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1.
Cell ; 186(6): 1230-1243.e14, 2023 03 16.
Article in English | MEDLINE | ID: mdl-36931246

ABSTRACT

Although Ca2+ has long been recognized as an obligatory intermediate in visual transduction, its role in plant phototransduction remains elusive. Here, we report a Ca2+ signaling that controls photoreceptor phyB nuclear translocation in etiolated seedlings during dark-to-light transition. Red light stimulates acute cytosolic Ca2+ increases via phyB, which are sensed by Ca2+-binding protein kinases, CPK6 and CPK12 (CPK6/12). Upon Ca2+ activation, CPK6/12 in turn directly interact with and phosphorylate photo-activated phyB at Ser80/Ser106 to initiate phyB nuclear import. Non-phosphorylatable mutation, phyBS80A/S106A, abolishes nuclear translocation and fails to complement phyB mutant, which is fully restored by combining phyBS80A/S106A with a nuclear localization signal. We further show that CPK6/12 function specifically in the early phyB-mediated cotyledon expansion, while Ser80/Ser106 phosphorylation generally governs phyB nuclear translocation. Our results uncover a biochemical regulatory loop centered in phyB phototransduction and provide a paradigm for linking ubiquitous Ca2+ increases to specific responses in sensory stimulus processing.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Phytochrome , Phytochrome B/genetics , Phytochrome B/metabolism , Phytochrome/genetics , Phytochrome/metabolism , Calcium/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Light , Light Signal Transduction , Mutation
2.
Mol Cell ; 82(16): 3015-3029.e6, 2022 08 18.
Article in English | MEDLINE | ID: mdl-35728588

ABSTRACT

Light and temperature in plants are perceived by a common receptor, phytochrome B (phyB). How phyB distinguishes these signals remains elusive. Here, we report that phyB spontaneously undergoes phase separation to assemble liquid-like droplets. This capacity is driven by its C terminus through self-association, whereas the intrinsically disordered N-terminal extension (NTE) functions as a biophysical modulator of phase separation. Light exposure triggers a conformational change to subsequently alter phyB condensate assembly, while temperature sensation is directly mediated by the NTE to modulate the phase behavior of phyB droplets. Multiple signaling components are selectively incorporated into phyB droplets to form concentrated microreactors, allowing switch-like control of phyB signaling activity through phase transitions. Therefore, light and temperature cues are separately read out by phyB via allosteric changes and spontaneous phase separation, respectively. We provide a conceptual framework showing how the distinct but highly correlated physical signals are interpreted and sorted by one receptor.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Phytochrome B/genetics , Phytochrome B/metabolism , Signal Transduction , Temperature
3.
Plant Cell ; 33(5): 1506-1529, 2021 07 02.
Article in English | MEDLINE | ID: mdl-33616669

ABSTRACT

Light-dependent seed germination is a vital process for many seed plants. A decisive event in light-induced germination is degradation of the central repressor PHYTOCHROME INTERACTING FACTOR 1 (PIF1). The balance between gibberellic acid (GA) and abscisic acid (ABA) helps to control germination. However, the cellular mechanisms linking PIF1 turnover to hormonal balancing remain elusive. Here, employing far-red light-induced Arabidopsis thaliana seed germination as the experimental system, we identified PLANTACYANIN (PCY) as an inhibitor of germination. It is a blue copper protein associated with the vacuole that is both highly expressed in mature seeds and rapidly silenced during germination. Molecular analyses showed that PIF1 binds to the miR408 promoter and represses miR408 accumulation. This in turn posttranscriptionally modulates PCY abundance, forming the PIF1-miR408-PCY repression cascade for translating PIF1 turnover to PCY turnover during early germination. Genetic analysis, RNA-sequencing, and hormone quantification revealed that PCY is necessary and sufficient to maintain the PIF1-mediated seed transcriptome and the low-GA-high-ABA state. Furthermore, we found that PCY domain organization and regulation by miR408 are conserved features in seed plants. These results revealed a cellular mechanism whereby PIF1-relayed external light signals are converted through PCY turnover to internal hormonal profiles for controlling seed germination.


