Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Iron deprivation affects aboveground cell wall biosynthesis in Populus and the role of PtrbHLH011 [RNA-seq]

ABSTRACT: Growing bioenergy crops like poplars on marginal land is appealing to minimize competition for arable land. However, this is hampered by a lack of insight into secondary cell wall (SCW) changes caused by environmental stress. Iron (Fe) deficiency is widespread and detrimental to plants. Here, we report that Fe deprivation increases SCW biosynthesis of poplar stem via the gene regulatory network (GRN) involving the transcription factor PtrbHLH011, whose expression is downregulated by Fe deprivation. PtrbHLH011 is a potent repressor of SCW, overexpression of which resulted in a reduction of stem SCW by over 65%. Furthermore, PtrbHLH011 overexpression induced foliar disease symptoms caused by reduced iron and flavonoid accumulations. By constructing PtrbHLH011-controlled GRN, we discovered that PtrbHLH011 binds to the AAAGACA sequence and represses essential genes for SCW biosynthesis, flavonoid biosynthesis, and iron homeostasis. Our results suggest that PtrbHLH011 functions as a co-regulator for the rapid activation of systematic Fe-deficiency responses.

ORGANISM(S): Populus tremula x Populus alba Populus trichocarpa

PROVIDER: GSE265825 | GEO | 2025/07/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Iron deprivation affects aboveground cell wall biosynthesis in Populus and the role of PtrbHLH011 [ChIP-seq]

Project description:Growing bioenergy crops like poplars on marginal land is appealing to minimize competition for arable land. However, this is hampered by a lack of insight into secondary cell wall (SCW) changes caused by environmental stress. Iron (Fe) deficiency is widespread and detrimental to plants. Here, we report that Fe deprivation increases SCW biosynthesis of poplar stem via the gene regulatory network (GRN) involving the transcription factor PtrbHLH011, whose expression is downregulated by Fe deprivation. PtrbHLH011 is a potent repressor of SCW, overexpression of which resulted in a reduction of stem SCW by over 65%. Furthermore, PtrbHLH011 overexpression induced foliar disease symptoms caused by reduced iron and flavonoid accumulations. By constructing PtrbHLH011-controlled GRN, we discovered that PtrbHLH011 binds to the AAAGACA sequence and represses essential genes for SCW biosynthesis, flavonoid biosynthesis, and iron homeostasis. Our results suggest that PtrbHLH011 functions as a co-regulator for the rapid activation of systematic Fe-deficiency responses.

2025-07-22 | GSE265823 | GEO

Cooperation of two mRNA-binding proteins drives metabolic adaptation to iron deficiency

Project description:Expression of the yeast Cth2 protein stimulates degradation of mRNAs encoding proteins with Fe-dependent functions in metabolism, in iron storage and in other cellular processes. We demonstrate that in response to Fe deprivation, the Cth2-homologue, Cth1, stimulates specific degradation of mRNAs involved in mitochondrially localized activities that include respiration and amino acid biosynthesis. Furthermore, yeast cells grown under Fe deprivation accumulate mRNAs encoding proteins that function in glucose metabolism. These studies demonstrate a reprogramming of cellular metabolism during Fe-starvation dependent on the coordinated activities of two mRNA binding proteins. Keywords: Messenger RNAs down regulated by Cth1 and Cth2 proteins in response to Fe-limitation

2008-07-15 | GSE11236 | GEO

Ectopic expression of FvVND4c promotes secondary cell wall thickening and flavonoid accumulation in Fragaria vesca

Project description:Secondary cell wall thickening (SCW) has a significant effect in the growth and development of plants, as well as in the resistance to various biotic and abiotic stresses. It is regulated by a multilevel transcriptional regulatory network, in which VASCULAR-RELATED NAC-DOMAINs (VNDs) act as key regulators. Lignin is an important component of SCW, it has a cooperative regulation with the biosynthesis of flavonoids which also originate from phenylpropanoid pathway. However, there are few studies on SCW thickening and flavonoid biosynthesis in flesh fruits. We want to investigate the role of FvVNDs on cell wall and fruit color development in Fragaria vesca.

