Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

White Leaf and Panicle 2 encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice (Oryza sativa L.)

ABSTRACT: We performed a transcriptomics analysis in the wild type and the mutant, and the expression levels of PEP-encoded genes, chloroplast development and heat-strss-related genes genes were affected inwlp2s mutant.

ORGANISM(S): Oryza sativa

PROVIDER: GSE98885 | GEO | 2018/03/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

White Leaf and Panicle 2, encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice.

Project description:The plastid-encoded RNA polymerase (PEP) plays an important role in the transcription machinery of mature chloroplasts, yet details of its function remain elusive in rice. Here, we identified a novel PEP-associated protein (PAP), WLP2, based on its two allelic white leaf and panicle mutants, wlp2s and wlp2w. The two mutants were albino lethal at high temperatures and showed decreased chlorophyll accumulation, abnormal chloroplast ultrastructure, and attenuated photosynthetic activity. Map-based cloning suggested that WLP2 encodes a putative pfkB-type carbohydrate kinase family protein, which is homologous to fructokinase-like 1 (AtFLN1) in Arabidopsis. WLP2 is mainly expressed in green tissues and its protein localizes in chloroplasts. Expression levels of PEP-encoded genes, chloroplast development genes and photosynthesis-related genes were compromised in wlp2 mutants, indicating that WLP2 is essential for normal chloroplast biogenesis. Moreover, WLP2 and its paralog OsFLN2 can physically interact with thioredoxin OsTRXz to form a TRX-FLN regulatory module, which not only regulates transcription of the PEP-encoded genes but also maintains the redox balance in chloroplasts under heat stress. Furthermore, the wlp2w mutant gene represents a potential advantage in enhancing seed purity and high-throughput breeding. Our results strongly indicate that WLP2 protects chloroplast development from heat stress via a TRX-FLN regulatory module in rice.

| S-EPMC5853965 | biostudies-literature

Yellow-Leaf 1 encodes a magnesium-protoporphyrin IX monomethyl ester cyclase, involved in chlorophyll biosynthesis in rice (Oryza sativa L.)

Project description:We performed a transcriptomics analysis in the wild type and the mutant, and the expression levels of photosynthesis and chloroplast development genes were affected in yl-1 mutant.

2017-06-29 | GSE96073 | GEO

<i>Panicle Apical Abortion 7</i> Regulates Panicle Development in Rice (<i>Oryza sativa</i> L.).

Project description:The number of grains per panicle significantly contributes to rice yield, but the regulatory mechanism remains largely unknown. Here, we reported a loss-of-function mutant, panicle apical abortion 7 (paa7), which exhibited panicle abortion and degeneration of spikelets on the apical panicles during the late stage of young panicle development in rice. High accumulations of H2O2 in paa7 caused programmed cell death (PCD) accompanied by nuclear DNA fragmentation in the apical spikelets. Map-based cloning revealed that the 3 bp "AGC" insertion and 4 bp "TCTC" deletion mutation of paa7 were located in the 3'-UTR regions of LOC_Os07g47330, which was confirmed through complementary assays and overexpressed lines. Interestingly, LOC_Os07g47330 is known as FRIZZY PANICLE (FZP). Thus, PAA7 could be a novel allele of FZP. Moreover, the severe damage for panicle phenotype in paa7/lax2 double mutant indicated that PAA7 could crosstalk with Lax Panicle 2 (LAX2). These findings suggest that PAA7 regulates the development of apical spikelets and interacts with LAX2 to regulate panicle development in rice.

| S-EPMC9409353 | biostudies-literature

29RNP kinase idetification - Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice)

Project description:The 29-kDa RNA protein (29RNP), which was originally identified in rice etioplasts, has increased phosphorylation levels during de-etiolation. Here, using heparin-sepharose enriched fractions, we identified a chloroplast kinase that phosphorylated 29RNP. The chloroplast kinase phosphorylated the 29RNP and exhibited CKII biochemical characteristics in a kinase reaction test. Proteomic analysis of the chloroplast heparin-sepharose enriched fractions revealed the presence of 70 proteins, including both abundant proteins, such as plastid encoded polymerase subunits, and low-abundance proteins, such as APO2 and DAG. An inclusion list method using Fourier transform ion cyclotron resonance mass spectrometer ( FT-ICR LTQ MS ) was subsequently used to analyze the chloroplast heparin-sepharose enriched fractions. The 29RNP kinase was positively identified as a CKII alpha family protein by the presence of two unique peptides.

2015-04-27 | PXD000951 | Pride

29RNP phosphorylation site - Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice)

Project description:Identfication 29RNP phosphorylation site by rice chloroplast CK2 alpha.

2015-04-27 | PXD000857 | Pride

RNA-Seq analysis of Oryza sativa, ssp. japonica, cv. Kitaake leaves from plants lacking carbonic anhydrase in the chloroplast

Project description:The aim of this experiment was to assess the impact on the transcriptome of relocalisaiton of carbonic anhydrase activity from the chloroplast to the cytosol in Oryza sativa, ssp. japonica, cv. Kitaake. Four genome edited lines and one wil-type control line were analysed.

2024-06-10 | E-MTAB-14111 | biostudies-arrayexpress

X-ray computed tomography to study rice (Oryza sativa L.) panicle development.

Project description:Computational tomography is an important technique for developing digital agricultural models that may help farmers and breeders for increasing crop quality and yield. In the present study an attempt has been made to understand rice seed development within the panicle at different developmental stages using this technique. During the first phase of cell division the Hounsfield Unit (HU) value remained low, increased in the dry matter accumulation phase, and finally reached a maximum at the maturation stage. HU value and seed dry weight showed a linear relationship in the varieties studied. This relationship was confirmed subsequently using seven other varieties. This is therefore an easy, simple, and non-invasive technique which may help breeders to select the best varieties. In addition, it may also help farmers to optimize post-anthesis agronomic practices as well as deciding the crop harvest time for higher grain yield.

| S-EPMC4623690 | biostudies-literature

29RNP kinase - Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice)

Project description:We firstly identified a chloroplast casein kinase 2 from rice heparin sepharose enrichmen which could phosphorylate the RNP29. Then we identified the phosphorylation site of RNP29. We also performed the phosophoproteome analysis of rice and compared the phosphorylation site between rice and arabidopsis.

2015-04-27 | PXD001168 | Pride

Structural basis of chloroplast transcription

Project description:Chloroplasts contain a dedicated genome, which encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. In this work, a 19-subunit PEP complex from Sinapis alba was purified by glycerol gradient centrifugation. All known subunits of the complex could be identified by LC-MS and the structure of the complex was determined by cryo-electron microscopy.

2024-02-19 | PXD048976 | Pride

Dynamic Profiles of transcriptome in Oryza sativa leaf

Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

2018-12-18 | GSE108204 | GEO

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