Subject(s)
Arabidopsis Proteins/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Germination , Light , Metalloproteins/metabolism , MicroRNAs/metabolism , Seeds/growth & development , Signal Transduction , Abscisic Acid/metabolism , Arabidopsis Proteins/genetics , Base Sequence , Basic Helix-Loop-Helix Transcription Factors/genetics , Conserved Sequence , Gene Expression Regulation, Plant/radiation effects , Gene Silencing , Genes, Plant , Germination/genetics , Gibberellins/metabolism , MicroRNAs/genetics , Models, Biological , Phylogeny , Promoter Regions, Genetic/genetics , Protein Binding/genetics , Protein Binding/radiation effects , Seedlings/radiation effects , Seeds/genetics , Signal Transduction/radiation effects , Vacuoles/metabolism , Vacuoles/radiation effects
4.
Proc Natl Acad Sci U S A ; 117(31): 18858-18868, 2020 08 04.
Article in English | MEDLINE | ID: mdl-32694206

ABSTRACT

Buried seedlings undergo dramatic developmental transitions when they emerge from soil into sunlight. As central transcription factors suppressing light responses, PHYTOCHROME-INTERACTING FACTORs (PIFs) and ETHYLENE-INSENSITIVE 3 (EIN3) actively function in darkness and must be promptly repressed upon light to initiate deetiolation. Microproteins are evolutionarily conserved small single-domain proteins that act as posttranslational regulators in eukaryotes. Although hundreds to thousands of microproteins are predicted to exist in plants, their target molecules, biological roles, and mechanisms of action remain largely unknown. Here, we show that two microproteins, miP1a and miP1b (miP1a/b), are robustly stimulated in the dark-to-light transition. miP1a/b are primarily expressed in cotyledons and hypocotyl, exhibiting tissue-specific patterns similar to those of PIFs and EIN3 We demonstrate that PIFs and EIN3 assemble functional oligomers by self-interaction, while miP1a/b directly interact with and disrupt the oligomerization of PIFs and EIN3 by forming nonfunctional protein complexes. As a result, the DNA binding capacity and transcriptional activity of PIFs and EIN3 are predominantly suppressed. These biochemical findings are further supported by genetic evidence. miP1a/b positively regulate photomorphogenic development, and constitutively expressing miP1a/b rescues the delayed apical hook unfolding and cotyledon development of plants overexpressing PIFs and EIN3 Our study reveals that microproteins provide a temporal and negative control of the master transcription factors' oligomerization to achieve timely developmental transitions upon environmental changes.


Subject(s)
Arabidopsis Proteins , DNA-Binding Proteins , Plant Development/radiation effects , Signal Transduction/radiation effects , Transcription Factors , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Plant/radiation effects , Light , Organ Specificity , Protein Multimerization/radiation effects , Transcription Factors/chemistry , Transcription Factors/genetics , Transcription Factors/metabolism
5.
J Integr Plant Biol ; 64(4): 812-820, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35060666

ABSTRACT

Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes. The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function. MicroProteins are small, single-domain proteins that directly bind target protein complexes and disrupt their assembly. Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level. In the last few decades, thousands of plant microProteins have been predicted by computational approaches, but only a few have been experimentally validated. Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species. Here, we review characterized microProteins, including their biological roles, regulatory targets, and modes of action. In particular, we focus on microProtein-directed allosteric modulation of key components in light signaling pathways, and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants. Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.


Subject(s)
Arabidopsis , Proteins , Proteomics
6.
Proc Natl Acad Sci U S A ; 115(25): 6482-6487, 2018 06 19.
Article in English | MEDLINE | ID: mdl-29844157

ABSTRACT

Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5 Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.