2023-05-01 | GSE225542 | GEO

Transcription profiling of S. cerevisiae cth1cth2 cells independently transformed with pRS416 (V), pRS416-CTH1 (C) or pRS416-CTH2 (T) reveals cooperation of two mRNA-binding proteins drives metabolic adaptation to iron deficiency

Project description:Expression of the yeast Cth2 protein stimulates degradation of mRNAs encoding proteins with Fe-dependent functions in metabolism, in iron storage and in other cellular processes. We demonstrate that in response to Fe deprivation, the Cth2-homologue, Cth1, stimulates specific degradation of mRNAs involved in mitochondrially localized activities that include respiration and amino acid biosynthesis. Furthermore, yeast cells grown under Fe deprivation accumulate mRNAs encoding proteins that function in glucose metabolism. These studies demonstrate a reprogramming of cellular metabolism during Fe-starvation dependent on the coordinated activities of two mRNA binding proteins. Experiment Overall Design: cth1cth2 cells independently transformed with pRS416 (V), pRS416-CTH1 (C) or pRS416-CTH2 (T) were grown in triplicate in SC-Ura containing 100 Î¼M BPS until exponential growth phase (approximately 6hrs) at 30 degrees, RNA was extracted using a standard glass beads protocol, labeled and hybridized to Yeast Genome S98 Afffymetrix arrays.

2008-10-20 | E-GEOD-11236 | biostudies-arrayexpress

Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteria

Project description:Oxygenic photosynthesis contains multiple proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Accordingly, its composition is heavily re-organized when iron becomes limiting as a nutrient factor, a situation that is frequently encountered in nature. However, the molecular mechanisms controlling the reorganization of the photosynthetic system upon iron deprivation have remained enigmatic. Here we show that the small regulatory RNA IsaR1 (Iron-stress activated RNA 1) plays a pivotal role in acclimation to low iron conditions. The transcription factor Fur cannot facilitate iron starvation dependent repression of it’s targets because it requires iron for DNA binding. We show that the Fur repressed sRNA IsaR1 fulfills this repressor function in iron homeostasis. The IsaR1 regulon consists of at least 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, the detoxification of anion radicals, citrate cycle, and in tetrapyrrole biogenesis. We demonstrate that IsaR1 is absolutely necessary to maintain physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (i) directly, via posttranscriptional repression of gene expression and indirectly, (ii) via the suppression of Fe/S cluster co-factor and (iii) pigment biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a riboregulator of central importance. These findings provide a new perspective for studies of the regulation of iron homeostasis in photosynthetic organisms.

2016-10-01 | GSE87496 | GEO

Salicylic acid accumulation is required for Fe-deficiency responses in Arabidopsis

Project description:Several phytohormones and other small molecules have been demonstrated to be involved in iron (Fe) homeostasis. However, how salicylic acid (SA), an essential hormone in plant immunity and defense responses, participates in Fe-deficiency responses in plants is largely unknown. Here, we took advantage of a SA biosynthesis defect mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. Under a Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significant higher in pad4 than Col-0 under the Fe-deficiency treatment, suggesting that a mutation in the PAD4 gene may alleviate the Fe-deficiency-induced symptoms by regulating the soluble Fe concentrations. Furthermore, a SA signaling maker line (PR1promoter: GUS) was used to investigate how Fe deficiency affects endogenous SA biosynthesis and metabolism. The data showed that Fe deficiency significantly induced SA accumulation in Col-0, and the loss function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines.

2016-10-01 | GSE74515 | GEO

Iron deficiency response of interactions between Brachypodium and Pseudomonas fluorescens SBW25 under controlled growth conditions.

Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.

2020-09-22 | GSE158273 | GEO

The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system.

2013-06-29 | GSE48416 | GEO

Iron uptake experiments in yeast

Project description:The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Using regression correlation

2006-02-07 | E-GEOD-4196 | biostudies-arrayexpress

The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress