Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field

ABSTRACT: Improving photosynthesis is a major approach to increase crop yield potential. Here we report a negative transcription factor of photosynthesis, which can be manipulated to increase rice photosynthesis and plant biomass in the field. This transcription factor named negative regulator of photosynthesis 1 (NRP1) (Os07g0471900) which was identified through a co-expression analysis using rice leaf RNA sequencing (RNA-seq) data. The NRP1 showed significantly negative correlation with the expression of many genes involved in photosynthesis. Knocking out NPR1 led to greater photosynthesis and increased biomass in the field, while overexpression of NRP1 decreased photosynthesis and biomass. Transcriptomic data analysis shows that NRP1 can negatively regulate the expression of photosynthetic genes. Protein transactivation experiments show that NRP1 is a transcription activator, implying that NRP1 may indirectly regulate photosynthesis gene expression through an unknown regulator. This study shows that combination of bioinformatics analysis with transgenic testing can be used to identify new regulators to improve photosynthetic efficiency in crops.

ORGANISM(S): Oryza sativa

PROVIDER: GSE136918 | GEO | 2019/10/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field

Project description:Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field

| PRJNA564036 | ENA

Over-expression of a transcription factor mEmBP-1a increases rice photosynthesis, biomass and yield by regulating the expression of multiple key photosynthesis genes

Project description:Improvement in the photosynthetic efficiency is a major approach to improve crop yield potential. So far, most of the demonstrated cases of photosynthesis improvement was achieved through manipulation of one or a few photosynthesis related genes. Present study found that over-expression of one maize transcription factor, mEmBP-1 gene, led to simultaneously increased expression of nearly all genes in photosynthesis pathway, including genes encoding chlorophyll a and b-binding proteins (Lhca and Lhcb), photosystem II (PsbR3 and PsbW) and PS I reaction center subunits (PsaK and PsaN), genes encoding for chloroplast ATP synthase subunit and electron transport reaction (Fd1 and PC), and also major genes in the Calvin Benson Bassham cycle, Rubisco, GAPDH, FBA, TK and PRK. This increased photosynthesis gene expression resulted in increased leaf chlorophyll pigment, photosynthetic rate, quantum yields, biomass growth and grain yield both in the greenhouse and also in natural field conditions. Using DNA-Protein binding experiment, we found that mEmBP-1a protein can directly bind to the promoter regions of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes upregulates expression of these genes. Hence, this study shows that mEmBP-1a is a major regulator of photosynthesis.

2020-01-08 | GSE143259 | GEO

Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.

Project description:Plants capture solar energy and atmospheric carbon dioxide (CO2) through photosynthesis, which is the primary component of crop yield, and needs to be increased considerably to meet the growing global demand for food. Environmental stresses, which are increasing with climate change, adversely affect photosynthetic carbon metabolism (PCM) and limit yield of cereals such as rice (Oryza sativa) that feeds half the world. To study the regulation of photosynthesis, we developed a rice gene regulatory network and identified a transcription factor HYR (HIGHER YIELD RICE) associated to PCM, which on expression in rice enhances photosynthesis under multiple environmental conditions, determining a morpho-physiological program leading to higher grain yield (GY) under normal, drought and high temperature stress conditions. We show HYR is a master regulator, directly activating photosynthesis genes, cascades of transcription factors and other downstream genes involved in PCM and yield stability under drought and high temperature environmental stress conditions. To assess the role of increased HYR expression in rice, whole-genome microarrays were used to generate gene expression profiles of rice cultivar Nipponbare transformed with an overexpression construct of the HYR gene (Loc_Os03g02650) under control of the CaMV 35S promoter, along with control wild-type (WT) lines.

2014-08-30 | GSE60936 | GEO

Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.

2014-08-30 | E-GEOD-60936 | biostudies-arrayexpress

Comparison of Splenic Nrp1- and Nrp1+ Treg Populations

Project description:To compare subpopulations of Treg cells in wild type mice based upon Nrp1 Expression, differentiating nTreg and iTreg Cells were FACS sorted based upon expression of CD4, Foxp3 and expression of Nrp1.

2012-08-30 | E-GEOD-40441 | biostudies-arrayexpress

A blueprint for C4 photosynthesis in the rice paddy: insights from the noxious weed Echinochloa glabrescens

Project description:The C4 pathway is a highly complex trait that increases photosynthetic efficiency in over sixty plant lineages. Although the majority of C4 plants occupy disturbed, arid and nutrient-poor habitats, some grow in high-nutrient, waterlogged conditions. One such example is Echinochloa glabrescens, which is an aggressive weed of rice paddies. We generated comprehensive transcriptome datasets for C4 E. glabrescens and C3 rice to identify genes associated with adaption to waterlogged, nutrient-replete conditions, but also used the data to better understand how C4 photosynthesis operates in these conditions. Similar to arid C4 species, leaves of E. glabrescens exhibited classical Kranz anatomy with lightly lobed mesophyll cells. As with rice and other hygrophytic C3 species, leaves of E. glabrescens accumulated a chloroplastic phosphoenolpyruvate carboxylase protein, albeit at reduced levels relative to rice. We identified a molecular signature associated with C4 photosynthesis in nutrient-replete, waterlogged conditions that is highly similar to those previously reported from C4 plants that grow in more arid conditions. We also identified a cohort of genes that have been subjected to a selective sweep associated with growth in paddy conditions. Overall, this approach highlights the value of using wild species such as weeds to identify adaptions to specific conditions associated with high-yielding crops in agriculture.

2015-08-11 | E-MTAB-4422 | biostudies-arrayexpress

Comparison of Splenic Nrp1- and Nrp1+ Treg Populations

Project description:To compare subpopulations of Treg cells in wild type mice based upon Nrp1 Expression, differentiating nTreg and iTreg

2012-08-30 | GSE40441 | GEO

Wildtype and NRP1 knockout macrophages

Project description:Obesity gives rise to metabolic complications by mechanisms that are poorly understood. While chronic inflammatory signaling in adipose tissue is typically associated with metabolic deficiencies linked to excessive weight gain, we identified a subset of NRP1-expressing myeloid cells that accumulate in adipose tissue and protect against obesity and metabolic syndrome. Ablation of NRP1 in macrophages compromised lipid uptake in these cells, which reduced substrates for fatty acid β-oxidation and shifted energy metabolism of these macrophages towards a more inflammatory glycolytic metabolism. Conditional deletion of NRP1 in LysM Cre-expressing cells lead to inadequate adipose vascularization, accelerated weight gain and reduced insulin sensitivity even independent of weight gain. Transfer of NRP1+ hematopoietic cells improved glucose homeostasis, resulting in the reversal of a prediabetic phenotype. Our findings suggest a pivotal role for adipose tissue resident NRP1+-expressing macrophages in driving healthy weight gain and maintaining glucose tolerance.

2018-02-11 | GSE110447 | GEO

Overexpression of the HRD gene in Arabidopsis

Project description:Freshwater is a limited and dwindling global resource; therefore, efficient water use is required for food crops that have high water demands, such as rice, or for the production of sustainable energy biomass. We show here that expression of the Arabidopsis HARDY (HRD) gene in rice improves water use efficiency, the ratio of biomass produced to the water used, by enhancing photosynthetic assimilation and reducing transpiration. These drought tolerant low-water-consuming rice plants exhibit increased shoot biomass under well irrigated conditions and an adaptive increase in root biomass under drought stress. The HRD gene, an AP2/ERF-like transcription factor, identified by a gain-of-function Arabidopsis mutant hrd-D having roots with enhanced strength, branching, and cortical cells, exhibits drought resistance and salt tolerance, accompanied by an enhancement in the expression of abiotic stress associated genes. Although HRD overexpression in Arabidopsis produces thicker leaves with more chloroplast-bearing mesophyll cells, in rice there is an increase in leaf biomass and bundle sheath cells that probably contribute to the enhanced photosynthesis assimilation and efficiency. HRD overexpression was also studied for clues of molecular mechanisms involved using microarrays. The results exemplify application of a gene identified from the model plant Arabidopsis for the improvement of water use efficiency coincident with drought resistance in the crop plant rice. Keywords: Genetic modification transcription factor overexpression mutant

2007-09-05 | GSE8936 | GEO

Heterosis of Arabidopsis C24 x Col hybrids is associated with increased photosynthesis capacity.

Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased. Whole plants in Col, C24, and their F1 hybrids with two replications

2012-03-06 | E-GEOD-36273 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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