Subject(s)
Gene Expression Regulation, Plant/genetics , Morphogenesis/genetics , Seedlings/genetics , Transcription Factors/genetics , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Carrier Proteins/genetics , DNA-Binding Proteins , Darkness , Genome-Wide Association Study/methods , Hypocotyl/genetics , Light , Mutation/genetics , Nuclear Proteins/genetics , Signal Transduction/genetics , Transcriptional Activation/genetics
7.
Int J Cancer ; 146(7): 1937-1949, 2020 04 01.
Article in English | MEDLINE | ID: mdl-31376289

ABSTRACT

Yes-associated protein (YAP) is a transcriptional coactivator that promotes cell proliferation, stem cell maintenance and tissue homeostasis. The YAP activity is primarily regulated through an inhibitory phosphorylation by the serine/threonine kinases of Hippo pathway. Here, we show that receptor tyrosine kinase (RTK) erythropoietin-producing hepatocellular receptor A2 (EphA2) interacts with and phosphorylates YAP protein, leading to stabilization, nuclear translocation and activation of YAP in gastric cancer (GC) cells. EphA2 induces chemotherapy-resistance by increasing YAP stability and nuclear YAP protein. Knockdown of YAP blocks EphA2-induced tumor growth in GC xenograft mouse models. Importantly, the coactivation of EphA2 and YAP is manifested in clinical human GC, and is related to GC recurrence. Thus, our results establish a novel EphA2-to-YAP pathway that drives GC growth, progression and therapy-resistance, targeting this pathway would be an efficient way for the treatment of GC, particularly chemotherapy-resistant GC.


Subject(s)
Cell Cycle Proteins/metabolism , Ephrin-A2/metabolism , Signal Transduction , Stomach Neoplasms/metabolism , Transcription Factors/metabolism , Animals , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Cell Proliferation , Disease Models, Animal , Drug Resistance, Neoplasm/genetics , Humans , Mice , Models, Biological , Phosphorylation , Protein Binding , Protein Transport , Receptor, EphA2 , Recurrence , Stomach Neoplasms/etiology , Stomach Neoplasms/pathology , Stomach Neoplasms/therapy , Xenograft Model Antitumor Assays
8.
Plant Cell ; 29(12): 3051-3067, 2017 12.
Article in English | MEDLINE | ID: mdl-29114016

ABSTRACT

In buried seedlings, chloroplasts are arrested at the etioplast stage, but they rapidly mature upon emergence of the seedling. Etioplast-chloroplast differentiation is halted through the integration of soil-induced signals, including pressure and the absence of light, although the details on how this information converges to regulate cellular decisions remain unclear. Here, we identify an interdependent transcription module that integrates the mechanical pressure and darkness signals to control chloroplast development in Arabidopsis thaliana Mutations of ETHYLENE-INSENSITIVE3 (EIN3), the primary transcription factor in the ethylene signaling pathway that is activated in response to mechanical pressure, cause early development of etioplasts in the dark and severe photobleaching upon light exposure. Genetic studies demonstrate that repression of etioplast differentiation by EIN3 requires PHYTOCHROME INTERACTING FACTOR3 (PIF3), a darkness-stabilized bHLH transcription factor. EIN3 and PIF3 directly interact and form an interdependent module to repress the expression of most LIGHT HARVESTING COMPLEX (LHC) genes; overexpressing even one LHC could cause premature development of etioplasts. The EIN3-PIF3 transcription module synergistically halts chloroplast development by interdependently co-occupying the promoters of LHC genes. Thus, our results define a transcriptional regulatory module and provide mechanistic insight on the concerted regulation of chloroplast development by multiple soil-induced signals.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Basic Helix-Loop-Helix Transcription Factors/metabolism , Chloroplasts/metabolism , Nuclear Proteins/metabolism , Seedlings/metabolism , Transcription Factors/metabolism , Arabidopsis/genetics , Arabidopsis/radiation effects , Arabidopsis/ultrastructure , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , Chloroplasts/radiation effects , Chloroplasts/ultrastructure , DNA-Binding Proteins , Etiolation/radiation effects , Gene Expression Regulation, Plant/radiation effects , Genes, Plant , Light , Nuclear Proteins/genetics , Oxidation-Reduction , Oxidative Stress/radiation effects , Promoter Regions, Genetic , Protein Binding/radiation effects , Protein Stability/radiation effects , Protochlorophyllide/metabolism , Seedlings/radiation effects , Seedlings/ultrastructure , Transcription Factors/genetics , Transcriptome/genetics
9.
Chem Res Toxicol ; 32(5): 861-868, 2019 05 20.
Article in English | MEDLINE | ID: mdl-30816036

