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International Conference SPS 2018 - Plant Sciences For the Future:  J-4 ! starts the 4th of July

International Conference SPS 2018 - Plant Sciences For the Future:  J-4 ! starts the 4th of July | SEED DEV LAB Biblio | Scoop.it
 

July 4-6, 2018

Centrale-Supélec - Eiffel building - Gif-sur-Yvette

Close to Paris (RER B)

ATTENTION: CHANGE OF LOCATION


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SUPPORTING BASIC PLANT SCIENCE  The June 2018 edition of the GARNish newsletter available for download:

SUPPORTING BASIC PLANT SCIENCE  The June 2018 edition of the GARNish newsletter available for download: | SEED DEV LAB Biblio | Scoop.it
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Genetic control of seed shattering during African rice domestication

Genetic control of seed shattering during African rice domestication | SEED DEV LAB Biblio | Scoop.it
Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from a core heartland and introgression from local wild rice. The cloning of ObSH3 not only provides new insights into a critical crop domestication process but also adds to the body of knowledge on the molecular mechanism of seed dispersal.
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Plant epigenetics and transposable elements - from basic research to plant breeding 29-31 October, 2018 Angers (FRANCE)

Plant epigenetics and transposable elements - from basic research to plant breeding  29-31 October, 2018  Angers (FRANCE) | SEED DEV LAB Biblio | Scoop.it

plant epigenetics and transposable elements - from basic research to plant breeding

29-31 October, 2018

Angers (FRANCE)

“Plant epi/genetics” is an international conference on epigenetics and transposable elements. The aim of this conference is to bring together experts, novices, students and breeders to exchange and discuss their latest results in the fields of epigenetics and transposable elements. The conference will range from fundamental research to applications in crop plants. Plant breeding companies are encouraged to join in and participate at this meeting.

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A maternally-deposited endosperm cuticle contributes to the physiological defects of transparent testa seeds

A maternally-deposited endosperm cuticle contributes to the physiological defects of transparent testa seeds | SEED DEV LAB Biblio | Scoop.it
Mature dry seeds are highly resilient plant structures where the encapsulated embryo is kept protected and dormant to facilitate its ultimate dispersion. Seed viability is heavily dependent on the seed coat's capacity to shield living tissues from mechanical and oxidative stress. In Arabidopsis (Arabidopsis thaliana) the seed coat, also called testa, arises after differentiation of maternal ovular integuments during seed development. We recently described a thick cuticle tightly embedded in the mature seed's endosperm cell wall. We show here that it is produced by the maternal inner integument 1 layer (ii1) and, remarkably, transferred to the developing endosperm. Arabidopsis transparent testa (tt) mutations are a class of maternally-inherited mutations causing seed coat pigmentation defects. TT gene products encode proteins involved in flavonoid metabolism and regulators of seed coat development. tt mutants have abnormally high seed coat permeability, resulting in lower seed viability and dormancy. However, the biochemical basis of this high permeability is not fully understood. We show that the cuticles of developing tt mutant integuments have profound structural defects, which are associated with enhanced cuticle permeability. Genetic analysis indicates that a functional proanthocyanidin (PA) synthesis pathway is required to limit cuticle permeability, and our results suggest that PAs could be intrinsic components of the cuticle. Together, these results show that the formation of a maternal cuticle is an intrinsic part of the normal integumental differentiation program leading to testa formation and is essential for the seed's physiological properties.
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EAR1 Negatively Regulates ABA Signaling by Enhancing 2C Protein Phosphatase Activity

