Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rice in splicing factor OsSKIPa knock-down and overexpressed rice

ABSTRACT: OsSKIPa is an SNW/SKIP protein in rice, which homolog to SKIP(human) and PRP45(yeast). OsSKIPa can rescue the lethal of yeast prp45 mutants. OsSKIPa-suppressed plants (S59R) show decrease of cell viability. Overexpression of OsSKIPa (S58S) increase the osmotic stresses tolerance. OsSKIPa is an important regulator and interacting with a lot of proteins which have varient functions. In order to find the genes expression information when OsSKIPa changed. We use microarray to find changed genes in S59R and S58S plants in the normal condition. Experiment Overall Design: Whole plants were collected from 1-month-old S58S (two replicates), S59R (three replicates) and wild type (three replicates).

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Kabin Xie

PROVIDER: E-GEOD-10054 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: Lysine crotonylation (Kcr), as a novel evolutionarily conserved type of PTM, is ubiquitous and essential in cell biology. However, its functions in tea plant, an important beverage crop, are largely unknown. Our study firstly attempted to describe Kcr proteins in tea leaves under NH4+ deficiency/resupply, and provided significant insights into exploring the physiological role of Kcr in plants for N utilization. Results: We performed the global analysis of crotonylome in tea plants under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 kcr sites on 971 proteins were identified, of which contained in 15 types of Kcr motifs. Most of Kcr proteins were located in chloroplast and cytoplasm. 120 and 151 Kcr proteins were significantly changed at 3 hours and 3days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed Kcr proteins participated in diverse biological processes such as photosynthesis, carbon fixation and amino acid metabolism, suggesting Kcr plays important roles in these processes. Interestingly, a large number of enzymes were crotonylated, and the activity and Kcr level of these enzymes changed significantly after NH4+ resupply, indicating a potential function of Kcr in the regulation of enzyme activities. Moreover, the protein-protein interaction analysis revealed that the diverse interactions of identified Kcr proteins mainly involved in photosynthesis, carbon fixation, amino acid metabolism and ribosome. Conclusions: The results suggested that lysine crotonylated proteins might play regulating roles in metabolic process in tea leaves under NH4+ deficiency/resupply. The critical regulatory roles mainly involved in diverse aspects of primary metabolic processes, especially in photosynthesis, carbon fixation and amino acid metabolism. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine crotonylation in tea plants.

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Transcription profiling of rice in splicing factor OsSKIPa knock-down and overexpressed rice

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