ABSTRACT

The topoisomerase II inhibitor idarubicin (Ida) is an effective anticancer anthracycline drug and has been used for clinical therapies of multiple cancers. It is well-known that Ida and its analogues can induce DNA double strand breakage (DSB) by inhibiting topoisomer II and kill tumor cells. To date, it remains unknown whether they alter DNA epigenomes. Here, we show that Ida significantly stimulates the oxidation of a key epigenetic mark DNA 5-methyl-2'-deoxycytidine (5mC), which results in elevation of 5-hydroxymethyl-2'-deoxycytidine (5hmC) in four tested cell lines. Similarly, Ida analogues also display elevated 5hmC. DSB-causing topoisomer II inhibitor etopside fails to induce 5hmC change even at very high dose, which suggests the independence of the DSB. Moreover, the structure comparison supports that the histone eviction-associated amino sugar moiety is a characteristic of the anthracyclines required to promote the 5hmC elevation. Noteworthy, we also found that the 5mC oxidation is also cell-cycle dependent and mainly occurs during the S and G2/M phases. TET2 depletion diminishes the observed 5hmC elevation, which suggests that the Ida stimulation of 5hmC formation is mainly TET2-dependent. Deep-sequencing shows that 5hmC increases in all regions of the tested genome of T47D cells. The observation of a novel effect of Ida as well as other anthracycline compounds on epigenetic DNA modifications may help to further elucidate their biological and clinical effects.


Subject(s)
5-Methylcytosine/chemistry , DNA-Binding Proteins/metabolism , Idarubicin/pharmacology , Proto-Oncogene Proteins/metabolism , S Phase Cell Cycle Checkpoints/drug effects , 5-Methylcytosine/analysis , Cell Line, Tumor , Cell Survival/drug effects , Chromatography, High Pressure Liquid , Dioxygenases , Humans , Idarubicin/analogs & derivatives , Oxidation-Reduction , Tandem Mass Spectrometry
10.
Proc Natl Acad Sci U S A ; 112(12): 3817-22, 2015 Mar 24.
Article in English | MEDLINE | ID: mdl-25775589

ABSTRACT

Seed is an essential propagation organ and a critical strategy adopted by terrestrial flowering plants to colonize the land. The ability of seeds to accurately respond to light is vital for plant survival. However, the underlying mechanism is largely unknown. In this study, we reveal a circuit of triple feed-forward loops adopted by Arabidopsis seeds to exclusively repress germination in dark conditions and precisely initiate germination under diverse light conditions. We identify that de-etiolated 1 (DET1), an evolutionarily conserved protein, is a central repressor of light-induced seed germination. Genetic analysis demonstrates that DET1 functions upstream of long hypocotyl in far-red 1 (HFR1) and phytochrome interacting factor 1 (PIF1), the key positive and negative transcription regulators in seed germination. We further find that DET1 and constitutive photomorphogenic 10 (COP10) target HFR1 for protein degradation by assembling a COP10-DET1-damaged DNA binding protein 1-cullin4 E3 ligase complex. Moreover, DET1 and COP10 directly interact with and promote the protein stability of PIF1. Computational modeling reveals that phytochrome B (phyB)-DET1-HFR1-PIF1 and phyB-DET1-Protease-PIF1 are new signaling pathways, independent of the previously identified phyB-PIF1 pathway, respectively mediating the rapid and time-lapse responses to light irradiation. The model-simulated results are highly consistent with their experimental validations, suggesting that our mathematical model captures the essence of Arabidopsis seed germination networks. Taken together, this study provides a comprehensive molecular framework for light-regulated seed germination, improving our understanding of how plants respond to changeable environments.