The reversible phosphorylation of proteins by kinases and phosphatases is an antagonistic process that modulates many cellular functions. Protein phosphatases are usually negatively regulated by inhibitor proteins. During abscisic acid (ABA) signaling, these inhibitor proteins comprise PYR1/PYL/RCAR ABA receptors, which inhibit the core negative regulators, the clade A type 2C protein phosphatases (PP2Cs). However, it is not known whether these PP2Cs are positively regulated by other proteins. Here, we identified an Arabidopsis thaliana ear1 (enhancer of aba co-receptor1) mutant that exhibits pleiotropic ABA-hypersensitive phenotypes. EAR1 encodes an uncharacterized protein that is conserved in both monocots and dicots. EAR1 interacts with the N-terminal inhibition domains of all six PP2Cs, ABA INSENSITIVE1 (ABI1), ABI2, HYPERSENSITIVE TO ABA1 (HAB1), HAB2, ABA-HYPERSENSITIVE GERMINATION1 (AHG1), and AHG3, during ABA signaling and enhances the activity of PP2Cs both in vitro and in vivo. ABA treatment caused EAR1 to accumulate in the nucleus. These results indicate that EAR1 is a negative regulator of ABA signaling that enhances the activity of PP2Cs by interacting with and releasing the N-terminal autoinhibition of these proteins.
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PLANT SCIENCES FOR THE FUTURE (4-6 of July), Gif/Yvette (Paris), International Conference SPS 2018 - deadline to register May 31

PLANT SCIENCES FOR THE FUTURE (4-6 of July), Gif/Yvette (Paris), International Conference SPS 2018 - deadline to register May 31 | SEED DEV LAB Biblio | Scoop.it

July 4-6, 2018
CNRS Campus - Building 21 - Gif-sur-Yvette
Close to Paris (RER B)

 

Only a few days left to register to the conference

and to the Gala Dinner at the Paris Wine Museum !!

Deadline : May 31 (midnight)


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Measures of Toxicity

Measures of Toxicity | SEED DEV LAB Biblio | Scoop.it
This article is co-written by biologist Iida Ruishalme (yours truly at Thoughtscapism) and neuroscientist Alison Bernstein, aka Mommy PhD from SciMoms. We live amidst a mind-bogglingly rich sea of molecules. Nowadays, we also have astonishingly sophisticated methods of chemical detection at our disposal, and are able to measure smaller and smaller traces of substances in…

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Purple Brassica oleracea var. capitata F. rubra is due to the loss of BoMYBL2–1 expression 

Purple Brassica oleracea var. capitata F. rubra is due to the loss of BoMYBL2–1 expression  | SEED DEV LAB Biblio | Scoop.it
Water-soluble anthocyanin pigments are important ingredients in health-improving supplements and valuable for the food industry. Although great attention has been paid to the breeding and production of crops containing high levels of anthocyanin, genetic variation in red or purple cabbages (Brassica oleracea var. capitata F. rubra) has not yet been characterized at the molecular level. In this study, we identified the mechanism responsible for the establishment of purple color in cabbages.
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Seed coat thickness in the evolution of angiosperms

Seed coat thickness in the evolution of angiosperms | SEED DEV LAB Biblio | Scoop.it
The seed habit represents a remarkable evolutionary advance in plant sexual reproduction. Since the Paleozoic, seeds carry a seed coat that protects, nourishes and facilitates the dispersal of the fertilization product(s). The seed coat architecture evolved to adapt to different environments and reproductive strategies in part by modifying its thickness. Here, we review the great natural diversity observed in seed coat thickness among angiosperms and its molecular regulation in Arabidopsis.
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A tension-adhesion feedback loop in plant epidermis

A tension-adhesion feedback loop in plant epidermis | SEED DEV LAB Biblio | Scoop.it

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Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa 

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa  | SEED DEV LAB Biblio | Scoop.it
Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA‐directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV‐dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV‐dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.
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The Rosa genome provides new insights into the domestication of modern roses 

The Rosa genome provides new insights into the domestication of modern roses  | SEED DEV LAB Biblio | Scoop.it
Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

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Epigenetic responses to abiotic stresses during reproductive development in cereals

