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1.
J Integr Plant Biol ; 66(7): 1313-1333, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38751035

ABSTRACT

Calcium oscillations are induced by different stresses. Calcium-dependent protein kinases (CDPKs/CPKs) are one major group of the plant calcium decoders that are involved in various processes including drought response. Some CPKs are calcium-independent. Here, we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize pool. We found that ZmCPK2 does not bind calcium, and its activity is mainly inhibited during short term abscisic acid (ABA) treatment, and dynamically changed in prolonged treatment. Interestingly, ZmCPK2 interacts with and is inhibited by calcium-dependent ZmCPK17, a positive regulator of drought resistance, which is activated by ABA. ZmCPK17 could prevent the nuclear localization of ZmCPK2 through phosphorylation of ZmCPK2T60. ZmCPK2 interacts with and phosphorylates and activates ZmYAB15, a negative transcriptional factor for drought resistance. Our results suggest that drought stress-induced Ca2+ can be decoded directly by ZmCPK17 that inhibits ZmCPK2, thereby promoting plant adaptation to water deficit.


Subject(s)
Abscisic Acid , Calcium , Droughts , Gene Expression Regulation, Plant , Plant Proteins , Protein Kinases , Zea mays , Zea mays/drug effects , Zea mays/metabolism , Zea mays/genetics , Zea mays/physiology , Calcium/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Abscisic Acid/metabolism , Abscisic Acid/pharmacology , Gene Expression Regulation, Plant/drug effects , Phosphorylation , Protein Kinases/metabolism , Plants, Genetically Modified , Stress, Physiological/drug effects , Protein Binding/drug effects
2.
J Integr Plant Biol ; 66(7): 1334-1350, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38804844

ABSTRACT

Drought stress has negative effects on crop growth and production. Characterization of transcription factors that regulate the expression of drought-responsive genes is critical for understanding the transcriptional regulatory networks in response to drought, which facilitates the improvement of crop drought tolerance. Here, we identified an Alfin-like (AL) family gene ZmAL14 that negatively regulates drought resistance. Overexpression of ZmAL14 exhibits susceptibility to drought while mutation of ZmAL14 enhances drought resistance. An abscisic acid (ABA)-activated protein kinase ZmSnRK2.2 interacts and phosphorylates ZmAL14 at T38 residue. Knockout of ZmSnRK2.2 gene decreases drought resistance of maize. A dehydration-induced Rho-like small guanosine triphosphatase gene ZmROP8 is directly targeted and repressed by ZmAL14. Phosphorylation of ZmAL14 by ZmSnRK2.2 prevents its binding to the ZmROP8 promoter, thereby releasing the repression of ZmROP8 transcription. Overexpression of ZmROP8 stimulates peroxidase activity and reduces hydrogen peroxide accumulation after drought treatment. Collectively, our study indicates that ZmAL14 is a negative regulator of drought resistance, which can be phosphorylated by ZmSnRK2.2 through the ABA signaling pathway, thus preventing its suppression on ZmROP8 transcription during drought stress response.


Subject(s)
Droughts , Gene Expression Regulation, Plant , Plant Proteins , Zea mays , Phosphorylation , Zea mays/genetics , Zea mays/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Abscisic Acid/metabolism , Stress, Physiological/genetics , Promoter Regions, Genetic/genetics , Drought Resistance
3.
J Integr Plant Biol ; 65(1): 203-222, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36541721

ABSTRACT

Minichromosome Maintenance protein 10 (MCM10) is essential for DNA replication initiation and DNA elongation in yeasts and animals. Although the functions of MCM10 in DNA replication and repair have been well documented, the detailed mechanisms for MCM10 in these processes are not well known. Here, we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker gene. Although plant MCM10 possesses a similar crystal structure as animal MCM10, AtMCM10 is not essential for plant growth or development in Arabidopsis. AtMCM10 can directly bind to histone H3-H4 and promotes nucleosome assembly in vitro. The nucleosome density is decreased in Atmcm10, and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1 (CAF-1). Loss of both AtMCM10 and CAF-1 is embryo lethal, indicating that AtMCM10 and CAF-1 are indispensable for replication-coupled nucleosome assembly. AtMCM10 interacts with both new and parental histones. Atmcm10 mutants have lower H3.1 abundance and reduced H3K27me1/3 levels with releasing some silenced transposons. We propose that AtMCM10 deposits new and parental histones during nucleosome assembly, maintaining proper epigenetic modifications and genome stability during DNA replication.