Subject(s)
Arabidopsis Proteins/physiology , Arabidopsis/physiology , Basic Helix-Loop-Helix Transcription Factors/physiology , DNA-Binding Proteins/physiology , Germination , Nuclear Proteins/physiology , Seeds/physiology , Chromosome Mapping , Crosses, Genetic , Gene Deletion , Genotype , Intracellular Signaling Peptides and Proteins , Mutation , Phenotype
11.
Anal Chem ; 89(11): 5702-5706, 2017 06 06.
Article in English | MEDLINE | ID: mdl-28520399

ABSTRACT

DNA 5-hydroxymethylcytosine (5hmC) is an important epigenetic modification found in various mammalian cells. Immunofluorescence imaging analysis essentially provides visual pictures for the abundance and distribution of DNA 5hmC in single cells. However, nuclear DNA is usually wrapped around nucleosomes, packaged into chromatins, and further bound with many functional proteins. These physiologically relevant events would generate barriers to the anti-5hmC antibody to selectively recognize 5hmC in DNA. By taking advantage of these naturally generated barriers, here, we present a strategy to evaluate the accessibility of DNA 5hmC in chromatins in situ. We demonstrate that a few of the 5hmC sites in DNA are exposed or accessible to anti-5hmC antibody under nondenaturing conditions, suggesting that these 5hmC sites are not covered by functional DNA-binding proteins in mouse embryonic stem cells. Consistently, these 5hmC foci were distributed in open euchromatin regions as revealed by the 4',6-diamidino-2-phenylindole (DAPI) staining. By overexpressing TET1 catalytic domain (responsible for oxidation 5mC to produce 5hmC) in human MCF-7 cells, we observed a significant increase in accessible 5hmC along with an increase in total 5hmC sites. Collectively, by the use of the nondenaturing immunofluorescence imaging approach, we could obtain a visual landscape on the accessibility of DNA 5hmC in chromatins.


Subject(s)
5-Methylcytosine/analogs & derivatives , Chromatin/metabolism , Fluorescent Antibody Technique/methods , Molecular Imaging/methods , 5-Methylcytosine/immunology , 5-Methylcytosine/metabolism , Animals , Antibodies , DNA , Embryonic Stem Cells , Humans , MCF-7 Cells , Mice , Mixed Function Oxygenases/metabolism , Proto-Oncogene Proteins/metabolism
12.
Plant Cell ; 26(2): 695-711, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24563203

ABSTRACT

Members of the DDB1-CUL4-associated factors (DCAFs) family directly bind to DAMAGED DNA BINDING PROTEIN1 (DDB1) and function as the substrate receptors in CULLIN4-based E3 (CUL4) ubiquitin ligases, which regulate the selective ubiquitination of proteins. Here, we describe a DCAF protein, ABD1 (for ABA-hypersensitive DCAF1), that negatively regulates abscisic acid (ABA) signaling in Arabidopsis thaliana. ABD1 interacts with DDB1 in vitro and in vivo, indicating that it likely functions as a CUL4 E3 ligase substrate receptor. ABD1 expression is induced by ABA, and mutations in ABD1 result in ABA- and NaCl-hypersensitive phenotypes. Loss of ABD1 leads to hyperinduction of ABA-responsive genes and higher accumulation of the ABA-responsive transcription factor ABA INSENSITIVE5 (ABI5), hypersensitivity to ABA during seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, ultimately, increased drought tolerance. ABD1 directly interacts with ABI5 in yeast two-hybrid assays and associates with ABI5 in vivo by coimmunoprecipitation, and the interaction was found in the nucleus by bimolecular fluorescence complementation. Furthermore, loss of ABD1 results in a retardation of ABI5 degradation by the 26S proteasome. Taken together, these data suggest that the DCAF-CUL4 E3 ubiquitin ligase assembled with ABD1 is a negative regulator of ABA responses by directly binding to and affecting the stability of ABI5 in the nucleus.


