ISD-starch (initiation, synthesis, and degradation): an integrated approach toward the understanding of starch metabolism and formation in plants
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE20964 | GEO | 2011/03/01
SECONDARY ACCESSION(S): PRJNA124529
REPOSITORIES: GEO
Similar Datasets
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out
2011-05-12 | GSE21793 | GEO
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out 48 dye-swap - CATMA arrays
2011-03-01 | E-GEOD-20964 | biostudies-arrayexpress
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out 48 dye-swap - CATMA arrays
2011-05-12 | E-GEOD-21793 | biostudies-arrayexpress
Project description:In starchless mutants of Arabidopsis, pgm, and wild type, Col0, there are small differences in transcript levels at the end of the day, but large differences at the end of the night. Many of the transcripts of genes involved in biosynthesis and growth are repressed in the pgm mutant (Thimm et al., 2004). It is hypothesized that a transient depletion in sugars at the end of the night inhibits carbon utilization at the beginning of the day (Gibon et al., 2004). In order to test if the same inhibition of transcripts involved in biosynthesis and growth also occurs in starch excess mutants of Arabidopsis, Affymetrix arrays will be generated for WT (Col0), and the following mutants: sex4-3 (Salk 102567), ptpkis2 (Salk 053285), and sex1-3 (Yu et al., 2001). WT, sex4-3, and ptpkis2 plants were grown for 30 days and sex1-3 plants were grown for 36 days. All plants were grown in a growth chamber with a 12 hour photoperiod, quantum flux 100 mol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2. Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA). Samples were then treated with DNaseI (Invitrogen, CA, USA). 12 samples were used in this experiment.
2009-12-04 | E-GEOD-19260 | biostudies-arrayexpress
Project description:In starchless mutants of Arabidopsis, pgm, and wild type, Col0, there are small differences in transcript levels at the end of the day, but large differences at the end of the night. Many of the transcripts of genes involved in biosynthesis and growth are repressed in the pgm mutant (Thimm et al., 2004). It is hypothesized that a transient depletion in sugars at the end of the night inhibits carbon utilization at the beginning of the day (Gibon et al., 2004). In order to test if the same inhibition of transcripts involved in biosynthesis and growth also occurs in starch excess mutants of Arabidopsis, Affymetrix arrays will be generated for WT (Col0), and the following mutants: sex4-3 (Salk 102567), ptpkis2 (Salk 053285), and sex1-3 (Yu et al., 2001). WT, sex4-3, and ptpkis2 plants were grown for 30 days and sex1-3 plants were grown for 36 days. All plants were grown in a growth chamber with a 12 hour photoperiod, quantum flux 100 mol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2. Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA). Samples were then treated with DNaseI (Invitrogen, CA, USA).
2009-12-05 | GSE19260 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106642 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106627 | GEO
Project description:Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.
2020-11-04 | GSE106684 | GEO
Project description:Usually starch is nearly depleted at the end of the night. To induce a gradual depletion of carbon, we have analysed the global response of transcripts during an extension of the night, where carbon becomes severely limiting from about four hours onwards. Keywords: time course
2008-02-14 | GSE10016 | GEO
Project description:Thermophilic fungus Myceliophthora thermophila with great capacity for polysaccharides degradation is attractive to be engineered into a cell factory to produce chemicals and biofuels directly from renewable polysaccharides such as starch. Understanding the molecular mechanism of starch degradation of the fungi would be helpful. To date, there has been no transcriptome analysis on starch in thermophilic fungi. In this study, we performed the transcriptomic profile of M. thermophila responding to soluble starch, and a 342-gene set was identified as “starch regulon”, including the major amylolytic enzyme (Mycth_72393), which was verified thereafter as the most important such hydrolase for starch degradation in this fungus. Moreover, the function of key amylolytic enzyme regulator AmyR in M. thermophila was evaluated by analyzing the performance of its deletion mutant using our CRISPR/Cas9 system, which showed significantly decreased amylase activity and poor growth on starch. Additionally, deletion of amyR led to resistance to carbon catabolite repression (CCR) and enhanced cellulases production. Our study provides an insight into understanding the molecular basis of starch degradation in this thermophilic fungus, and will accelerate the fungal strain rational engineering for starch-based biochemical production.
2021-02-02 | GSE110062 | GEO