Dataset Information

Quantitative Analysis of Global Proteome in Arabidopsis thaliana

ABSTRACT: In total, 5,840 protein groups were identified, among which 5,188 proteins were quantified. The fold-change cutoff was set when proteins with quantitative ratios above 1.5 or below 0.667 are deemed significant. Among the quantified proteins, 95 proteins are up-regulated and 155 proteins are down-regulated in group gr1-seedling/WT-seedling.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: xiaomei li

LAB HEAD: lirong sun

PROVIDER: PXD011814 | Pride | 2019-11-12

REPOSITORIES: Pride

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Publications

Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis.

Sun Lirong L Xu Yuxing Y Bai Shenglong S Bai Xue X Zhu Huijie H Dong Huan H Wang Wei W Zhu Xiaohong X Hao Fushun F Song Chun-Peng CP

Journal of experimental botany 20191001 19

Pseudouridine (Ψ) is widely distributed in mRNA and various non-coding RNAs in yeast and mammals, and the specificity of its distribution has been determined. However, knowledge about Ψs in the RNAs of plants, particularly in mRNA, is lacking. In this study, we performed genome-wide pseudouridine-sequencing in Arabidopsis and for the first time identified hundreds of Ψ sites in mRNA and multiple Ψ sites in non-coding RNAs. Many predicted and novel Ψ sites in rRNA and tRNA were detected. mRNA was ...[more]

PMID: 31173101

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Project description:Background: Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8C, LT accompanied by flooding (LTF) and CK (control) treatments were established for three days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. Results: LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. Conclusion: Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.

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Dataset Information

Quantitative Analysis of Global Proteome in Arabidopsis thaliana

Dataset's files

Publications

Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis.

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