The maintenance of cellular phosphate(Pi)homeostasis is of great importance in living organisms.The SPX domain-containing protein 1(SPX1)proteins from both Arabidopsis and rice have been proposed to act as sensors of ...The maintenance of cellular phosphate(Pi)homeostasis is of great importance in living organisms.The SPX domain-containing protein 1(SPX1)proteins from both Arabidopsis and rice have been proposed to act as sensors of Pi status.The molecular signal indicating the cellular Pi status and regulating Pi homeostasis in plants,however,remains to be identified,as Pi itself does not bind to the SPX domain.Here,we report the identification of the inositol pyrophosphate lnsP8 as a signaling molecule that regulates Pi homeostasis in Arabidopsis.Polyacrylamide gel electrophoresis profiling of InsPs revealed that lnsP8 level positively correlates with cellular Pi concentration.We demonstrated that the homologs of diphosphoinositol pentaki-sphosphate kinase(PPIP5K),VIH1 and VIH2,function redundantly to synthesize lnsP8,and that the vih1 vih2 double mutant overaccumulates Pi.SPX1 directly interacts with PHR1,the central regulator of Pi starvation responses,to inhibit its function under Pi-replete conditions.However,this interaction is compromised in the vih1 vih2 double mutant,resulting in the constitutive induction of Pi starvation-induced genes,indicating that plant cells cannot sense cellular Pi status without lnsP8.Furthermore,we showed that lnsP8 could directly bind to the SPX domain of SPX1 and is essential for the interaction between SPX1 and PHR1.Collectively,our study suggests that lnsP8 is the intracellular Pi signaling molecule serving as the ligand of SPX1 for controlling Pi homeostasis in plants.展开更多
DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and de...DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence(MEMS) in the promoter of the DNA demethylase gene ROS_1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS_1 expression. How DNA methylation in the MEMS region promotes ROS_1 expression is not known. Here, we show that several Su(var)3-9 homologs(SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS_1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS.Mutations in the SUVHs lead to decreased ROS_1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.展开更多
DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation a...DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.展开更多
Plasticity in root system architecture(RSA)allows plants to adapt to changing nutritional status in the soil.Phosphorus availability is a major determinant of crop yield,and RSA remodeling is critical to increasing th...Plasticity in root system architecture(RSA)allows plants to adapt to changing nutritional status in the soil.Phosphorus availability is a major determinant of crop yield,and RSA remodeling is critical to increasing the efficiency of phosphorus acquisition.Although substantial progress has been made in understanding the signaling mechanism driving phosphate starvation responses in plants,whether and how epigenetic regulatory mechanisms contribute is poorly understood.Here,we report that the Switch defective/sucrose non-fermentable(SWI/SNF)ATPase BRAHMA(BRM)is involved in the local response to phosphate(Pi)starvation.The loss of BRM function induces iron(Fe)accumulation through increased LOW PHOSPHATE ROOT1(LPR1)and LPR2 expression,reducing primary root length under Pi deficiency.We also demonstrate that BRM recruits the histone deacetylase(HDA)complex HDA6-HDC1 to facilitate histone H3 deacetylation at LPR loci,thereby negatively regulating local Pi deficiency responses.BRM is degraded under Pi deficiency conditions through the 26 S proteasome pathway,leading to increased histone H3 acetylation at the LPR loci.Collectively,our data suggest that the chromatin remodeler BRM,in concert with HDA6,negatively regulates Fe-dependent local Pi starvation responses by transcriptionally repressing the RSA-related genes LPR1 and LPR2 in Arabidopsis thaliana.展开更多
Tomato is an important vegetable crop and fluctuating available soil phosphate(Pi)level elicits several morpho-physiological responses driven by underlying molecular responses.Therefore,understanding these molecular r...Tomato is an important vegetable crop and fluctuating available soil phosphate(Pi)level elicits several morpho-physiological responses driven by underlying molecular responses.Therefore,understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency.A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato.Apart from changes in the expression levels of genes,there were also alterations in the expression of alternatively-spliced transcripts.Physiological responses such as anthocyanin accumulation,reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses(PSR).Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato.Overall,our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare.Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.展开更多
Phosphorus is a building block in various biomolecules such as nucleic acids,proteins,and phospholipids.It also plays pivotal roles in many metabolic pathways,including photosynthesis and respiration(Bowler et al.,201...Phosphorus is a building block in various biomolecules such as nucleic acids,proteins,and phospholipids.It also plays pivotal roles in many metabolic pathways,including photosynthesis and respiration(Bowler et al.,2010).Plants take up phosphorus as inorganic phosphate(Pi),which is limited in most soils,and Pi constraints affect plant growth and development and hence agricultural productivity.To cope with low Pi availability in soil,plants have evolved complex mechanisms to maintain Pi homeostasis at the whole-plant and cellular level,which includes Pi uptake,storage,and redistribution.展开更多
Phosphorus(P)is obtained by plants as phosphate(Pi)from the soil and low Pi levels affects plant growth and development.Adaptation to low Pi condition entails sensing internal and external Pi levels and translating th...Phosphorus(P)is obtained by plants as phosphate(Pi)from the soil and low Pi levels affects plant growth and development.Adaptation to low Pi condition entails sensing internal and external Pi levels and translating those signals to molecular and morphophysiological changes in the plant.In this review,we present findings related to local and systemin Pi sensing with focus the molecular mechanisms behind root system architectural changes and the impact of hormones and epigenetic mechanisms affecting those changes.We also present some of the recent advances in the Pi sensing and signaling mechanisms focusing on inositol pyrophosphate InsP8 and its interaction with SPX domain proteins to regulate the activity of the central regulator of the Pi starvation response,PHR.展开更多
