The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression

Evaluation of Chemical-Inducible Gene Expression Systems for Beet Cyst Nematode Infection Assays in Arabidopsis thaliana

Cyst nematodes co-opt plant developmental programs for the establishment of a permanent feeding site called a syncytium in plant roots. In recent years, the role of plant developmental genes in syncytium formation has gained much attention. One main obstacle in studying the function of development-related genes in syncytium formation is that mutation or ectopic expression of such genes can cause pleiotropic phenotypes, making it difficult to interpret nematode-related phenotypes or, in some cases, impossible to carry out infection assays due to aberrant root development. Here, we tested three commonly used inducible gene expression systems for their application in beet cyst nematode infection assays of the model plant Arabidopsis thaliana. We found that even a low amount of ethanol diminished nematode development, deeming the ethanol-based system unsuitable for use in cyst nematode infection assays, whereas treatment with estradiol or dexamethasone did not negatively affect cyst nematode viability. Dose and time course responses showed that in both systems, a relatively low dose of inducer (1 μM) is sufficient to induce high transgene expression within 24 h of treatment. Transgene expression peaked at 3 to 5 days post-induction and began to decline thereafter, providing a perfect window for inducible transgenes to interfere with syncytium establishment while minimizing any adverse effects on root development. These results indicate that both estradiol- and dexamethasone-based inducible gene expression systems are suitable for cyst nematode infection assays. The employment of such systems provides a powerful tool to investigate the function of essential plant developmental genes in syncytium formation. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

AtERF13 and AtERF6 double knockout fine-tunes growth and the transcriptome to promote cadmium tolerance in Arabidopsis

The toxic heavy metal cadmium (Cd) restricts plant growth. However, how plants fine-tune their growth to modulate Cd resistance has not been determined. Ethylene response factors (ERFs) are key regulators of Cd stress, and Arabidopsis thaliana ERF13 and ERF6 (AtERF13 and AtERF6) negatively regulate growth. We previously demonstrated that AtERF13 is a transcriptional activator that binds a Cd-responsive element. Herein, we report that Arabidopsis plants improve Cd tolerance by repressing AtERF13 and AtERF6. We found that AtERF13 and AtERF6 were strongly downregulated by Cd stress and that AtERF6 weakly bound Cd-responsive elements. Moreover, AtERF13 physically interacted with AtERF6. Importantly, AtERF13 and AtERF6 double knockout mutants, but not single mutants or overexpression lines, grew better, tolerated more Cd and had higher Cd contents than did the wild type. Comparative transcriptome analysis revealed that the double mutants regulate the defense response to cope with Cd toxicity. Accordingly, we propose that, upon Cd stress, Arabidopsis plants repress AtERF13 and AtERF6 to relieve their growth inhibition effects and adjust the transcriptome to adapt to Cd stress, leading to increased Cd tolerance. Our findings thereby provide deep mechanical insights into how dual-function transcription factors fine-tune growth and the transcriptome to promote Cd tolerance in plants.

CXIP4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis

Zinc knuckle (ZCCHC) motif-containing proteins are present in unicellular and multicellular eukaryotes and most ZCCHC proteins with known functions participate in the metabolism of various classes of RNA, such as mRNAs, ribosomal RNAs, and microRNAs. The Arabidopsis (Arabidopsis thaliana) genome encodes 69 ZCCHC-containing proteins, but the functions of most remain unclear. One of these proteins is CAX-INTERACTING PROTEIN 4 (CXIP4), which has been classified as a PTHR31437 family member, along with human SREK1-interacting protein 1 (SREK1IP1), which is thought to function in pre-mRNA splicing and RNA methylation. Metazoan SREK1IP1-like and plant CXIP4-like proteins only share a ZCCHC motif, and their functions remain almost entirely unknown. We studied two loss-of-function alleles of Arabidopsis CXIP4, the first mutations in PTHR31437 family genes described to date: cxip4-1 is likely null and shows early lethality, and cxip4-2 is hypomorphic and viable, with pleiotropic morphological defects. The cxip4-2 mutant exhibited deregulation of defense genes and upregulation of transcription factor encoding genes, some of which might explain its developmental defects. This mutant also exhibited increased intron retention events, and the specific functions of misspliced genes, such as those involved in "gene silencing by DNA methylation" and "mRNA polyadenylation factor" suggest that CXIP4 has additional functions. The CXIP4 protein localizes to the nucleus in a pattern resembling nuclear speckles, which are rich in splicing factors. Therefore, CXIP4 is required for plant survival and proper development, and mRNA maturation.

Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1

Seed dormancy governs germination timing, with both evolutionary and applied consequences. Despite extensive studies on the hormonal and genetic control of these processes, molecular mechanisms directly linking dormancy and germination remain poorly understood. By screening a collection of lines overexpressing Arabidopsis transcription factors, we identified ERF50 as a key gene to control dormancy and germination. To study its regulation, we measured seed-related physiological parameters in loss-of-function mutants and carried out transactivation, protein interaction and ChIP-PCR analyses. We found direct ERF50-mediated repression of DOG1 and activation of EXPA2 transcription, which results in enhanced seed germination. Although ERF50 expression is increased by DOG1 in dormant seeds, ERF50 germination-promoting activity is blocked by RGL2. The physiological, genetic and molecular evidence gathered here supports that ERF50 controls germination timing by regulating DOG1 levels to leverage its role as enhancer of seed germination, via RGL2 antagonism on EXPA2 expression. Our results highlight the central role of ERF50 as a feedback regulator to couple and fine-tune seed dormancy and germination.

Fast and Efficient Root Phenotyping via Pose Estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Arabidopsis BBX14 is involved in high light acclimation and seedling development

The development of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways and receives input from the biogenic signal integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light (HL) levels and biogenic signals, which was studied by using inhibitors of chloroplast development. Our chromatin immunoprecipitation-Seq experiments revealed that BBX14 is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 may function as a regulator of the circadian clock. In addition, BBX14 plays a role in chlorophyll biosynthesis during early onset of light. Knockout of BBX14 results in a long hypocotyl phenotype dependent on a retrograde signal. Furthermore, the expression of BBX14 and BBX15 during biogenic signaling requires GUN1. Investigation of the role of BBX14 and BBX15 in GUN-type biogenic (gun) signaling showed that the overexpression of BBX14 or BBX15 caused de-repression of CA1 mRNA levels, when seedlings were grown on norflurazon. Notably, transcripts of the LHCB1.2 marker are not de-repressed. Furthermore, BBX14 is required to acclimate plants to HL stress. We propose that BBX14 is an integrator of biogenic signals and that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module. However, we do not classify BBX14 or BBX15 overexpressors as gun mutants based on a critical evaluation of our results and those reported in the literature. Finally, we discuss a classification system necessary for the declaration of new gun mutants.

PDR9 allelic variation and MYB63 modulate nutrient-dependent coumarin homeostasis in Arabidopsis

Plant roots release phytochemicals into the soil environment to influence nutrient availability and uptake. Arabidopsis thaliana roots release phenylpropanoid coumarins in response to iron (Fe) deficiency, likely to enhance Fe uptake and improve plant health. This response requires sufficient phosphorus (P) in the root environment. Nonetheless, the regulatory interplay influencing coumarin production under varying availabilities of Fe and P is not known. Through genome-wide association studies, we have pinpointed the influence of the ABC transporter G family member, PDR9, on coumarin accumulation and trafficking (homeostasis) under combined Fe and P deficiency. We show that genetic variation in the promoter of PDR9 regulates its expression in a manner associated with coumarin production. Furthermore, we find that MYB63 transcription factor controls dedicated coumarin production by regulating both COUMARIN SYNTHASE (COSY) and FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) expression while orchestrating secretion through PDR9 genes under Fe and P combined deficiency. This integrated approach illuminates the intricate connections between nutrient signaling pathways in coumarin response mechanisms.