Epigenetic responses to abiotic stresses during reproductive development in cereals | SEED DEV LAB Biblio | Scoop.it
Abiotic stresses, including heat, drought, cold, flooding, and salinity, negatively impact crop productivity. Various stages during reproductive development are especially sensitive to environmental stresses, which may lead to complete sterility and severe yield losses. Plants exhibit diverse responses to ameliorate stress damage. Changes in DNA methylation, histone modification as well as regulation of small RNA and long noncoding RNA pathways have been shown to represent key modulators in plant stress responses. During reproductive development in cereals, various protein complexes controlling histone and DNA methylation have been identified, revealing conserved and novel mechanisms regulating abiotic stress responses in cereals and other plant species. New findings highlight the role of transposable elements during stress periods. Here, we review our current understanding of epigenetic stress responses during male and female gametophyte formation (germline development), fertilization, early seed devolvement, and seed maturation in cereals. An integrative model of epigenetic responses during reproductive development in cereals is proposed, emphasizing the role of DNA methylation and histone modifications during abiotic stresses.
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JMJ30‐mediated H3K9me3 demethylation drives tissue identity changes to promote callus formation in Arabidopsis 

JMJ30‐mediated H3K9me3 demethylation drives tissue identity changes to promote callus formation in Arabidopsis  | SEED DEV LAB Biblio | Scoop.it
Summary
Plant somatic cells can be reprogrammed by in vitro tissue culture methods, and massive genome‐wide chromatin remodeling occurs particularly during callus formation. Since callus tissue resembles root primordium, tissue identity conversion is essentially required when leaf explants are used. Consistent with the fact that differentiation state is defined by chromatin structure that permits limited gene profiles, epigenetic changes underlie the cellular reprogramming for tissue identity changes. Although a histone methylation process suppressing leaf identity during leaf‐to‐callus transition has been demonstrated, the epigenetic factor involved in activation of lateral root identity is still elusive. Here, we report that JUMONJI C DOMAIN‐CONTAINING PROTEIN 30 (JMJ30) stimulates callus formation by promoting expression of a subset of LATERAL ORGAN BOUNDARIES‐DOMAIN (LBD) genes that establish root primordia. The JMJ30 protein binds to promoters of the LBD16 and LBD29 genes along with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and activates LBD expression. Consistently, JMJ30‐deficient mutant displays reduced callus formation with low LBD transcript levels. The ARF‐JMJ30 complex catalyzes the removal of methyl groups from H3K9me3 especially at the LBD16 and LBD29 loci to activate their expression during leaf‐to‐callus transition. Moreover, the ARF‐JMJ30 complex further recruits ARABIDOPSIS TRITHORAX‐RELATED 2 (ATXR2), which promotes H3K36me3 deposition at the LBD16 and LBD29 promoters, and the tripartite ensures stable LBD activation during callus formation. These results indicate that the coordinated epigenetic modifications promote callus formation by establishing root primordium identity.

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Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants | SEED DEV LAB Biblio | Scoop.it
In plants, cytosine methylation, an epigenetic mark critical for transposon silencing, is maintained over generations by key enzymes that directly methylate DNA and is facilitated by chromatin remodelers, like DECREASE IN DNA METHYLATION 1 (DDM1). Short-interfering RNAs (siRNAs) also mediate transposon DNA methylation through a process called RNA-directed DNA methylation (RdDM). In tomato (Solanum lycopersicum), siRNAs are primarily mapped to gene-rich chromosome arms, and not to pericentromeric regions as in Arabidopsis thaliana. Tomato encodes two DDM1 genes. To better understand their functions and interaction with the RdDM pathway, we targeted the corresponding genes via the CRISPR/Cas9 technology, resulting in the isolation of Slddm1a and Slddm1b knockout mutants. Unlike the single mutants, Slddm1a Slddm1b double mutant plants display pleiotropic vegetative and reproductive phenotypes, associated with severe hypomethylation of the heterochromatic transposons in both the CG and CHG methylation contexts. The methylation in the CHH context increased for some heterochromatic transposons and conversely decreased for others localised in euchromatin. We found that the number of heterochromatin-associated siRNAs, including RdDM-specific small RNAs, increased significantly, likely limiting the transcriptional reactivation of transposons in Slddm1a Slddm1b. Taken together, we propose that the global production of siRNAs and the CHH methylation mediated by the RdDM pathway are restricted to chromosome arms in tomato. Our data suggest that both pathways are greatly enhanced in heterochromatin when DDM1 functions are lost, at the expense of silencing mechanisms normally occurring in euchromatin.
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Seed tissue and nutrient partitioning, a case for the nucellus

