Plant Growth In Arabidopsis Research Articles

BRZ-INSENSITIVE-LONG HYPOCOTYL8 inhibits kinase-mediated phosphorylation to regulate brassinosteroid signaling.

Glycogen synthase kinase 3 (GSK3) is an evolutionarily conserved serine/threonine protein kinase in eukaryotes. In plants, the GSK3-like kinase BRASSINOSTEROID-INSENSITIVE 2 (BIN2) functions as a central signaling node through which hormonal and environmental signals are integrated to regulate plant development and stress adaptation. BIN2 plays a major regulatory role in brassinosteroid (BR) signaling and is critical for phosphorylating/inactivating BRASSINAZOLE-RESISTANT 1 (BZR1), also known as BRZ-INSENSITIVE-LONG HYPOCOTYL 1 (BIL1), a master transcription factor of BR signaling, but the detailed regulatory mechanism of BIN2 action has not been fully revealed. In this study, we identified BIL8 as a positive regulator of BR signaling and plant growth in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses showed that BIL8 is downstream of the BR receptor BRASSINOSTEROID-INSENSITIVE 1 (BRI1) and promotes the dephosphorylation of BIL1/BZR1. BIL8 interacts with and inhibits the activity of the BIN2 kinase, leading to the accumulation of dephosphorylated BIL1/BZR1. BIL8 suppresses the cytoplasmic localization of BIL1/BZR1, which is induced via BIN2-mediated phosphorylation. Our study reveals a regulatory factor, BIL8, that positively regulates BR signaling by inhibiting BIN2 activity.

The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis

Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.

Trichoderma virens Big Ras GTPase-1, a molecular switch for transforming a mutualistic fungus to plants in a deleterious microbe

Trichoderma spp. are ascomycete filamentous fungi widely distributed worldwide that establish mutualistic relationships with plants by antagonizing phytopathogens in the rhizosphere and colonizing the plant roots, hence, promoting plant growth and triggering the systemic resistance against phytopathogens. During the first stages of root colonization by Trichoderma, plants recognize the fungus as an invader by inducing the plant defense system, including the production of reactive oxygen species (ROS). Some members of the small Ras GTPases regulate NADPH oxidases and, therefore, ROS production. However, their role in mutualistic microorganisms that colonize plant roots is poorly understood. It has been demonstrated that Trichoderma virens strains lacking TBRG-1, a member of a new family of the Ras GTPases, impair their biocontrol capability and behave like a pathogen on tomato seeds and seedlings. Here, we found that TBRG-1 is essential in T. virens to maintain the mutualistic relationship with plants because a mutant-lacking tbrg-1 gen could not induce plant growth in Arabidopsis and tomatoes. Furthermore, treatment of Arabidopsis seedlings with Δtbrg-1 induced strongly PR-1a, the systemic acquired resistance (SAR) marker gene at early times of the interaction, which correlated with enhanced foliar damage by Botrytis cinerea, resembling the behavior of a biotrophic phytopathogen. Additionally, leaves of plants treated with either T. virens wild-type (wt) or Δtbrg-1 and challenged or not with Botrytis showed ROS production to a different extent, as well as differential expression of cell detoxification-related genes, CAT1, and APX1. Root colonization assays of sid-2 and jar1 mutant lines affected in SAR and induced systemic resistance (ISR) by Δtbrg-1 and the wt strain, suggest an important role of both pathways in the recognition of the fungus and that TBRG-1 plays a pivotal role in root colonization. Furthermore, we found that TBRG-1 is a negative regulator of NoxR expression, which may impact the mutualistic interaction.

Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis.

Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.

