Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA126947 | ENA |
REPOSITORIES: ENA
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Project description:ISD-starch (initiation, synthesis, and degradation): an integrated approach toward the understanding of starch metabolism and formation in plants
| PRJNA124529 | ENA
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root
2009-01-04 | GSE8973 | GEO
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root Genes expression was compared between cotton stems that were low in starch and accumulating starch. Gene expression was also compared between cotton roots that were low in starch and accumulating starch. A total of three microarrays were used. One dye swap was used. Material from the field were harvested 2 weeks apart. Greenhouse grown material were planted at two week intervals and harvested at the same time. NOTE that the channel representing the low starch material only gave about half of the total signal than the high starch samples. QPCR of 9 genes confirmed differential expression of 8 of them. QPCR also confirmed similar expression of two genes not predicted to be differentially expressed by the microarray analysis. Therefore no correction was made for the apparent difference in the hybridization of high and low starch samples.
2010-06-24 | E-GEOD-8973 | biostudies-arrayexpress
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
Project description:To uncover the mechanisms underlying pear fruit response to boron application, a comprehensive transcriptome analysis was performed. Boron application significantly induced expression of sorbitol metabolism and sucrose metabolism genes.Boron application also increased the expression of starch degradation, fatty acid synthesis, IAA degradation, GA synthesis and inhibit the expression of ethylene synthesis gene.
2022-03-08 | GSE193221 | GEO
Project description:The enzyme lycopene β-cyclase (LYCB) is responsible for the synthesis of β-carotene, a valuable component of the human diet. To understand the effect of the high β-Carotene content accumulation on plants carotenoid biosynthesis and global genes expression，a tomato engineered to constitutively express Lycb-1 accumulated a high level of β-carotene was used in this reasearch.Microarray analysis in the ripe stage revealed that the constitutive expression of Lycb-1 differentially regulated a number of genes involved in the synthesis of fatty acids, flavones, flavonols, flavonoids and phenylpropanoids, in the degradation of limonene and pinene, in starch and sucrose metabolism and in photosynthesis.
2012-12-12 | GSE33435 | GEO
Project description:<p _msttexthash='586474785' _msthash='612'>White tea (WT) develops unique aged quality during long-term storage, characterized by progressive changes in sensory properties and chemical composition. However, integrated insights into the sensory, metabolites, and microbial contribution underlying this process remain limited. This study systematically investigated the quality evolution of Bai Mudan tea (a typical WT) over 0 to 11 years of storage using an integrated multi-omics approach. Sensory analysis revealed a flavor transition from fresh (grassy, fruity) to aged (woody, stale) characteristics. Volatilomics identified 72 volatile compounds, with cedrol and isophorone as aged characteristic aroma compounds (rOAV ≥ 1, VIP ≥ 1, p ≤ 0.05). Metabolomics identified 1146 non-metabolites, showing accumulation of fatty acyls and flavonoids, and a decrease in amino acids. Metagenomic sequencing analysis revealed that bacterial communities (mainly Sphingomonas, Pedobacter, Methylobacterium, and Chryseobacterium) dominated during the first 7 years of storage, followed by a potential shift toward a bacterial - fungal synergy pattern in later stages as the abundances of Monascus and Aspergillus increased. KEGG annotation highlighted the roles of carbohydrate metabolism and amino acid metabolism, and flavonoid biosynthesis was activated during storage. Multi-omics correlation networks demonstrated that fungi positively regulated volatile flavors, while bacteria may be involved in taste balance. Monascus, Sphingomonas, Sphingobium, and Novosphingobium were identified as core functional taxa that may contribute to WT quality formation during storage through aged flavor synthesis, flavonoid accumulation, and lipid degradation. In conclusion, this study provides a multi-dimensional scientific basis for a comprehensive understanding of the formation mechanism of aged quality in white tea during storage.</p>
2025-11-18 | MTBLS13336 | MetaboLights
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits.
2012-05-04 | GSE32522 | GEO