Subject(s)
Arabidopsis , Histones , Animals , Arabidopsis/genetics , Arabidopsis/metabolism , Chromatin Assembly and Disassembly , Chromatin Assembly Factor-1/genetics , Chromatin Assembly Factor-1/metabolism , DNA Replication/genetics , Histone Chaperones/genetics , Histone Chaperones/metabolism , Histones/metabolism , Nucleosomes/metabolism
4.
Dev Cell ; 57(23): 2638-2651.e6, 2022 12 05.
Article in English | MEDLINE | ID: mdl-36473460

ABSTRACT

Plant root architecture flexibly adapts to changing nitrate (NO3-) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3--mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3- in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3- availability. Under low-NO3- availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.


Subject(s)
Nitrates , Transcription Factors , Nitrates/pharmacology , Transcription Factors/genetics
5.
J Integr Plant Biol ; 64(11): 2075-2096, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36083579

ABSTRACT

Repression of embryonic traits during the seed-to-seedling phase transition requires the inactivation of master transcription factors associated with embryogenesis. How the timing of such inactivation is controlled is unclear. Here, we report on a novel transcriptional co-repressor, Arabidopsis thaliana SDR4L, that forms a feedback inhibition loop with the master transcription factors LEC1 and ABI3 to repress embryonic traits post-imbibition. LEC1 and ABI3 regulate their own expression by inducing AtSDR4L during mid to late embryogenesis. AtSDR4L binds to sites upstream of LEC1 and ABI4, and these transcripts are upregulated in Atsdr4l seedlings. Atsdr4l seedlings phenocopy a LEC1 overexpressor. The embryonic traits of Atsdr4l can be partially rescued by impairing LEC1 or ABI3. The penetrance and expressivity of the Atsdr4l phenotypes depend on both developmental and external cues, demonstrating the importance of AtSDR4L in seedling establishment under suboptimal conditions.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Plant Dormancy/genetics , Co-Repressor Proteins/metabolism , Gene Expression Regulation, Plant/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Seedlings/genetics , Seedlings/metabolism , Seeds/metabolism
6.
iScience ; 25(5): 104313, 2022 May 20.
Article in English | MEDLINE | ID: mdl-35602970

ABSTRACT

A genome-wide analysis in Schizosaccharomyces pombe indicated that double-deletion mutants of Chl1 and histone H3K9 methyltransferase complex factors are synthetically sick. Here, we show that loss of Chl1 increases the accumulation of RNA-DNA hybrids at pericentromeric dg and dh repeats in the absence of the H3K9 methyltransferase Clr4, which leads to genome instability, including more severe defects in chromosome segregation and increased chromatin accessibility. Localization of Chl1 at pericentromeric regions depends on a subunit of replication protein A (RPA), Ssb1. In wild-type (WT) cells, transcriptionally repressed heterochromatin prevents the formation of RNA-DNA hybrids. When Clr4 is deleted, dg and dh repeats are highly transcribed. Then Ssb1 associates with the displaced single-stranded DNA (ssDNA) and recruits Chl1 to resolve the RNA-DNA hybrids. Together, our data suggest that Chl1 coordinates with Clr4 to eliminate RNA-DNA hybrids, which contributes to the maintenance of genome integrity.

7.
Science ; 375(6587): eabg7985, 2022 03 25.
Article in English | MEDLINE | ID: mdl-35324310

ABSTRACT

A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. We found that the quantitative trait locus KRN2 in maize and its rice ortholog, OsKRN2, experienced convergent selection. These orthologs encode WD40 proteins and interact with a gene of unknown function, DUF1644, to negatively regulate grain number in both crops. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-offs in other agronomic traits. Furthermore, genome-wide scans identified 490 pairs of orthologous genes that underwent convergent selection during maize and rice evolution, and these were enriched for two shared molecular pathways. KRN2, together with other convergently selected genes, provides an excellent target for future crop improvement.