Lead-Resistant Morganella morganii Rhizobacteria Reduced Lead Toxicity in Arabidopsis thaliana by Improving Growth, Physiology, and Antioxidant Activities

Biological remediation serves as a powerful technique for addressing heavy metals toxicity in metals-contaminated soils. The present study aimed to evaluate the efficacy of lead (Pb)-resistant rhizobacterial strains on growth, photosynthetic traits, and antioxidant activities of the Arabidopsis plant under lead toxicity in pot conditions. Two pre-isolated and pre-characterized Pb-resistant Morganella morganii (ABT3) and Morganella morganii (ABT9) strains were used for inoculating Arabidopsis plants grown under varying Pb concentrations (1.5 mM and 2.5 mM) using PbNO3 as the lead source. The treatments were set up in a completely randomized design with four replications. Data on growth parameters, physiological characteristics, lipid peroxidation, and antioxidant activities were recorded at harvesting. It was observed that Pb contamination caused a significant reduction in Arabidopsis growth, chlorophyll content and quantum yield at both lead concentrations. The Pb concentration of 2.5 mM, showed a substantial decrease in all parameters, including shoot fresh weight (58.72%), shoot dry weight (59.31%), root fresh weight (67.31%), root dry weight (67.28%), chlorophyll content (48.69%), quantum yield (62.36%), catalase activity (65.30%), superoxide dismutase (60.88%), and peroxidase activity (60.54%) while increasing lipid peroxidation (113.8%). However, the inoculation with Pb-resistant M. morganii strains (ABT3 and ABT9) improved plant growth, photosynthesis and antioxidant activities, while reduced the malondialdehyde content of Arabidopsis compared to control plants without inoculation. The M. morganii strain ABT9 showed a maximum increase in the shoot fresh weight (67.18%), shoot dry weight (67.96%), root fresh weight (94.04%), root dry weight (93.92%), shoot length (148.88%), root length (123.33%), chlorophyll content (52.53%), quantum yield (58.57%), catalase activity (39.46%), superoxide dismutase (21.84%), and peroxidase activity (22.34%) while decreasing lipid peroxidation (35.28%). PCA analysis further showed that all nine treatments scattered differently across the PC1 and PC2, having 81.4% and 17.0% data variance, respectively, indicating the efficiency of Pb-resistant strains. The heatmap further validated that the introduction of Pb-resistant strains positively correlated with the growth parameters, quantum yield, chlorophyll content and antioxidant activities of Arabidopsis seedlings. Both Pb-resistant strains improved Arabidopsis plant growth and photosynthetic efficiency under lead stress conditions. Thus, both Morganella morganii ABT3 and Morganella morganii ABT9 strains can be considered as bio-fertilizer for reducing lead toxicity thereby improving plant growth and physiology in metal-contaminated agricultural soils.

ADP-ribosylation factor D1 modulates Golgi morphology, cell plate formation, and plant growth in Arabidopsis.

ADP-ribosylation factor (ARF) family proteins, one type of small guanine-nucleotide-binding (G) proteins, play a central role in regulating vesicular traffic and organelle structures in eukaryotes. The Arabidopsis (Arabidopsis thaliana) genome contains more than 21 ARF proteins, but relatively little is known about the functional heterogeneity of ARF homologs in plants. Here, we characterized the function of a unique ARF protein, ARFD1B, in Arabidopsis. ARFD1B exhibited both cytosol and punctate localization patterns, colocalizing with a Golgi marker in protoplasts and transgenic plants. Distinct from other ARF1 homologs, overexpression of a dominant-negative mutant form of ARFD1B did not alter the localization of the Golgi marker mannosidase I (ManI)-RFP in Arabidopsis cells. Interestingly, the ARFD1 artificial microRNA knockdown mutant arfd1 displayed a deleterious growth phenotype, while this phenotype was restored in complemented plants. Further, confocal imaging and transmission electron microscopy analyses of the arfd1 mutant revealed defective cell plate formation and abnormal Golgi morphology. Pull-down and liquid chromatography-tandem mass spectrometry analyses identified Coat Protein I (COPI) components as interacting partners of ARFD1B, and subsequent bimolecular fluorescence complementation, yeast (Saccharomyces cerevisiae) two-hybrid, and co-immunoprecipitation assays further confirmed these interactions. These results demonstrate that ARFD1 is required for cell plate formation, maintenance of Golgi morphology, and plant growth in Arabidopsis.

Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis

When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth–defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.