Pectin methylesterase 31 is transcriptionally repressed by ABI5 to negatively regulate ABA-mediated inhibition of seed germination

Pectin methylesterase (PME), a family of enzymes that catalyze the demethylation of pectin, influences seed germination. Phytohormone abscisic acid (ABA) inhibits seed germination. However, little is known about the function of PMEs in response to ABA-mediated seed germination. In this study, we found the role of PME31 in response to ABA-mediated inhibition of seed germination. The expression of PME31 is prominent in the embryo and is repressed by ABA treatment. Phenotype analysis showed that disruption of PME31 increases ABA-mediated inhibition of seed germination, whereas overexpression of PME31 attenuates this effect. Further study found that ABI5, an ABA signaling bZIP transcription factor, is identified as an upstream regulator of PME31. Genetic analysis showed that PME31 functions downstream of ABI5 in ABA-mediated seed germination. Detailed studies showed that ABI5 directly binds to the PME31 promoter and inhibits its expression. In the plants, PME31 expression is reduced by ABI5 in ABA-mediated seed germination. Taken together, PME31 is transcriptionally inhibited by ABI5 and negatively regulates ABA-mediated seed germination inhibition. These findings shed new light on the mechanisms of PMEs in response to ABA-mediated seed germination.

A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1

The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::β-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.

Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution

Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth. Consequently, using root growth as a readout for signal perception can help decipher which external cues are perceived by roots, and how these signals are integrated. To date, studies measuring root growth responses using large numbers of roots have been limited by a lack of high-throughput image acquisition, poor scalability of analytical methods, or low spatiotemporal resolution. Here, we developed the Root Walker pipeline, which uses automated microscopes to acquire time-series images of many roots exposed to controlled treatments with high spatiotemporal resolution, in conjunction with fast and automated image analysis software. We demonstrate the power of Root Walker by quantifying root growth rate responses at different time and throughput scales upon treatment with natural auxin and two mitogen-associated protein kinase cascade inhibitors. We find a concentration-dependent root growth response to auxin and reveal the specificity of one MAPK inhibitor. We further demonstrate the ability of Root Walker to conduct genetic screens by performing a genome-wide association study on 260 accessions in under 2 weeks, revealing known and unknown root growth regulators. Root Walker promises to be a useful toolkit for the plant science community, allowing large-scale screening of root growth dynamics for a variety of purposes, including genetic screens for root sensing and root growth response mechanisms.

Fast and efficient root phenotyping via pose estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

The MKK3-MPK7 cascade phosphorylates ERF4 and promotes its rapid degradation to release seed dormancy in Arabidopsis

Seeds establish dormancy to delay germination until the arrival of a favorable growing season. In this study, we identify a fate switch comprised of the MKK3-MPK7 kinase cascade and the ethylene response factor ERF4 that is responsible for the seed state transition from dormancy to germination. We show that dormancy-breaking factors activate the MKK3-MPK7 module, which affects the expression of some α-EXPANSIN (EXPA) genes to control seed dormancy. Furthermore, we identify a direct downstream substrate of this module, ERF4, which suppresses the expression of these EXPAs by directly binding to the GCC boxes in their exon regions. The activated MKK3-MPK7 module phosphorylates ERF4, leading to its rapid degradation and thereby releasing its inhibitory effect on the expression of these EXPAs. Collectively, our work identifies a signaling chain consisting of protein phosphorylation, degradation, and gene transcription , by which the germination promoters within the embryo sense and are activated by germination signals from ambient conditions.

An IRE1-proteasome system signalling cohort controls cell fate determination in unresolved proteotoxic stress of the plant endoplasmic reticulum

Excessive accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress, which is an underlying cause of major crop losses and devastating human conditions. ER proteostasis surveillance is mediated by the conserved master regulator of the unfolded protein response (UPR), Inositol Requiring Enzyme 1 (IRE1), which determines cell fate by controlling pro-life and pro-death outcomes through as yet largely unknown mechanisms. Here we report that Arabidopsis IRE1 determines cell fate in ER stress by balancing the ubiquitin-proteasome system (UPS) and UPR through the plant-unique E3 ligase, PHOSPHATASE TYPE 2CA (PP2CA)-INTERACTING RING FINGER PROTEIN 1 (PIR1). Indeed, PIR1 loss leads to suppression of pro-death UPS and the lethal phenotype of an IRE1 loss-of-function mutant in unresolved ER stress in addition to activating pro-survival UPR. Specifically, in ER stress, PIR1 loss stabilizes ABI5, a basic leucine zipper (bZIP) transcription factor, that directly activates expression of the critical UPR regulator gene, bZIP60, triggering transcriptional cascades enhancing pro-survival UPR. Collectively, our results identify new cell fate effectors in plant ER stress by showing that IRE1's coordination of cell death and survival hinges on PIR1, a key pro-death component of the UPS, which controls ABI5, a pro-survival transcriptional activator of bZIP60.