Subject(s)
Abscisic Acid/metabolism , Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Carrier Proteins/metabolism , Cullin Proteins/metabolism , DNA-Binding Proteins/metabolism , Signal Transduction , Ubiquitin-Protein Ligases/metabolism , Abscisic Acid/pharmacology , Adaptation, Physiological/drug effects , Amino Acid Sequence , Arabidopsis/drug effects , Arabidopsis/genetics , Arabidopsis/growth & development , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/genetics , Basic-Leucine Zipper Transcription Factors/metabolism , Carrier Proteins/chemistry , DNA-Binding Proteins/genetics , Droughts , Gene Expression Regulation, Plant/drug effects , Germination/drug effects , Germination/genetics , Molecular Sequence Data , Plant Stomata/drug effects , Plant Stomata/genetics , Plant Stomata/physiology , Protein Binding/drug effects , Protein Stability/drug effects , Proteolysis/drug effects , Seeds/drug effects , Seeds/genetics , Seeds/growth & development , Signal Transduction/drug effects , Signal Transduction/genetics , Sodium Chloride/pharmacology , Substrate Specificity/drug effects
13.
Proc Natl Acad Sci U S A ; 111(11): 3913-20, 2014 Mar 18.
Article in English | MEDLINE | ID: mdl-24599595

ABSTRACT

The early life of terrestrial seed plants often starts under the soil in subterranean darkness. Over time and through adaptation, plants have evolved an elaborate etiolation process that enables seedlings to emerge from soil and acquire autotrophic ability. This process, however, requires seedlings to be able to sense the soil condition and relay this information accordingly to modulate both the seedlings' growth and the formation of photosynthetic apparatus. The mechanism by which soil overlay drives morphogenetic changes in plants, however, remains poorly understood, particularly with regard to the means by which the cellular processes of different organs are coordinated in response to disparate soil conditions. Here, we illustrate that the soil overlay quantitatively activates seedlings' ethylene production, and an EIN3/EIN3-like 1-dependent ethylene-response cascade is required for seedlings to successfully emerge from the soil. Under soil, an ERF1 pathway is activated in the hypocotyl to slow down cell elongation, whereas a PIF3 pathway is activated in the cotyledon to control the preassembly of photosynthetic machinery. Moreover, this latter PIF3 pathway appears to be coupled to the ERF1-regulated upward-growth rate. The coupling of these two pathways facilitates the synchronized progression of etioplast maturation and hypocotyl growth, which, in turn, ultimately enables seedlings to maintain the amount of protochlorophyllide required for rapid acquisition of photoautotrophic capacity without suffering from photooxidative damage during the dark-to-light transition. Our findings illustrate the existence of a genetic signaling pathway driving soil-induced plant morphogenesis and define the specific role of ethylene in orchestrating organ-specific soil responses in Arabidopsis seedlings.


Subject(s)
Arabidopsis/growth & development , Ethylenes/metabolism , Etiolation/physiology , Germination/physiology , Seedlings/growth & development , Soil/chemistry , Arabidopsis Proteins/metabolism , Chromatography, Gas , DNA-Binding Proteins , Histocytochemistry , Microscopy, Confocal , Microscopy, Fluorescence , Nuclear Proteins/metabolism , Peptide Termination Factors/metabolism , Protochlorophyllide/biosynthesis , Real-Time Polymerase Chain Reaction , Transcription Factors/metabolism
14.
Plant Cell ; 25(10): 3770-84, 2013 Oct.
Article in English | MEDLINE | ID: mdl-24179122

ABSTRACT

Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that phytochrome-interacting factor1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, long hypocotyl in far-red1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1-PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1-PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1-PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.