Seed tissue and nutrient partitioning, a case for the nucellus | SEED DEV LAB Biblio | Scoop.it
Flowering plants display a large spectrum of seed architectures. The volume ratio of maternal versus zygotic seed tissues changes considerably among species and underlies different nutrient-storing strategies. Such diversity arose through the evolution of cell elimination programs that regulate the relative growth of one tissue over another to become the major storage compartment. The elimination of the nucellus maternal tissue is regulated by developmental programs that marked the origin of angiosperms and outlined the most ancient seed architectures. This review focuses on such a defining mechanism for seed evolution and discusses the role of nucellus development in seed tissues and nutrient partitioning at the light of novel discoveries on its molecular regulation.
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The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11

The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11 | SEED DEV LAB Biblio | Scoop.it
Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpic seed abortion determined by the SEED DEVELOPMENT INHIBITOR (SDI) locus is the usual source of seedlessness in commercial grapevine (Vitis vinifera) cultivars, the underlying sdi mutation remains unknown. Here, we undertook an integrative approach to identify the causal mutation. Quantitative genetics and fine mapping in two 'Crimson Seedless' (CS)-derived F1 mapping populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a 323-kb region on chromosome 18. RNA-seq comparing seed traces of seedless and seeds of seeded F1 individuals identified processes triggered during sdi-determined seed abortion, including activation of salicylic acid-dependent defenses. The RNA-seq dataset was investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide changes in coding sequences of the seedless haplotype were predicted in two genes within the sdi fine mapping interval. Targeted re-sequencing of the two genes in a collection of 124 grapevine cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene AGAMOUS-LIKE 11 (VviAGL11) was fully linked with stenospermocarpy. The concurrent post-zygotic variation identified for this missense polymorphism and seedlessness phenotype in seeded somatic variants of the original stenospermocarpic cultivar supports a causal effect. We postulate that seed abortion caused by this amino acid substitution in VviAGL11 is the major cause of seedlessness in cultivated grapevine. This information can be exploited to boost seedless grape breeding.
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Meeting resistance

Meeting resistance | SEED DEV LAB Biblio | Scoop.it

"Almost as soon as antibiotics were discovered to be valuable in medicine, resistance emerged among bacteria. Whenever mutating or recombining organisms are faced with extirpation, those individuals with variations that avert death will survive and reproduce to take over the population. This can happen rapidly among organisms that reproduce fast and outpace our efforts to combat them. Thus, our use of chemical entities to rid ourselves of clinical, domestic, and agricultural pathogens and pests has selected for resistance."

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FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis | SEED DEV LAB Biblio | Scoop.it
The chromatin remodeling activities of the FACT (facilitates chromatin transactions) complex are required for many cellular functions, including transcription, DNA replication, and repair. Here, we demonstrate that the two FACT subunits, SSRP1 and SPT16, are also required for genome-wide DNA demethylation and regulation of gene imprinting during Arabidopsis reproduction. Without FACT, Arabidopsis seeds undergo abnormal development and exhibit aberrant DNA hypermethylation, including at imprinting control region loci. We show that FACT associates with the DEMETER (DME) DNA demethylase, facilitating DNA demethylation at over half of DME’s targets, specifically those which reside in heterochromatin. These results provide insight into upstream events in the DNA demethylation pathway and reveal the importance of chromatin remodeling for DNA demethylation during Arabidopsis reproduction.
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More than 40 PhD projects from the SPS LabEx teams in the Doctoral Schools' competitions !!

More than 40 PhD projects from the SPS LabEx teams in the Doctoral Schools' competitions !! | SEED DEV LAB Biblio | Scoop.it


- The application deadline depends on the subject.

