Therefore, we speculated that OsSnRK1a expression positively regulates SnRK1 activity in response to low sucrose availability in rice sheaths. Through phosphoproteomics and further PRM verification, 20 phosphosites that depend on SnRK1 and are correlated with NSC transport were obtained. Based on the function of these sites and proteins, we found that SnRK1 regulates starch degradation, sucrose metabolism, phloem transport, sugar transport across tonoplast, and glycolysis via phosphorylation to promote sheath NSC transport. Overall, our results revealed the importance, function and regulatory mechanism of SnRK1 in sheath NSC transport.
2022-03-18 | PXD024670 | Pride
Project description:Insufficient leaf photosynthesis promotes sheath NSC transport to the panicle during grain filling. SnRK1 regulates assimilate distribution between plant tissues and organs. However, the mechanism by which SnRK1 regulates sheath NSC transport to the panicle and its response to limited leaf assimilation remain unclear. Here, we performed leaf cutting (LC) at anthesis to simulate insufficient leaf assimilation and set no treatment as a CK. In response to LC, SnRK1 activity increased rapidly, and NSC transport was advanced. Sheath NSCs were not transported in a snrk1a mutant with deficient SnRK1 activity. These results indicated that SnRK1 activity is important for sheath NSC transport. The high correlation of T6P and sucrose and the inhibition of SnRK1 by T6P in sheaths in vitro implied that T6P slightly inhibits SnRK1 activity in rice sheaths in response to sucrose availability. The increase in SnRK1 activity was accompanied by an increase in OsSnRK1a expression and a low sucrose content. Low sucrose signaling increases SnRK1 transcription. Therefore, we speculated that OsSnRK1a expression positively regulates SnRK1 activity in response to low sucrose availability in rice sheaths. Through phosphoproteomics and further PRM verification, 20 phosphosites that depend on SnRK1 and are correlated with NSC transport were obtained. Based on the function of these sites and proteins, we found that SnRK1 regulates starch degradation, sucrose metabolism, phloem transport, sugar transport across tonoplast, and glycolysis via phosphorylation to promote sheath NSC transport. Overall, our results revealed the importance, function and regulatory mechanism of SnRK1 in sheath NSC transport.
2022-03-18 | PXD024675 | Pride
Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h). 22 dye-switch - treated vs untreated comparison
2013-06-28 | E-GEOD-48181 | biostudies-arrayexpress
Project description:Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.
2014-10-25 | GSE62671 | GEO