Subject(s)
Edible Grain , Oryza , Plant Proteins/genetics , Selection, Genetic , WD40 Repeats , Zea mays , Edible Grain/genetics , Genes, Plant , Oryza/genetics , Phylogeny , Plant Breeding , Plant Proteins/classification , WD40 Repeats/genetics , Zea mays/genetics
8.
Plant Cell ; 34(1): 633-654, 2022 01 20.
Article in English | MEDLINE | ID: mdl-34741605

ABSTRACT

Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/physiology , Basic-Leucine Zipper Transcription Factors/genetics , Phytochrome A/genetics , Signal Transduction , Transcription Factors/genetics , Up-Regulation , Arabidopsis/genetics , Arabidopsis Proteins/metabolism , Basic-Leucine Zipper Transcription Factors/metabolism , Gene Expression Regulation, Plant , Phytochrome A/metabolism , Transcription Factors/metabolism
9.
Int J Mol Sci ; 22(22)2021 Nov 19.
Article in English | MEDLINE | ID: mdl-34830369

ABSTRACT

It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world.


Subject(s)
DNA Copy Number Variations/genetics , Plants, Genetically Modified/genetics , Transgenes/genetics , Zea mays/genetics , DNA Primers , Gene Dosage/genetics , Plant Breeding
10.
Plant Cell ; 33(12): 3675-3699, 2021 12 03.
Article in English | MEDLINE | ID: mdl-34469582

ABSTRACT

Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophic Verticillium dahliae-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leaves in vitro but enhances the resistance to V. dahliae when overexpressed in Arabidopsis or cotton without affecting the plant growth and development. VDAL protein interacts with Arabidopsis E3 ligases plant U-box 25 (PUB25) and PUB26 and is ubiquitinated by PUBs in vitro. However, VDAL is not degraded by PUB25 or PUB26 in planta. Besides, the pub25 pub26 double mutant shows higher resistance to V. dahliae than the wild-type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist the V. dahliae infection without causing a hypersensitive response (HR); alternatively, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/physiology , Ascomycota/physiology , Fungal Proteins/genetics , Plant Diseases/genetics , Ubiquitin-Protein Ligases/genetics , Arabidopsis/genetics , Arabidopsis/microbiology , Arabidopsis Proteins/metabolism , Ascomycota/genetics , Disease Resistance/genetics , Fungal Proteins/metabolism , Plant Diseases/microbiology , Ubiquitin-Protein Ligases/metabolism
11.
Nat Commun ; 12(1): 4713, 2021 08 05.
Article in English | MEDLINE | ID: mdl-34354054

ABSTRACT

Maize (Zea mays L.) is a cold-sensitive species that often faces chilling stress, which adversely affects growth and reproduction. However, the genetic basis of low-temperature adaptation in maize remains unclear. Here, we demonstrate that natural variation in the type-A Response Regulator 1 (ZmRR1) gene leads to differences in chilling tolerance among maize inbred lines. Association analysis reveals that InDel-35 of ZmRR1, encoding a protein harboring a mitogen-activated protein kinase (MPK) phosphorylation residue, is strongly associated with chilling tolerance. ZmMPK8, a negative regulator of chilling tolerance, interacts with and phosphorylates ZmRR1 at Ser15. The deletion of a 45-bp region of ZmRR1 harboring Ser15 inhibits its degradation via the 26 S proteasome pathway by preventing its phosphorylation by ZmMPK8. Transcriptome analysis indicates that ZmRR1 positively regulates the expression of ZmDREB1 and Cellulose synthase (CesA) genes to enhance chilling tolerance. Our findings thus provide a potential genetic resource for improving chilling tolerance in maize.


Subject(s)
Zea mays/genetics , Zea mays/physiology , Alleles , Cold Temperature , Gene Expression Profiling , Gene Expression Regulation, Plant , Genes, Plant , Genetic Variation , Glucosyltransferases/genetics , Glucosyltransferases/metabolism , In Vitro Techniques , Mitogen-Activated Protein Kinases/genetics , Mitogen-Activated Protein Kinases/metabolism , Models, Biological , Phosphorylation , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Stress, Physiological/genetics
12.
Front Plant Sci ; 12: 517742, 2021.
Article in English | MEDLINE | ID: mdl-33746991

ABSTRACT

Potassium (K+) is one of essential mineral elements for plant growth and development. K+ channels, especially AKT1-like channels, play crucial roles in K+ uptake in plant roots. Maize is one of important crops; however, the K+ uptake mechanism in maize is little known. Here, we report the physiological functions of K+ channel ZMK1 in K+ uptake and homeostasis in maize. ZMK1 is a homolog of Arabidopsis AKT1 channel in maize, and mainly expressed in maize root. Yeast complementation experiments and electrophysiological characterization in Xenopus oocytes indicated that ZMK1 could mediate K+ uptake. ZMK1 rescued the low-K+-sensitive phenotype of akt1 mutant and enhanced K+ uptake in Arabidopsis. Overexpression of ZMK1 also significantly increased K+ uptake activity in maize, but led to an oversensitive phenotype. Similar to AKT1 regulation, the protein kinase ZmCIPK23 interacted with ZMK1 and phosphorylated the cytosolic region of ZMK1, activating ZMK1-mediated K+ uptake. ZmCIPK23 could also complement the low-K+-sensitive phenotype of Arabidopsis cipk23/lks1 mutant. These findings demonstrate that ZMK1 together with ZmCIPK23 plays important roles in K+ uptake and homeostasis in maize.

13.
New Phytol ; 230(6): 2355-2370, 2021 06.
Article in English | MEDLINE | ID: mdl-33666235

ABSTRACT

The farmland of the world's main corn-producing area is increasingly affected by salt stress. Therefore, the breeding of salt-tolerant cultivars is necessary for the long-term sustainability of global corn production. Previous studies have shown that natural maize varieties display a large diversity of salt tolerance, yet the genetic variants underlying such diversity remain poorly discovered and applied, especially those mediating the tolerance to salt-induced osmotic stress (SIOS). Here we report a metabolomics-driven understanding and genetic improvement of maize SIOS tolerance. Using a LC-MS-based untargeted metabolomics approach, we profiled the metabolomes of 266 maize inbred lines under control and salt conditions, and then identified 37 metabolite biomarkers of SIOS tolerance (METO1-37). Follow-up metabolic GWAS (mGWAS) and genotype-to-phenotype modeling identified 10 candidate genes significantly associating with the SIOS tolerance and METO abundances. Furthermore, we validated that a citrate synthase, a glucosyltransferase and a cytochrome P450 underlie the genotype-METO-SIOS tolerance associations, and showed that their favorable alleles additively improve the SIOS tolerance of elite maize inbred lines. Our study provides a novel insight into the natural variation of maize SIOS tolerance, which boosts the genetic improvement of maize salt tolerance, and demonstrates a metabolomics-based approach for mining crop genes associated with this complex agronomic trait.


Subject(s)
Plant Breeding , Zea mays , Metabolomics , Osmotic Pressure , Phenotype , Zea mays/genetics
14.
Plant Cell ; 32(7): 2196-2215, 2020 07.
Article in English | MEDLINE | ID: mdl-32371543