Proteome profiling of a S‐Nitrosoglutathione reductase (GSNOR) null mutant reveals that aldo‐keto reductases form a new class of enzymes involved in nitric oxide homeostasis

Nitric oxide (NO) is a short‐lived gas that acts as a signaling molecule in all higher organisms, including plants. Despite the involvement of NO in multiple plant processes, including germination, root growth and fertility, a basic understanding of the mechanisms by which NO exerts its effects is lacking. NO and its derivatives impact these physiological processes through reversible S‐nitrosation of critical protein cysteines. In cells, regulation of NO‐levels is predominantly achieved by reaction of reactive nitrogen species (RNS) with glutathione (GSH), thereby forming S‐nitrosoglutathione (GSNO), a principal NO reservoir. Mutation of Arabidopsis thaliana S‐nitrosoglutathione reductase (GSNOR) leads to higher intracellular concentrations of S‐nitrosothiols, confirming that the GSNOR reduction of GSNO is a major route of GSNO catabolism in plants and other eukaryotes1. We demonstrate in Arabidopsisthat absence of GSNOR results in differential regulation of proteins involved in chlorophyll metabolism, the general stress response and photosynthesis2. In addition, our proteomic analysis identified a significant increase in proteins that belong to the aldo‐keto reductase (AKR) protein superfamily, AKR4C8 and 9. Since specific AKRs have been linked to NO metabolism in mammals, we expressed and purified ArabidopsisAKR4C8 and 9 and close homologues AKR4C10 and 11 and determined that they have NADPH‐dependent activity in GSNO and S‐nitroso‐coenzyme A (SNO‐CoA) reduction. Plants lacking GSNOR also show increased activity of NADPH‐dependent GSNO reduction, consistent with increased AKR activity2. To address the in vivo role of these AKRs, CRISPR/Cas9‐mediated mutant lines will be generated, and their capacity to metabolize RNS assessed. In addition, by subjecting AKR mutant plants to different abiotic and nitrosative stresses, results will uncover the importance of AKR proteins in NO homeostasis during both optimal growth and stress conditions. Taken together, these data define a new, NADPH‐dependent component of NO metabolism that may be integrated with NADH‐dependent GSNOR activity to control NO homeostasis in plants and other organisms.1. Lee, U., Wie, C., Fernandez, B. O., Feelisch, M. & Vierling, E. Modulation of nitrosative stress by S‐nitrosoglutathione reductase is critical for thermotolerance and plant growth in Arabidopsis. Plant Cell 20, 786–802 (2008).2. Treffon, P., Rossi, J., Gabellini, G., Trost, P., Zaffagnini, M., Vierling, E. Quantitative proteome profiling of a S‐nitrosoglutathione reductase (GSNOR) null mutant reveals a new class of enzymes involved in nitric oxide homeostasis in plants. Accepted. Front. Plant Sci. (2021).

Proteins Interacting with S‐Nitrosoglutathione reductase to Regulate Nitric Oxide Homeostasis

In plants, nitric oxide (NO) is a crucial signaling molecule involved in many physiological processes and stress pathways. NO can influence plant germination, flowering, and root development1. NO is usually found in an adduct with glutathione, forming S‐nitrosoglutathione (GSNO), which can affect protein S‐nitrosation, an important post‐translational modification that can alter protein activity and stability. The enzyme S‐nitrosoglutathione reductase (GSNOR) catalyzes the irreversible NADH‐dependent reduction of GSNO. GSNOR’s ability to regulate GSNO levels and subsequently affect S‐nitrosation activity makes it a critical enzyme in NO signaling2. The objective of this project is to identify proteins that interact with GSNOR to regulate its activity and stability, thereby impacting NO homeostasis. Based on previous experiments, we hypothesize that thioredoxins and catalase may be recovered as interacting candidates. We are utilizing enzyme‐catalyzed proximity labeling with the biotin ligase, TurboID, coupled to mass spectrometry to identify interacting partners of GSNOR in the plant model Arabidopsis thaliana. Currently, we have shown that a GSNOR‐TurboID fusion protein that has been transformed into a GSNOR null mutant can rescue the mutant phenotype without displaying any adverse effects on plant growth. As controls, A. thaliana lines carrying TurboID fused to YFP and targeted to the nucleus or cytosol have also been characterized. Importantly, upon treatment with biotin, TurboID produces strong biotinylation signals in these lines. These findings indicate that TurboID is suitable for use in A. thalianaand that biotinylated proteins can be recovered for identification by mass spectrometry. These experiments will advance the current understanding of GSNOR’s regulation, leading to an improved model of NO signaling.1. Xu, S., D. Guerra, U. Lee, & E. Vierling. S‐Nitrosoglutathione reductases are low‐copy number, cysteine‐rich proteins in plants that control multiple developmental and defense responses in Arabidopsis. Front. Plant Sci. 4: 1‐13 (2013). doi: 10.3389/fpls.2013.00430. 2. Lee, U., Wie, C., Fernandez, B. O., Feelisch, M. & Vierling, E. Modulation of nitrosative stress by S‐nitrosoglutathione reductase is critical for thermotolerance and plant growth in Arabidopsis. Plant Cell. 20: 786–802 (2008). doi: 10.1105/tpc/107.052647.