Repressive ZINC FINGER OF ARABIDOPSIS THALIANA proteins promote programmed cell death in the Arabidopsis columella root cap

Developmental programmed cell death (dPCD) controls a plethora of functions in plant growth and reproduction. In the root cap of Arabidopsis (Arabidopsis thaliana), dPCD functions to control organ size in balance with the continuous stem cell activity in the root meristem. Key regulators of root cap dPCD including SOMBRERO/ANAC033 (SMB) belong to the NAC family of transcription factors. Here, we identify the C2H2 zinc finger protein ZINC FINGER OF ARABIDOPSIS THALIANA 14 ZAT14 as part of the gene regulatory network of root cap dPCD acting downstream of SMB. Similar to SMB, ZAT14-inducible misexpression leads to extensive ectopic cell death. Both the canonical EAR motif and a conserved L-box motif of ZAT14 act as transcriptional repression motifs and are required to trigger cell death. While a single zat14 mutant does not show a cell death-related phenotype, a quintuple mutant knocking out 5 related ZAT paralogs shows a delayed onset of dPCD execution in the columella and the adjacent lateral root cap. While ZAT14 is co-expressed with established dPCD-associated genes, it does not activate their expression. Our results suggest that ZAT14 acts as a transcriptional repressor controlling a so far uncharacterized subsection of the dPCD gene regulatory network active in specific root cap tissues.

The SMC5/6 complex recruits the PAF1 complex to facilitate DNA double-strand break repair in Arabidopsis

DNA double-strand breaks (DSBs) are one of the most toxic forms of DNA damage, which threatens genome stability. Homologous recombination is an error-free DSB repair pathway, in which the evolutionarily conserved SMC5/6 complex (SMC5/6) plays essential roles. The PAF1 complex (PAF1C) is well known to regulate transcription. Here we show that SMC5/6 recruits PAF1C to facilitate DSB repair in plants. In a genetic screen for DNA damage response mutants (DDRMs), we found that the Arabidopsis ddrm4 mutant is hypersensitive to DSB-inducing agents and is defective in homologous recombination. DDRM4 encodes PAF1, a core subunit of PAF1C. Further biochemical and genetic studies reveal that SMC5/6 recruits PAF1C to DSB sites, where PAF1C further recruits the E2 ubiquitin-conjugating enzymes UBC1/2, which interact with the E3 ubiquitin ligases HUB1/2 to mediate the monoubiquitination of histone H2B at DSBs. These results implicate SMC5/6-PAF1C-UBC1/2-HUB1/2 as a new axis for DSB repair through homologous recombination, revealing a new mechanism of SMC5/6 and uncovering a novel function of PAF1C.

Genome-wide analysis of R2R3-MYB transcription factors reveals their differential responses to drought stress and ABA treatment in desert poplar (Populus euphratica)