ABSTRACT

Phytochromes are red (R) and far-red (FR) light photoreceptors in plants, and PHYTOCHROME-INTERACTING FACTORS (PIFs) are a group of basic helix-loop-helix family transcription factors that play central roles in repressing photomorphogenesis. Here, we report that MYB30, an R2R3-MYB family transcription factor, acts as a negative regulator of photomorphogenesis in Arabidopsis (Arabidopsis thaliana). We show that MYB30 preferentially interacts with the Pfr (active) forms of the phytochrome A (phyA) and phytochrome B (phyB) holoproteins and that MYB30 levels are induced by phyA and phyB in the light. It was previously shown that phytochromes induce rapid phosphorylation and degradation of PIFs upon R light exposure. Our current data indicate that MYB30 promotes PIF4 and PIF5 protein reaccumulation under prolonged R light irradiation by directly binding to their promoters to induce their expression and by inhibiting the interaction of PIF4 and PIF5 with the Pfr form of phyB. In addition, our data indicate that MYB30 interacts with PIFs and that they act additively to repress photomorphogenesis. In summary, our study demonstrates that MYB30 negatively regulates Arabidopsis photomorphogenic development by acting to promote PIF4 and PIF5 protein accumulation under prolonged R light irradiation, thus providing new insights into the complicated but delicate control of PIFs in the responses of plants to their dynamic light environment.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Basic Helix-Loop-Helix Transcription Factors/metabolism , Transcription Factors/metabolism , Arabidopsis/physiology , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , Gene Expression Regulation, Plant , Light , Phytochrome A/metabolism , Phytochrome B/metabolism , Plants, Genetically Modified , Promoter Regions, Genetic , Seedlings/physiology , Transcription Factors/genetics
15.
EMBO J ; 39(13): e103630, 2020 07 01.
Article in English | MEDLINE | ID: mdl-32449547

ABSTRACT

Light and temperature are two core environmental factors that coordinately regulate plant growth and survival throughout their entire life cycle. However, the mechanisms integrating light and temperature signaling pathways in plants remain poorly understood. Here, we report that CBF1, an AP2/ERF-family transcription factor essential for plant cold acclimation, promotes hypocotyl growth under ambient temperatures in Arabidopsis. We show that CBF1 increases the protein abundance of PIF4 and PIF5, two phytochrome-interacting bHLH-family transcription factors that play pivotal roles in modulating plant growth and development, by directly binding to their promoters to induce their gene expression, and by inhibiting their interaction with phyB in the light. Moreover, our data demonstrate that CBF1 promotes PIF4/PIF5 protein accumulation and hypocotyl growth at both 22°C and 17°C, but not at 4°C, with a more prominent role at 17°C than at 22°C. Together, our study reveals that CBF1 integrates light and temperature control of hypocotyl growth by promoting PIF4 and PIF5 protein abundance in the light, thus providing insights into the integration mechanisms of light and temperature signaling pathways in plants.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Hypocotyl/growth & development , Temperature , Trans-Activators/metabolism , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Hypocotyl/genetics , Trans-Activators/genetics
16.
Mol Plant ; 13(3): 414-430, 2020 03 02.
Article in English | MEDLINE | ID: mdl-32059872

ABSTRACT

PHYTOCHROME-INTERACTING FACTORS (PIFs) are a group of basic helix-loop-helix transcription factors that can physically interact with photoreceptors, including phytochromes and cryptochromes. It was previously demonstrated that PIFs accumulated in darkness and repressed seedling photomorphogenesis, and that PIFs linked different photosensory and hormonal pathways to control plant growth and development. In this study, we show that PIFs positively regulate the ABA signaling pathway during the seedling stage specifically in darkness. We found that PIFs positively regulate ABI5 transcript and protein levels in darkness in response to exogenous ABA treatment by binding directly to the G-box motifs in the ABI5 promoter. Consistently, PIFs and the G-box motifs in the ABI5 promoter determine ABI5 expression in darkness, and overexpression of ABI5 could rescue the ABA-insensitive phenotypes of pifq mutants in the dark. Moreover, we discovered that PIFs can physically interact with the ABA receptors PYL8 and PYL9, and that this interaction is not regulated by ABA. Further analyses showed that PYL8 and PYL9 promote PIF4 protein accumulation in the dark and enhance PIF4 binding to the ABI5 promoter, but negatively regulate PIF4-mediated ABI5 activation. Taken together, our data demonstrate that PIFs interact with ABA receptors to orchestrate ABA signaling in darkness by controlling ABI5 expression, providing new insights into the pivotal roles of PIFs as signal integrators in regulating plant growth and development.