DiZF-C3H1, a zinc finger transcription factor from the dove tree (Davidia involucrata Baill.), plays a negative role in seed development and plant growth in Arabidopsis and tobacco

Low seed fertility seriously limits the survival and adaption of rare plant species. Here, we identified a seed-specific gene, DiZF-C3H1, from the dove tree and verified its function. Overexpression of DiZF-C3H1 caused retarded root development, delayed anthesis, abnormal floral organs, and deformed siliques in transgenic Arabidopsis lines. No offspring were obtained in transgenic Arabidopsis lines due to serious seed abortion. Therefore, we performed further verification in tobacco. Similarly, overexpression of DiZF-C3H1 retarded root development and reduced berry size and seed yield in transgenic tobacco lines. Moreover, although transgenic tobacco offspring were obtained, the viability of transgenic seeds was reduced and their germination was delayed. In addition, faded flowers were observed in transgenic tobacco lines. Taken together, DiZF-C3H1 was verified to play a negative role in root growth, floral organ development, and especially seed development in Arabidopsis and tobacco. This appears to be a deleterious gene for these model plants with high seed fertility. However, this function might be of special significance for Davidia, whose seed dormancy period is extremely long; DiZF-C3H1 might play a critical role in the distinctive reproduction strategy adopted by this rare and endangered species.

Retraction Note: Three SAUR proteins SAUR76, SAUR77 and SAUR78 promote plant growth in Arabidopsis

Retraction Note: Three SAUR proteins SAUR76, SAUR77 and SAUR78 promote plant growth in Arabidopsis

Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis.

The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant's stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.

Heterologous transformation of Camelina sativa with high-speed chimeric myosin XI-2 promotes plant growth and leads to increased seed yield.

Camelina sativa is a Brassicaceae oilseed plant used as a biotechnology platform for biofuel and healthy vegetable oil. As Camelina is closely related to the model plant Arabidopsis, the genetic tools of Arabidopsis are considered useful when applied to Camelina. Myosin XI-2 is one of the major motive forces driving cytoplasmic streaming in Arabidopsis. In our previous study, high-speed chimeric myosin XI-2, a myosin XI-2 artificially modified by genetically exchanging the motor domain of Arabidopsis myosin XI-2 with the faster Chara myosin XI, was shown to accelerate cytoplasmic streaming and promote plant growth in Arabidopsis. Here, we heterologously transformed this high-speed Chara-Arabidopsis chimeric myosin XI-2 gene in Camelina. The transgenic plants exhibited not only enhancement of leaf development and main stem elongation but also early flowering and seed setting, indicating that the high-speed chimeric myosin XI-2 can improve plant growth in Camelina. Interestingly, total seed yield was significantly increased in the transgenic plants as the total seed number increased. Our results suggest that the high-speed myosin XI system might also be effective to improve the growth of other closely related plant species.

The Glycine- and Proline-Rich Protein AtGPRP3 Negatively Regulates Plant Growth in Arabidopsis.