Subject(s)
Arabidopsis Proteins/physiology , Arabidopsis/physiology , Basic Helix-Loop-Helix Transcription Factors/physiology , DNA-Binding Proteins/physiology , Germination/genetics , Light , Nuclear Proteins/physiology , Arabidopsis/genetics , Arabidopsis/radiation effects , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Plant , Gene Regulatory Networks , Nuclear Proteins/genetics , Phytochrome B/physiology , Protein Multimerization , Transcriptome
15.
Electrophoresis ; 36(24): 3088-93, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26377303

ABSTRACT

The free solution electrophoretic behavior of DNA-protein complexes depends on their charge and mass in a certain experimental condition, which are two fundamental properties of DNA-protein complexes in free solution. Here, we used CE LIF to study the free solution behavior of DNA-methyl-CpG-binding domain protein (MBD2b) complexes through exploring the relationship between the mobilities, charge, and mass of DNA-protein complexes. This method is based on the effective separation of free DNA and DNA-protein complexes because of their different electrophoretic mobility in a certain electric field. In order to avoid protein adsorption, a polyacrylamide-coated capillary was used. Based on the evaluation of the electrophoretic behavior of formed DNA-MBD2b complexes, we found that the values of (µ0 /µ)-1 were directly proportional to the charge-to-mass ratios of formed complexes, where the µ0 and µ are the mobility of free DNA probe and DNA-protein complex, respectively. The models were further validated by the complex mobilities of protein with various lengths of DNA probes. The deviation of experimental and calculated charge-to-mass ratios of formed complexes from the theoretical data was less than 10%, suggesting that our models are useful to analyze the DNA-binding properties of the purified MBD2b protein and help to analyze other DNA-protein complexes. Additionally, this study enhances the understanding of the influence of the charge-to-mass ratios of formed DNA-protein complexes on their separation and electrophoretic behaviors.


Subject(s)
DNA-Binding Proteins/chemistry , DNA/chemistry , Electrophoresis, Capillary/methods , Multiprotein Complexes/chemistry , DNA/analysis , DNA-Binding Proteins/analysis , Fluorescence , Humans , Molecular Weight , Multiprotein Complexes/analysis , Protein Binding , Reproducibility of Results
16.
Plant Cell ; 24(3): 875-92, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22438023

ABSTRACT

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single-base-pair resolution the DNA methylomes of Arabidopsis thaliana Landsberg erecta and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs, implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to methylome remodeling were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes circadian clock associated1 and late elongated hypocotyl. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA enhancer1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in heterosis.


Subject(s)
Arabidopsis/genetics , DNA Methylation , DNA, Plant/metabolism , Ecotype , Hybrid Vigor , Arabidopsis Proteins/metabolism , Chimera/genetics , Gene Expression Regulation, Plant , Genome, Plant , Genomic Library , RNA, Plant/genetics , Transcriptome
17.
Methods Mol Biol ; 2795: 105-111, 2024.
Article in English | MEDLINE | ID: mdl-38594532

ABSTRACT

In this method, we employed HEK293T cells to express the plant photoreceptor phytochrome B (phyB). Through the application of various treatments such as phycocyanobilin (PCB) supplementation, red light exposure, and temperature adjustments, the phyB proteins exhibited liquid-liquid phase separation, leading to the formation of biomolecular condensates. Here, we present a comprehensive description of the protein expression, cell treatment, and imaging capture procedures. This detailed guide provides step-by-step instructions on how to induce phase separation of phyB proteins in HEK293T cells. By utilizing this approach, researchers can investigate the physicochemical characteristics and dynamic formation process of phyB photobodies with precision.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Phytochrome , Humans , Phytochrome B/metabolism , Phytochrome/metabolism , Arabidopsis Proteins/metabolism , HEK293 Cells , Arabidopsis/metabolism , Phase Separation , Transcription Factors/metabolism , Light , Photoreceptor Cells/metabolism
18.
Curr Biol ; 34(14): 3152-3164.e6, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-38971148

