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Co-immunoprecipitation coupled with mass for RNR10 in rice&Identification of ubiquitination sites in rice DNR1

ABSTRACT: RNR10 is a key factor that regulates the response of rice roots to nitrogen.In an attempt to determine the target(s) of RNR10, we performed co-immunoprecipitation (Co-IP) coupled with mass spectrometry analysis to search for RNR10 interactors.DNR1 is a downstream target gene of RNR10.Previous studies have shown that rice DNR1 is subjected to ubiquitination modification. In order to identify the ubiquitination modification sites of DNR1,we performed mass spectrometry analyses.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Yunzhi Huang

LAB HEAD: Yunzhi Huang

PROVIDER: PXD043400 | Pride | 2023-09-30

REPOSITORIES: Pride

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Project description:Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array. keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray

			Action	DRS
	DNR1_ubi.dat	Other
	DNR1_ubi.mgf	Mgf
	DNR1_ubi.raw	Raw
	RNR10.dat	Other
	RNR10_IP-MS_1.mgf	Mgf

Dataset Information

Co-immunoprecipitation coupled with mass for RNR10 in rice&Identification of ubiquitination sites in rice DNR1

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