Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Acetylome analyses in the germinating rice seed

ABSTRACT: Seed germination is a complicated physiological process, during which structures of mitochondria and plastids are recovered, and metabolisms are re-activated (Han and Yang, 2015). It has been shown that metabolism reactivation is very important for rice germination (He et al., 2011b;Han et al., 2014a). It is still unknown if protein acetylation involved in and regulate these metabolisms during rice seed germination. To answer this question, we globally profiled the acetylome in rice embryos from the germinating seeds. A number of acetylated enzymes were identified. The results provide more information about the metabolism regulation in germinating seeds.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Seed

SUBMITTER: Zhang Hui

LAB HEAD: ping fang Yang

PROVIDER: PXD002739 | Pride | 2016-01-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PTM20140928MI01_Rice_Kac.peak	Other
	PTM20140928MI01_Rice_Kac.xls	Xls
	Rice_Kac_1.raw	Raw
	Rice_Kac_2.raw	Raw
	Rice_Kac_3.raw	Raw

Items per page:

1 - 5 of 6

Publications

Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed.

He Dongli D Wang Qiong Q Li Ming M Damaris Rebecca Njeri RN Yi Xingling X Cheng Zhongyi Z Yang Pingfang P

Journal of proteome research 20160128 3

Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses ...[more]

PMID: 26767346

Similar Datasets

Transcription profiling of barley maturing and germinating grains

Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.

2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress

N-glycoproteomic analysis of rice germinating embryo

Project description:N-glycoproteomic analysis of rice germinating embryo at 24 hours after inhibition

2017-03-29 | PXD004417 | Pride

AMPK activator 991 specifically activates SnRK1 and thereby affects seed germination in rice

Project description:Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) is a central regulator of metabolism and developmental transition in plant. Compound 991 is a well-known 5′-adenosine monophosphate activated protein kinase (AMPK) activator in mammals. SnRK1 and AMPK are highly conserved. However, whether 991 could also act as a SnRK1 activator is unknown. Adding 991 significantly increased the activity of SnRK1 in desalted extracts from germinating rice seeds in vitro. To determine whether 991 has biological activity in plant, rice seeds were treated with different concentrations of 991. Low concentration of 991 promoted rice seed germination, while high concentration of 991 inhibited rice germination. The effect of 991 on rice germination is similar to the effect of OsSnRK1a overexpression on germination. To explore whether 991 affects germination by specifically affecting SnRK1, the germination status of the snrk1a mutant and WT under 1 μM 991 treatment were compared. The snrk1a mutant exhibited insensitivity to 991. Through phosphoproteomic analysis, we found that the differential phosphopeptides caused by 991 treatments and overexpression of OsSnRK1a are largely overlapped. Phosphoproteomic analysis also revealed that SnRK1 might affect rice germination by regulating the phosphorylation levels of S285-PIP2;4, S1013-SOS1 and S110-ABI5. These results showed that 991 is a specific and workable SnRK1 activator in rice. The promotion and inhibition of 991 treatments on germination also exist in wheat seeds. 991 is expected to be used for exploring the function of SnRK1 in more detail and depth and chemical regulation of growth and development in crops.

2024-02-04 | PXD044360 | Pride

Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds. MicroRNA profiles in 2 different seed libraries (mature seeds and a pool of germinating seed stages) of Glycine max by deep sequencing (Illumina GAII).

2015-05-25 | E-GEOD-38373 | biostudies-arrayexpress

Identification of target genes of the DELLA protein RGL2 during the repression of seed germination

Project description:To shed light on the genetic events downstream of DELLA proteins, we have employed a microarray expression profiling of Arabidopsis thaliana seeds to identify target genes of the DELLA protein RGL2. Seeds of the germinating ga1-3 rga-t2 rgl2-1 and the non-germinating ga1-3 rga-t2 mutant were stratified, and RNA was extracted after five days. Transcript profiles of the non-germinating seeds closely resemble profiles of dormant seeds, and several transcription factors involved in light- and phytohormone-regulated signalling pathways appear to be up-regulated, suggesting that RGL2 controls various physiological aspects to inhibit seed germination. Gene expression five days after stratification was measured in ga1-3 rga-t2 seeds, using seeds of the ga1-3 rga-t2 rgl2-1 mutant as reference. Two biological replicates were performed for each sample.