ABSTRACT

Seed germination represents a determinant for plants to enter ecosystems and is thus regarded as a key ecological and agronomic trait. It is tightly regulated by a variety of environmental cues to ensure that seeds germinate under favorable conditions. Here, we characterize BBX32, a B-box zinc-finger protein, as an imbibition-stimulated positive regulator of seed germination. Belonging to subgroup V of the BBX family, BBX32 exhibits distinct characteristics compared with its close counterparts within the same subgroup. BBX32 is transiently induced at both the transcriptional and post-transcriptional levels in the embryo upon water absorption. Genetic evidence indicates that BBX32 acts upstream of the master transcription factor PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) to facilitate light-induced seed germination. BBX32 directly interacts with PIF1, suppressing its protein-interacting and DNA-binding capabilities, thereby relieving PIF1's repression on seed germination. Furthermore, the imbibition-stimulated BBX32 functions in parallel with the light-induced transcription regulator HFR1 to collectively attenuate the transcriptional activities of PIF1. The BBX32-PIF1 de-repression module serves as a molecular connection that enables plants to integrate signals of water availability and light exposure, effectively coordinating the initiation of seed germination.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Gene Expression Regulation, Plant , Germination , Seedlings , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis/growth & development , Arabidopsis/physiology , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Seedlings/growth & development , Seedlings/genetics , Seedlings/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics , Zinc Fingers
19.
Cancer Rep (Hoboken) ; 7(5): e2064, 2024 May.
Article in English | MEDLINE | ID: mdl-38711262

ABSTRACT

BACKGROUND: Breast cancer (BC) is the most commonly diagnosed female cancer. Homeobox protein MEIS2, a key transcription factor, is involved in the regulation of many developmental and cellular processes. However, the role of MEIS2 in the development of breast cancer is still unclear. AIMS: We aimed to examine the role of myeloid ecotropic insertion site (MEIS2) in breast cancer and the association of MEIS2 with breast cancer clinical stages and pathological grades. We revealed the underlying mechanism by which MEIS2 affected breast cancer cell growth and tumor development. METHODS AND RESULTS: Using human BC cell lines, clinical samples and animal xenograft model, we reveal that MEIS2 functions as a tumor suppressor in breast cancer. The expression of MEIS2 is inversely correlated with BC clinical stages and pathological grades. MEIS2 knockdown (MEIS2-KD) promotes while MEIS2 overexpression suppresses breast cancer cell proliferation and tumor development in vitro and in animal xenograft models, respectively. To determine the biological function of MEIS2, we screen the expression of a group of MEIS2 potential targeting genes in stable-established cell lines. Results show that the knockdown of MEIS2 in breast cancer cells up-regulates the IL10 expression, but MEIS2 overexpression opposed the effect on IL10 expression. Furthermore, the suppressive role of MEIS2 in breast cancer cell proliferation is associated with the IL10 expression and myeloid cells infiltration. CONCLUSION: Our study demonstrates that the tumor suppressor of MEIS2 in breast cancer progression is partially via down regulating the expression of IL10 and promoting myeloid cells infiltration. Targeting MEIS2 would be a potentially therapeutic avenue for BC.


Subject(s)
Breast Neoplasms , Cell Proliferation , Gene Expression Regulation, Neoplastic , Homeodomain Proteins , Interleukin-10 , Transcription Factors , Humans , Female , Breast Neoplasms/pathology , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Animals , Mice , Transcription Factors/genetics , Transcription Factors/metabolism , Interleukin-10/metabolism , Interleukin-10/genetics , Cell Line, Tumor , Down-Regulation , Xenograft Model Antitumor Assays , Mice, Nude
20.
Cancers (Basel) ; 16(3)2024 Jan 31.
Article in English | MEDLINE | ID: mdl-38339348

ABSTRACT

FtsJ RNA 2'-O-methyltransferase 1 (FTSJ1) is a member of the methyltransferase superfamily and is involved in the processing and modification of ribosomal RNA. We herein demonstrate that FTSJ1 favors TNBC progression. The knockdown of FTSJ1 inhibits TNBC cell proliferation and development, induces apoptosis of cancer cells, and increases the sensitivity of TNBC cells to T-cell-mediated cytotoxicity. Furthermore, the high expression of FTSJ1 in TNBC attenuates CD8+T cell infiltration in the tumor microenvironment (TME) correlated with poorer prognosis for clinical TNBC patients. In this study, we establish that FTSJ1 acts as a tumor promotor, is involved in cancer immune evasion, and may serve as a potential immunotherapy target in TNBC.

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