Subject(s)
Abscisic Acid/metabolism , Arabidopsis Proteins/metabolism , Arabidopsis/cytology , Arabidopsis/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Darkness , Intracellular Signaling Peptides and Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/radiation effects , Arabidopsis Proteins/genetics , Base Sequence , Basic-Leucine Zipper Transcription Factors/genetics , Gene Expression Regulation, Plant/radiation effects , Promoter Regions, Genetic/genetics , Protein Binding/radiation effects , RNA, Messenger/genetics , Signal Transduction/radiation effects
17.
Exp Ther Med ; 19(2): 999-1005, 2020 Feb.
Article in English | MEDLINE | ID: mdl-32010262

ABSTRACT

The aim of the present study was to determine the role of long intergenic non-protein coding RNA 858 (LINC00858) in retinoblastoma (RB) and investigate the underlying molecular mechanisms. RB tissues and paracancerous tissues of 27 RB cases were obtained. RB cell lines (SO-RB50, Y79, HXO-RB44 and WERI-Rb1) and a normal retinal epithelial cell line (ARPE-19) were cultured for in vitro experiments. Batches of SO-RB50 and Y79 cells were assigned to groups transfected with small interfering RNA targeting LINC00858 (si-LINC00858 group), microRNA (miR)-3182 mimics or inhibitor, or the respective controls. A Cell Counting Kit-8 and Transwell assays were performed to assess the effect of the transfections on the proliferation, migration and invasion of SO-RB50 and Y79 cells. A luciferase reporter assay was performed using SO-RB50 cells to demonstrate the direct binding of LINC00858 and miR-3182. Reverse transcription-quantitative PCR was employed to detect LINC00858 and miR-3182 expression. Pearson correlation analysis was used to assess the correlation between the expression of LINC00858 and miR-3182. The results indicated that RB tissues and cells exhibited aberrantly elevated LINC00858 expression (P<0.05). Compared with those in the control-transfected group, SO-RB50 and Y79 cells of the si-LINC00858 group had a lower cell proliferation, as well as a lower number of migrated and invaded cells (all P<0.05). miR-3182 was proven to be a target gene of LINC00858, to be abnormally downregulated in RB tissues and cells (P<0.05) and to be negatively correlated with LINC00858 expression. Compared with those in the si-LINC00858 + inhibitor-negative control group, SO-RB50 and Y79 cells of the si-LINC00858 + miR-3182 inhibitor group exhibited a significantly higher relative proliferation, migration and invasion (all P<0.05). In conclusion, LINC00858 promoted RB cell proliferation, migration and invasion, at least partially by inhibiting miR-3182.

18.
Plant Physiol ; 181(1): 249-261, 2019 09.
Article in English | MEDLINE | ID: mdl-31331996

ABSTRACT

DNA methylation and histone modification are important epigenetic marks that coregulate gene expression and genome stability. To identify factors involved in chromatin silencing, we carried out a forward genetic screen for mutants that release the silenced Pro-35S:LUCIFERASE (35SP-LUC) in Arabidopsis (Arabidopsis thaliana). We identified an epigenetic regulator, METHIONINE SYNTHASE1 (ATMS1), which catalyzes the synthesis of methionine (Met) in the one-carbon metabolism pathway. The ATMS1 mutation releases the silenced 35SP-LUC and the majority of endogenous genes and transposons. The effect of ATMS1 on chromatin silencing is related to decreased levels of DNA methylation (CG, CHG, and CHH) and histone-3 lysine-9 dimethylation. The ATMS1 mutation caused a significant decrease in the ratio of S-adenosylmethionine to S-adenosylhomocysteine. Exogenous application of Met rescued the phenotype of atms1-1 ATMS1 plays a predominant role in DNA and histone methylations among the three Met synthetase homologs. These results suggest that ATMS1 is required for DNA and histone methylations through its function in the one-carbon metabolism pathway, indicating the complex interplay between metabolism and epigenetic regulation.


Subject(s)
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/metabolism , Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , Epigenesis, Genetic , Histones/metabolism , Protein Processing, Post-Translational , 5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/genetics , Arabidopsis/genetics , Arabidopsis Proteins/genetics , DNA Methylation , Gene Silencing , Lysine/metabolism , Methionine/metabolism
19.
Proc Natl Acad Sci U S A ; 116(21): 10576-10585, 2019 05 21.
Article in English | MEDLINE | ID: mdl-31064880