文摘The maintenance of cellular phosphate(Pi)homeostasis is of great importance in living organisms.The SPX domain-containing protein 1(SPX1)proteins from both Arabidopsis and rice have been proposed to act as sensors of Pi status.The molecular signal indicating the cellular Pi status and regulating Pi homeostasis in plants,however,remains to be identified,as Pi itself does not bind to the SPX domain.Here,we report the identification of the inositol pyrophosphate lnsP8 as a signaling molecule that regulates Pi homeostasis in Arabidopsis.Polyacrylamide gel electrophoresis profiling of InsPs revealed that lnsP8 level positively correlates with cellular Pi concentration.We demonstrated that the homologs of diphosphoinositol pentaki-sphosphate kinase(PPIP5K),VIH1 and VIH2,function redundantly to synthesize lnsP8,and that the vih1 vih2 double mutant overaccumulates Pi.SPX1 directly interacts with PHR1,the central regulator of Pi starvation responses,to inhibit its function under Pi-replete conditions.However,this interaction is compromised in the vih1 vih2 double mutant,resulting in the constitutive induction of Pi starvation-induced genes,indicating that plant cells cannot sense cellular Pi status without lnsP8.Furthermore,we showed that lnsP8 could directly bind to the SPX domain of SPX1 and is essential for the interaction between SPX1 and PHR1.Collectively,our study suggests that lnsP8 is the intracellular Pi signaling molecule serving as the ligand of SPX1 for controlling Pi homeostasis in plants.
文摘DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence(MEMS) in the promoter of the DNA demethylase gene ROS_1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS_1 expression. How DNA methylation in the MEMS region promotes ROS_1 expression is not known. Here, we show that several Su(var)3-9 homologs(SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS_1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS.Mutations in the SUVHs lead to decreased ROS_1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.
基金the Chinese Academy of Sciences and the National Natural Science Foundation of China(31970580)to M.L.the National Key R&D Program(2016YFA0503200)+1 种基金Shenzhen Science and Technology Program(JCYJ20200109110403829 and KQTD20190929173906742)Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006)to J.D.
文摘DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3)as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.
基金the Shanghai Natural Science Foundation(22ZR1469200)the National Natural Science Foundation of China(31970580)。
文摘Plasticity in root system architecture(RSA)allows plants to adapt to changing nutritional status in the soil.Phosphorus availability is a major determinant of crop yield,and RSA remodeling is critical to increasing the efficiency of phosphorus acquisition.Although substantial progress has been made in understanding the signaling mechanism driving phosphate starvation responses in plants,whether and how epigenetic regulatory mechanisms contribute is poorly understood.Here,we report that the Switch defective/sucrose non-fermentable(SWI/SNF)ATPase BRAHMA(BRM)is involved in the local response to phosphate(Pi)starvation.The loss of BRM function induces iron(Fe)accumulation through increased LOW PHOSPHATE ROOT1(LPR1)and LPR2 expression,reducing primary root length under Pi deficiency.We also demonstrate that BRM recruits the histone deacetylase(HDA)complex HDA6-HDC1 to facilitate histone H3 deacetylation at LPR loci,thereby negatively regulating local Pi deficiency responses.BRM is degraded under Pi deficiency conditions through the 26 S proteasome pathway,leading to increased histone H3 acetylation at the LPR loci.Collectively,our data suggest that the chromatin remodeler BRM,in concert with HDA6,negatively regulates Fe-dependent local Pi starvation responses by transcriptionally repressing the RSA-related genes LPR1 and LPR2 in Arabidopsis thaliana.
文摘Tomato is an important vegetable crop and fluctuating available soil phosphate(Pi)level elicits several morpho-physiological responses driven by underlying molecular responses.Therefore,understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency.A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato.Apart from changes in the expression levels of genes,there were also alterations in the expression of alternatively-spliced transcripts.Physiological responses such as anthocyanin accumulation,reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses(PSR).Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato.Overall,our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare.Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.
基金This work was supported by the Chinese Academy of Sciences(CAS)and the Shanghai Natural Science Foundation(22ZR1469200).
文摘Phosphorus is a building block in various biomolecules such as nucleic acids,proteins,and phospholipids.It also plays pivotal roles in many metabolic pathways,including photosynthesis and respiration(Bowler et al.,2010).Plants take up phosphorus as inorganic phosphate(Pi),which is limited in most soils,and Pi constraints affect plant growth and development and hence agricultural productivity.To cope with low Pi availability in soil,plants have evolved complex mechanisms to maintain Pi homeostasis at the whole-plant and cellular level,which includes Pi uptake,storage,and redistribution.
文摘Phosphorus(P)is obtained by plants as phosphate(Pi)from the soil and low Pi levels affects plant growth and development.Adaptation to low Pi condition entails sensing internal and external Pi levels and translating those signals to molecular and morphophysiological changes in the plant.In this review,we present findings related to local and systemin Pi sensing with focus the molecular mechanisms behind root system architectural changes and the impact of hormones and epigenetic mechanisms affecting those changes.We also present some of the recent advances in the Pi sensing and signaling mechanisms focusing on inositol pyrophosphate InsP8 and its interaction with SPX domain proteins to regulate the activity of the central regulator of the Pi starvation response,PHR.
