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ABSTRACT:
PROVIDER: PRJNA915477 | ENA |
REPOSITORIES: ENA
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Project description:An increasing amount of evidence attest that the tea made by albino tea cultivars processes characteristic aroma and taste, which has been considered as a new potential product in the market. Therefore, flavor formation mechanism of albino tea cultivars have drawn exceeding attention from researchers. In this study, transcriptome, metabolomics, and whole-genome bisulfite sequencing (WGBS) were employed to investigate shading effects on leaf color conversion and biosynthesis of three major secondary metabolites in the Albino tea cultivar ‘Yujinxiang’. The increase of leaf chlorophyll level is the major cause of shaded leaf greening from young pale or yellow leaf. Transcriptome analysis showed differentially expressed genes (DEGs) mainly participated in biosynthesis of amino acids, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, sulfur metabolism, purine metabolism, and pentose and glucuronate interconversions in shading period compared with control group. The result of metabolomics indicated the total catechins level of shading group was significantly decreased than the control; however, the abundance of caffeine was markedly increased, and theanine level was nearly not influenced. Whole-genome DNA methylation analysis revealed that the global genomic DNA methylation patterns of shading period were remarkably altered compared with the control. Furthermore, differentially methylated regions (DMRs) and the DMR-related DEGs between shading and non-shading analysis indicated the DMR-related DEGs were the critical participants in biosynthesis of three major secondary metabolites. To sum up, these findings suggested that the altered levels of DNA methylation may be the main cause for biosynthesis changes of three major secondary metabolites in ‘Yujinxiang’.
2022-12-29 | GSE142753 | GEO
Project description:Background: Lysine succinylation of proteins has potential impacts on protein structure and function, which occurred on post-translation level. However, the information about the lysine succinylation of proteins in tea plants is limited. In the present study, the significant signal of succinylation in tea plants was found by western blot. Subsequently, we performed qualitative analyses to globally identify lysine succinylation substrates by using high accuracy nano LC-MS/MS combined with affinity purification. Results: As a result, a total of 142 lysine succinylation sites were identified in 86 proteins. The identified succinylated proteins are involved in various biological processes and a large proportion of the succinylation sites are present on proteins in the primary metabolism pathway, including glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle and glycine, serine and threonine metabolism. Moreover, 10 new succinylated sites on histones were detected in tea plants either. Conclusions: These results suggested that succinylated proteins in tea plants might play critical regulatory roles in biological processes, especially in the primary metabolism. This study not only globally analysed the functional annotation of lysine succinylation in tea plants, but also provided valuable information for further investigating the functions of lysine succinylation in tea plants.
2022-02-23 | PXD011717 | Pride
Project description:In field conditions, tea plants are often exposed to drought stress, which has profound effects on the growth and development of tea plants. However, most studies on tea plants in response to drought stress focused on single gene or protein expression, and transcriptome or proteome profiles, the impact of drought stress on ubiquitination in proteins remains unearthed. We performed a global profile of ubiquitinated (Kub) proteins in tea leaves under drought stress. In total, 1,409 lysine Kub sites in 781 proteins were identified, of which 14 sites in 12 proteins were up-regulated and 123 sites in 91 proteins were down-regulated compared with drought and control. Furthermore, we analyzed the Kub proteins related to ubiquitin-mediated proteolysis, catechins biosynthesis, and carbohydrate and amino acid metabolism in tea leaves under drought stress. The results indicated that many Kub proteins involved in ubiquitin-mediated proteolysis played important roles in protein degradation. Several Kub proteins related to catechins biosynthesis were positively correlated with each other because of their co-expression and co-localization. Our study preliminarily revealed the global profiling of Kub proteins in metabolic pathways and provided an important resource for further study on the functions of Kub proteins in tea plants under drought stress.
2019-11-12 | PXD011688 | Pride
Project description:Cysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.)) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, to date, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in multiple subcellular compartments, especially in the chloroplast and cytoplasm. The analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in carbon metabolism, especially in Calvin cycle and TCA cycle. These results suggested that S-nitrosylated proteins in tea leaves might play critical regulatory roles in the carbon metabolism. Overall, this study not only globally analyzed the functional annotation of cysteine S-nitrosylation in tea leaves, but also preliminarily provided the valuable information for further investigating the functions of cysteine S-nitrosylation in tea plants.
2020-05-26 | PXD012443 | Pride
Project description:CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci. We undertook a microarray analysis of 14-day-old plants and found that PKL continues to play an important role in expression of H3K27me3-enriched genes and in specification of developmental identity after germination. We used microarray to identify genes that are differentialy expressed in 14-day-old pkl seedlings and used chormatin immunoprecipitation to identify genes that are the direct targets of PKL.
2012-01-01 | GSE31639 | GEO
Project description:In order to identify primed (and memorized) genes resulting from BTH and/ or flg22 application, we performed a series of microarray-based transcription profiles. 7 days after germination Arabidopsis plants were treated the first time with the indicated treatment and second time 10 days after germination with the indicated treatment. Plants were harvested and RNA was extracted 21 days after germination. BTH was applied as formulated compound Bion. The sample name reflects the treatment order. Samples with the name water_water are control treatments which were treated 7 and 10 days after germination with water. The sample with the name Bion_flg22 was treated 7 days after germination with BTH and 10 days after germination flg22.
2018-12-04 | GSE123073 | GEO
Project description:In this work we studied the participation of RdDM pathway in response to salinity during germination, we found that the RdDM promotes germination while AGO4 null mutant negatively regulates the germination process.
2020-08-13 | GSE156093 | GEO
Project description:We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity.
2022-09-28 | GSE167503 | GEO
Project description:We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity.
2022-09-28 | GSE167505 | GEO