ABSTRACT

Epigenetic markers, such as histone acetylation and DNA methylation, determine chromatin organization. In eukaryotic cells, metabolites from organelles or the cytosol affect epigenetic modifications. However, the relationships between metabolites and epigenetic modifications are not well understood in plants. We found that peroxisomal acyl-CoA oxidase 4 (ACX4), an enzyme in the fatty acid ß-oxidation pathway, is required for suppressing the silencing of some endogenous loci, as well as Pro35S:NPTII in the ProRD29A:LUC/C24 transgenic line. The acx4 mutation reduces nuclear histone acetylation and increases DNA methylation at the NOS terminator of Pro35S:NPTII and at some endogenous genomic loci, which are also targeted by the demethylation enzyme REPRESSOR OF SILENCING 1 (ROS1). Furthermore, mutations in multifunctional protein 2 (MFP2) and 3-ketoacyl-CoA thiolase-2 (KAT2/PED1/PKT3), two enzymes in the last two steps of the ß-oxidation pathway, lead to similar patterns of DNA hypermethylation as in acx4 Thus, metabolites from fatty acid ß-oxidation in peroxisomes are closely linked to nuclear epigenetic modifications, which may affect diverse cellular processes in plants.


Subject(s)
Arabidopsis/metabolism , DNA Methylation , Epigenesis, Genetic , Fatty Acids/metabolism , Peroxisomes/metabolism , ATP Citrate (pro-S)-Lyase/metabolism , Acetylation , Acyl-CoA Oxidase/genetics , Acyl-CoA Oxidase/metabolism , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Gene Expression Regulation, Plant , Histones/metabolism , Oxidation-Reduction , Plants, Genetically Modified , Potassium Channels, Voltage-Gated/metabolism
20.
Int Ophthalmol ; 39(10): 2223-2235, 2019 Oct.
Article in English | MEDLINE | ID: mdl-30607864

ABSTRACT

OBJECTIVE: To understand the involvement of the mGluR5-mediated JNK signaling pathway in rats with diabetic retinopathy (DR). METHODS: This study established rat models of diabetes mellitus (DM), which were divided into Normal, DM, DM + CHPG (mGluR5 agonist CHPG), and DM + MTEP (mGluR5 antagonist MTEP) groups. The blood glucose and weight of rats were recorded. EB staining was used for observation of blood-retinal barrier (BRB) damage. Neural retina function was measured by pattern electroretinogram (ERG). PAS and NG2 immunohistochemistry were conducted to evaluate the retinal vascular morphology. The TUNEL assay and active caspase-3 immunohistochemistry were performed to detect retinal cell apoptosis. Additionally, the expression levels of superoxide dismutase (SOD) and methylenedioxyamphetamine (MDA) were measured. Moreover, expression levels of mGluR5 and JNK pathway-related proteins were detected by western blot. RESULTS: When compared with control rats, rats in the DM group showed decreased amplitude and latency of the peak times in the ERG test; further, DM group rats presented increases in blood glucose, BRB permeability, a retinal capillary area density, retinal cell apoptosis with an increased number of active caspase-3-positive cells, MDA level, mGluR5 levels, and the ratio of p-JNK/JNK, and they showed reductions in body weight and SOD activity, as well as in the number of pericytes and in the pericyte coverage (all P < 0.05). However, rats in DM + CHPG group had stronger negative effects than those in DM group (all P < 0.05). Rats from DM + MTEP group showed an opposite trend compared with the DM rats (all P < 0.05). CONCLUSION: The level of mGluR5 in DR rats was upregulated, whereas inhibition of mGluR5 alleviated retinal pathological damage and decreased cell apoptosis to improve DR via suppression of the JNK signaling pathway, which provided a scientific theoretical basis for the clinical treatment of DR.


Subject(s)
Diabetic Retinopathy/physiopathology , MAP Kinase Signaling System/physiology , Receptor, Metabotropic Glutamate 5/physiology , Animals , Blood Glucose/metabolism , Blood-Retinal Barrier/pathology , Diabetes Mellitus, Experimental , Diabetic Retinopathy/metabolism , Electroretinography , Male , Rats , Rats, Sprague-Dawley , Receptor, Metabotropic Glutamate 5/metabolism , Retina/physiopathology , Retinal Vessels/pathology
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