Glycine- and proline-rich proteins (GPRPs) comprise a small conserved family that is widely distributed in the plant kingdom. GPRPs are relatively short peptides (<200 amino acids) that contain three typical domains, including an N-terminal XYPP-repeat domain, a middle hydrophobic domain rich in alanine, and a C-terminal HGK-repeat domain. These proteins have been proposed to play fundamental roles in plant growth and environmental adaptation, but their functions remain unknown. In this study, we selected an Arabidopsis GPRP (AtGPRP3) to profile the physiological role of GPRPs. Transcripts of AtGPRP3 could be detected in the whole Arabidopsis plant, but greater amounts were found in the rosette, followed by the cauline. The AtGPRP3::GFP fusion protein was mainly localized in the nucleus. The overexpression and knockout of AtGPRP3, respectively, retarded and accelerated the growth of Arabidopsis seedlings, while the increase in the growth rate of atgprp3 plants was offset by the complementary expression of AtGPRP3. CAT2 and CAT3, but not CAT1, interacted with AtGPRP3 in the nuclei of Arabidopsis protoplasts. The knockout of CAT2 by CRISPR-Cas9 retarded the growth of the Arabidopsis seedlings. Together, our data suggest that AtGPRP3 negatively regulates plant growth, potentially through CAT2 and CAT3.

Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants.

Phosphorus (P) is an essential macronutrient required for plant growth and development. The involvement of cytokinin response factors (CRFs) in phosphate (Pi) homeostasis and lateral root (LR) initiation in Arabidopsis has been revealed. However, little is known in oil crops. Here, we performed genome-wide dissection of the CRF family in Brassica napus to identify 44 members, which were evolutionally classified into 6 subgroups. Among them, four BnaCRF8 genes were strongly upregulated by P deprivation, and were selected to be further investigated. Time course qRT-PCR analyses showed that four BnaCRF8 genes were enhanced dramatically after 12 h of P stress. Analyses of the subcellular localization in tobacco leaves indicated that BnaA7.CRF8 and BnaC2.CRF8 were localized in the nucleus. The expression of BnaCRF8 genes had constant negative effects on primary root growth and LR initiation and growth, and it reduced Pi acquisition and plant growth in Arabidopsis. Moreover, the expression of Pi homeostasis-related genes was modulated in BnaA7.CRF8 overexpression plants. These results suggest that BnaCRF8 genes might negatively regulate root architecture and plant growth through transcriptional modification of Pi homeostasis-related components. Overall, this study suggests that upregulation of BnaCRF8 genes might be a smart adaptive strategy to cope with continuous Pi deficiency in the environment.

Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis.

DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.

Arabidopsis ZUOTIN RELATED FACTOR1 Proteins Are Required for Proper Embryonic and Post-Embryonic Root Development.

The H2A/UBIQUITIN-binding proteins AtZRF1a/b have been reported as key regulators involved in multiple processes of Arabidopsis plant growth and development. Yet, the cellular and molecular mechanisms underlying the mutant phenotype remain largely elusive. Here we show that loss-of-function of AtZRF1a/b causes defective root elongation and deformed root apical meristem organization in seedlings. The premature termination of the primary root in the atzrf1a;atzrf1b double mutant is associated with an advanced onset of endoreduplication and subsequent consumption of reservoir stem cells. Cytological analyses using cell type-specific markers and florescent dyes indicate that AtZRF1a/b are involved in maintenance of proper cell layer organization, determinacy of cell identity, and establishment of auxin gradient and maximum at the root tip. During embryogenesis AtZRF1a/b act dominantly in regulating the maintenance of ground tissue initial cells and production of lateral root cap. Lastly, quantitative real-time polymerase chain reaction analysis shows mis-expression of some key genes involved in regulating cell patterning, cell proliferation and/or hormone pathways. Our results provide important insight into AtZRF1a/b function in cell fate determinacy and in establishment and maintenance of proper stem cell reservoir during embryonic and post-embryonic root development.

PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana

Plant-growth-promoting rhizobacteria (PGPR) improve plant growth by altering the root architecture, although the mechanisms underlying this alteration have yet to be unravelled. Through microarray analysis of PGPR-treated rice roots, a large number of differentially regulated genes were identified. Ectopic expression of one of these genes, OsASR6 (ABA STRESS RIPENING6), had a remarkable effect on plant growth in Arabidopsis. Transgenic lines over-expressing OsASR6 had larger leaves, taller inflorescence bolts and greater numbers of siliques and seeds. The most prominent effect was observed in root growth, with the root biomass increasing four-fold compared with the shoot biomass increase of 1.7-fold. Transgenic OsASR6 over-expressing plants showed higher conductance, transpiration and photosynthesis rates, leading to an ˜30% higher seed yield compared with the control. Interestingly, OsASR6 expression led to alterations in the xylem structure, an increase in the xylem vessel size and altered lignification, which correlated with higher conductance. OsASR6 is activated by auxin and, in turn, increases auxin responses and root auxin sensitivity, as observed by the increased expression of auxin-responsive genes, such as SAUR32 and PINOID, and the key auxin transcription factor, ARF5. Collectively, these phenomena led to an increased root density. The effects of OsASR6 expression largely mimic the beneficial effects of PGPRs in rice, indicating that OsASR6 activation may be a key factor governing PGPR-mediated changes in rice. OsASR6 is a potential candidate for the manipulation of rice for improved productivity.

The Blue-Light Receptor CRY1 Interacts with BZR1 and BIN2 to Modulate the Phosphorylation and Nuclear Function of BZR1 in Repressing BR Signaling in Arabidopsis

The blue-light receptor cryptochrome 1 (CRY1) primarily mediates blue-light inhibition of hypocotyl elongation in Arabidopsis. However, the underlying mechanisms remain largely elusive. We report here that CRY1 inhibits hypocotyl elongation by repressing brassinosteroid (BR) signaling. A genetic interaction assay reveals the negative regulatory effect of CRY1 on the function of BZR1, a core transcription factor in the BR signaling pathway. We demonstrated that CRY1 interacts with the DNA-binding domain of BZR1 to interfere with the DNA-binding ability of BZR1, and represses its transcriptional activity. Furthermore, we found that CRY1 promotes the phosphorylation of BZR1 and inhibits the nuclear accumulation of BZR1. Interestingly, we discovered that CRY1 interacts with the GSK3-like kinase BIN2 and enhances the interaction of BIN2 and BZR1 in a light-dependent manner. Our findings revealed that CRY1 negatively regulates the function of BZR1 through at least two mechanisms: interfering with the DNA-binding ability of BZR1 and promoting the phosphorylation of BZR1. Therefore, we uncover a novel CRY1-BIN2-BZR1 regulatory module that mediates crosstalk between blue light and BR signaling to coordinate plant growth in Arabidopsis.

A TOR-YAK1 signaling axis controls cell cycle, meristem activity and plant growth in Arabidopsis.

TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic phosphatidylinositol-3-kinase-related kinase that plays a major role in regulating growth and metabolism in response to environment in plants. We performed a genetic screen for Arabidopsis ethylmethane sulfonate mutants resistant to the ATP-competitive TOR inhibitor AZD-8055 to identify new components of the plant TOR pathway. We found that loss-of-function mutants of the DYRK (dual specificity tyrosine phosphorylation regulated kinase)/YAK1 kinase are resistant to AZD-8055 and, reciprocally, that YAK1 overexpressors are hypersensitive to AZD-8055. Significantly, these phenotypes were conditional on TOR inhibition, positioning YAK1 activity downstream of TOR. We further show that the ATP-competitive DYRK1A inhibitor pINDY phenocopies YAK1 loss of function. Microscopy analysis revealed that YAK1 functions to repress meristem size and induce differentiation. We show that YAK1 represses cyclin expression in the different zones of the root meristem and that YAK1 is essential for TOR-dependent transcriptional regulation of the plant-specific SIAMESE-RELATED (SMR) cyclin-dependent kinase inhibitors in both meristematic and differentiating root cells. Thus, YAK1 is a major regulator of meristem activity and cell differentiation downstream of TOR.