2012-08-31 | E-GEOD-40485 | biostudies-arrayexpress

Transcriptomic analysis of regulatory gene expression profiles by NF-YCs, and RGL2 under paclobutrazol (PAC) condition

Project description:To understand how the NF-YC-RGL2 complex functions in repressing seed germination, a genome-wide transcriptomic analysis was carried out using germinating seeds of rgl2, nf-ycT and the wild-type (Col) grown on the medium containing 5 uM PAC and Col grown on mock treatment. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in Col_PAC vs Col_mock, nf-ycT_PAC vs Col_PAC, and rgl2_PAC vs Col_PAC subsets, which are referred to as PAC-, NF-YC-, and RGL2-regulated genes.These data reveal that NF-YCs and RGL2 co-target a set of common genes in response to phytohormone signals, strongly supporting the role of NF-YC-RGL2 in seed germination regulation. Digital gene expression tag profiles of wild type (Col), nf-ycT mutant, and rgl2 mutant germinating seed for 12 h after stratification were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

2016-07-25 | E-GEOD-84753 | biostudies-arrayexpress

affy_compartimentation_rice_albumen_embryon-Transcriptomic study of the rice seed compartimentation during germination

Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30M-BM-0C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in M-bM-^@M-^\EM-bM-^@M-^] while the endosperm samples are abbreviated M-bM-^@M-^\AM-bM-^@M-^]. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition). 36 arrays - rice; organ comparison,time course

2013-07-01 | E-GEOD-43780 | biostudies-arrayexpress

Transcriptome analysis during seed germination of elite Chinese bread wheat cultivar Jimai 20

Project description:Wheat seed germination is highly related to seedling survival rate and subsequent vegetative growth,and therefore directly affects the conformation of wheat yield and quality. So wheat seed germination is not only important to itself, but the whole human society. However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinese bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed germination. Seed germination involves in the regulation of large number of genes, whether these genes are normal activated or not is very important to seed germination. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in five phases of wheat cultivar Jimai 20 seed germination. Our results provide a new insights into the thoroughly metabolic changes of seed germination as well as the relationship between some significant genes. The five groups including germinating seeds were harvest at five successive phases, which were 0 (P0), 12 (P1), 24 (P2), 36 (P3), 48 (P4) hour after imbibition respectively. Three independent experiments were performed for each group.

2013-08-14 | E-GEOD-49821 | biostudies-arrayexpress

Carrot (Daucus carota L.) seed germination was promoted by hydro-electro hybrid priming through regulating the accumulation of proteins involved in carbohydrate and protein metabolism

Project description:Asynchronized and nonuniform seed germination is causing obstacles to the large-scale cultivation of carrot (Daucus carota L.). In the present study, the combination of high voltage electrostatic field treatment (EF) with hydropriming (HYD), namely hydro-electro hybrid priming (HEHP), significantly improved all germination indicators of carrot seeds, and the promoting effect was superior to that of the HYD treatment. A TMT-based proteomic analysis was conducted on the carrot seeds, and the maximum number of differentially abundant proteins (DAPs) appeared between CK and HEHP. KEGG analysis revealed that the upregulated DAPs were mainly enriched in the pathways related to protein synthesis and degradation such as “ribosome” and “proteasome”, while the downregulated DAPs were mainly enriched in photosynthesis-related pathways. Furthermore, the maximum DAPs were annotated in carbohydrate metabolism. Some proteins identified as key enzymes of the glyoxylate cycle, the tricarboxylate cycle, glycolysis and the pentose phosphate pathway showed enhanced abundance in priming treatments. The activities of several key enzymes involved in carbohydrate metabolism were also enhanced by the priming treatments, especially the HEHP treatment. Real-time quantitative PCR (qRT-PCR) analysis revealed that the effect of priming is mainly reflected before sowing. In conclusion, the optimal effect of HEHP is to regulate the synthesis and degradation of proteins in seeds to meet the requirements of germination and initiate the utilization of seed storage reserves and respiratory metabolism. The present work expanded the understanding of the response mechanism of carrot seed germination to priming and the biological effects of high voltage electrostatic field.

2022-04-04 | PXD030133 | Pride

Lepidium sativum seed germination timecourse

Project description:This series analyses germinating Lepidium sativum seeds with both temporal and spatial detail. This is a cross species microarray normalisation on Arabidopsis thaliana chips. Performed as part of the vSEED project Lepidium seeds were dissected into four compartments at seven time points during seed germination. The compartments were the micropylar endosperm (CAP), the non-micropylar endosperm (NME), the radicle and lower hypocotyl (RAD) and the cotyledons (COT). At testa and endosperm rupture the seeds were split into pre- and post- ruptured populations. Dry seeds were also sampled: as a whole seed (DRY), the radicle and endosperm part (DRYRC) and the dry seed part containing the non-micropylar endosperm and part of the cotyledons (DRYNMC).

2015-02-20 | E-GEOD-55702 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data