- Those subjects are registered to various Doctoral Schools. For the modalities of application, please refer to the Doctoral School related to the subject.


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Autophagy is essential for optimal Fe translocation to seeds in Arabidopsis

Autophagy is essential for optimal Fe translocation to seeds in Arabidopsis | SEED DEV LAB Biblio | Scoop.it
Micronutrient deficiencies affect a large part of the world population. They are mostly due to the consumption of grains with insufficient content of Fe or Zn. It is therefore important to improve our knowledge of the mechanisms of micronutrient loading to seeds. Nutrient loaded in seeds originate either from de novo uptake by roots or recycling from leaves. Autophagy is a conserved mechanism for nutrient recycling in eukaryotes and was shown to be involved in nitrogen remobilization to seeds. Measuring the distribution of metal nutrients at the end of the life in Arabidopsis thaliana plants impaired in autophagy, we have investigated the role of autophagy in metal micronutrient translocation to seeds. We found that several Arabidopsis genotypes impaired in autophagy display defects in nutrient remobilization to seeds. In atg5-1, which is completely defective in autophagy, the efficiency of Fe translocation from vegetative organs to seeds was severely decreased even when Fe was provided during seed formation. Combining atg5-1 with sid2 mutation that counteracts premature senescence associated to autophagy deficiency and using 57Fe pulse labelling, we could propose a two step mechanism in which iron taken up de novo during seed formation is first accumulated in vegetative organs and subsequently remobilized to seeds. Finally, we showed that translocations of zinc and manganese to seeds are also dependent on autophagy. Our results highlight the importance of autophagy for optimal micronutrient remobilization to seeds. Fine tuning autophagy during seed formation opens new possibilities to improve this trait.
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Synthetic hormone-responsive transcription factors can monitor and re-program plant development

Synthetic hormone-responsive transcription factors can monitor and re-program plant development | SEED DEV LAB Biblio | Scoop.it

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Nice synthetic in vivo   sensors to monitor  auxin, JA and GA levels !

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Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle

Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle | SEED DEV LAB Biblio | Scoop.it
Vinblastine, a potent anticancer drug, is produced by Madagascar periwinkle in small quantities: heterologous reconstitution of vinblastine biosynthesis could provide an additional source of this drug. The chemistry underlying vinblastine synthesis makes identification of the biosynthetic genes challenging. Here we identify the two missing steps of vinblastine biosynthesis in this plant, namely an oxidase and a reductase that isomerize stemmadenine acetate into dihydroprecondylocarpine acetate, which is then deacetoxylated and cyclized to either catharanthine or tabersonine via two herein characterized hydrolases. The pathways show how plants create chemical diversity and also enable development of heterologous platforms for generation of stemmadenine-derived bioactive compounds.
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CORNICHON sorting and regulation of GLR channels underlie pollen tube Ca2+ homeostasis

CORNICHON sorting and regulation of GLR channels underlie pollen tube Ca2+ homeostasis | SEED DEV LAB Biblio | Scoop.it
Compared to animals, evolution of plant calcium (Ca2+) physiology has led to a loss of proteins for influx and small ligand–operated control of cytosolic Ca2+, leaving many Ca2+ mechanisms unaccounted for. Here, we show a mechanism for sorting and activation of glutamate receptor–like channels (GLRs) by CORNICHON HOMOLOG (CNIH) proteins. Single mutants of pollen-expressed Arabidopsis thaliana GLRs (AtGLRs) showed growth and Ca2+ flux phenotypes expected for plasma membrane Ca2+ channels. However, higher-order mutants of AtGLR3.3 revealed phenotypes contradicting this assumption. These discrepancies could be explained by subcellular AtGLR localization, and we explored the implication of AtCNIHs in this sorting. We found that AtGLRs interact with AtCNIH pairs, yielding specific intracellular localizations. AtCNIHs further trigger AtGLR activity in mammalian cells without any ligand. These results reveal a regulatory mechanism underlying Ca2+ homeostasis by sorting and activation of AtGLRs by AtCNIHs.
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