Unknown,Transcriptomics,Genomics,Proteomics

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Temporal dependency of the transcriptional response to carbohydrate depletion contrasts with conservation of the rapid response to sucrose readdition

ABSTRACT: To investigate whether the transcriptional response to carbon (C) depletion and sucrose re-addition depend on the duration of C-depletion, Arabidopsis thaliana seedlings growing in liquid culture in weak continuous light were harvested 3, 6, 12, 24, 48 and 72 h after removing sucrose from the medium, and 30 min after resupplying sucrose at each of these times. After removing sucrose, soluble sugars fell strongly within 3 h, and starch was gradually depleted over 24 h, and hexose phosphates and ATP declined gradually over 72 h. Expression profiling using ATH arrays pointed to Overall the transcriptional response pointed to early transcriptional remodelling of metabolism to conserve C, followed by induction of photosynthesis and pathways that recycle C, and repression of growth-related processes. The time-dependent transcriptional response to C-depletion differed from that during a light/dark cycle and an extended night. Re-supplying sucrose for 30 min led to near-complete recovery of seedling sucrose levels, partial recovery of reducing sugars and phosphorylated intermediates, but no immediate change of starch or ATP. The rapid transcriptional response to sucrose readdition was conserved across the entire C-depletion time course, became larger with time. , and was highly enriched for regulatory genes. Whilst there was a rapid decrease of many C-depletion-induced transcripts, fewer transcripts increased. The majority of the transcripts that responded rapidly after resupplying sucrose also decreased after treating C-depleted seedlings with the transcriptional inhibitor cordycepin A, pointing to an important role for transcript turnover in the rapid response to sucrose.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Sarah Cookson

PROVIDER: E-MTAB-3143 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using M-bM-^@M-^Xomics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes. Arabidopsis seedlings were grown in 30 mL of sterile liquid full nutrition (FN) medium (3 mM sulphate) or 150 M-NM-<M sulphate medium. Transferring pre-grown 7-days old seedlings to a sulphate depleted medium (0 M-NM-<M sulphate) assured immediate and continued sulphate starvation during the next two days of plant cultivation. On day 9 subsets of the sulphate depleted cultures were supplied with sulphate (500 M-NM-<M) and samples taken 30 min and 3 hours after re-supply. Four time points (full nutrition (FN), plants starved for 48 h (-S), plants re-supplied with sulphate for 30 minutes (30M-bM-^@M-^Y S) and plants re-supplied with sulphate for 3 hours (3 h S)) were subjected to the microarray analysis. Two biological repetitions of each sample were analyzed.

Project description:Huntington's disease (HD) is a dominantly inherited genetic disease caused by mutant huntingtin (htt) protein with expanded polyglutamine tracts. A neuropathological hallmark of HD is the presence of neuronal inclusions of mutant htt. p62 is an important regulatory protein in selective autophagy, a process by which aggregated proteins are degraded, and it is associated with several neurodegenerative disorders including HD. Here we investigated the effect of p62 depletion in three HD model mice: R6/2, HD190QG and HD120QG mice. We found that loss of p62 in these models led to longer lifespans and reduced nuclear inclusions, although cytoplasmic inclusions increased with polyglutamine length. In mouse embryonic fibroblasts (MEFs) with or without p62, mutant htt with a nuclear localization signal (NLS) showed no difference in nuclear inclusion between the two MEF types. In the case of mutant htt without NLS, however, p62 depletion increased cytoplasmic inclusions. Furthermore, to examine the effect of impaired autophagy in HD model mice, we crossed R6/2 mice with Atg5 conditional knockout mice. These mice also showed decreased nuclear inclusions and increased cytoplasmic inclusions, similar to HD mice lacking p62. These data suggest that the genetic ablation of p62 in HD model mice enhances cytoplasmic inclusion formation by interrupting autophagic clearance of polyQ inclusions. This reduces polyQ nuclear influx and paradoxically ameliorates disease phenotypes by decreasing toxic nuclear inclusions. Gene expression profiles were analyzed to examine the effects of p62 depletion in mouse with or without mutant huntingtin exon 1 To examine the effect of p62 depletion on the transcriptome of Huntington's disease model mice, we crossed p62 knockout mice with HD model mice. We extracted total RNA from the striatum of these mice at 8 weeks and used for a microaaray analysis. The samples are HD transgenic mice with p62 knockout (HD_p62KO), HD mice with normal p62 (HD_p62WT), non-HD-transgenic mice with p62 knockout (NT_p62KO), and non-HD-transgenic mice with normal p62 (NT_p62WT).

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Temporal dependency of the transcriptional response to carbohydrate depletion contrasts with conservation of the rapid response to sucrose readdition

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