The R2R3-MYB transcription factors are widely involved in the regulation of plant growth, biotic and abiotic stress responses. Meanwhile, seed germination, which is stimulated by internal and external environments, is a critical stage in the plant life cycle. However, the identification, characterization, and expression profiling of the Populus euphratica R2R3-MYB family in drought response during seed germination have been unknown. Our study attempted to identify and characterize the R2R3-MYB genes in P. euphratica (PeR2R3-MYBs) and explore how R2R3-MYBs trigger the drought and abscisic acid (ABA) response mechanism in its seedlings. Based on the analysis of comparative genomics, 174 PeR2R3-MYBs were identified and expanded driven by whole genome duplication or segment duplication events. The analysis of Ka/Ks ratios showed that, in contrast to most PeR2R3-MYBs, the other PeR2R3-MYBs were subjected to positive selection in P. euphratica. Further, the expression data of PeR2R3-MYBs under drought stress and ABA treatment, together with available functional data for Arabidopsis thaliana MYB genes, supported the hypothesis that PeR2R3-MYBs involved in response to drought are dependent or independent on ABA signaling pathway during seed germination, especially PeR2R3-MYBs with MYB binding sites (MBS) cis-element and/or tandem duplication. This study is the first report on the genome-wide analysis of PeR2R3-MYBs, as well as the other two Salicaceae species. The duplication events and differential expressions of PeR2R3-MYBs play important roles in enhancing the adaptation to drought desert environment. Our results provide a reference for prospective functional studies of R2R3-MYBs of poplars and lay the foundation for new breeding strategies to improve the drought tolerance of P. euphratica.

Synthesis, Regulatory Factors, and Signaling Pathways of Estrogen in the Ovary

New insights have been thrown for understanding the significant role of estrogen on various systems of humans. Increasing evidences have determined the significant roles of estrogen in female reproductive system. So, the normal synthesis and secretion of estrogen play important roles in maintaining the function of tissues and organs. The ovaries are the main synthetic organs of estrogen. In this review, we summarized the current knowledge of the estrogen synthesis in the ovaries. A series of factors and signaling pathways that regulate the synthesis of estrogen are expounded in detail. Understanding the regulating factors and potential mechanism related to estrogen synthesis will be beneficial for understanding estrogen disorder related diseases and may provide novel therapeutic targets.

Flavonoids in vegetables: improvement of dietary flavonoids by metabolic engineering to promote health

Flavonoids are the most abundant polyphenols in plants, and have antioxidant effects as well as other bioactivities (e.g., anti-inflammatory, anti-cancer, anti-allergic, and neuroprotective effects). Vegetables are rich in flavonoids and are indispensable in our daily diet. Moreover, the vegetables as chassis for producing natural products would emerge as a promising means for cost-effective and sustainable production of flavonoids. Understanding the metabolic engineering of flavonoids in vegetables allows us to improve their nutrient composition. In this review, a comprehensive overview of flavonoids in vegetables, including the characterized types and distribution, health-promoting effects, associated metabolic pathways, and applied metabolic engineering are provided. We also introduce breakthroughs in multi-omics approaches that pertain to the elucidation of flavonoids metabolism in vegetables, as well as prospective and potential genome-editing technologies. Based on the varied composition and content of flavonoids among vegetables, dietary suggestions are further provided for human health.

Trihelix transcription factors GTL1 and DF1 prevent aberrant root hair formation in an excess nutrient condition

Root hair growth is tuned in response to the environment surrounding plants. While most previous studies focused on the enhancement of root hair growth during nutrient starvation, few studies investigated the root hair response in the presence of excess nutrients. We report that the post-embryonic growth of wild-type Arabidopsis plants is strongly suppressed with increasing nutrient availability, particularly in the case of root hair growth. We further used gene expression profiling to analyze how excess nutrient availability affects root hair growth, and found that RHD6 subfamily genes, which are positive regulators of root hair growth, are downregulated in this condition. However, defects in GTL1 and DF1, which are negative regulators of root hair growth, cause frail and swollen root hairs to form when excess nutrients are supplied. Additionally, we observed that the RHD6 subfamily genes are mis-expressed in gtl1-1 df1-1. Furthermore, overexpression of RSL4, an RHD6 subfamily gene, induces swollen root hairs in the face of a nutrient overload, while mutation of RSL4 in gtl1-1 df1-1 restore root hair swelling phenotype. In conclusion, our data suggest that GTL1 and DF1 prevent unnecessary root hair formation by repressing RSL4 under excess nutrient conditions.

A collection of inducible transcription factor-glucocorticoid receptor fusion lines for functional analyses in Arabidopsis thaliana

Arabidopsis possesses approximately 2000 transcription factors (TFs) in its genome. They play pivotal roles in various biological processes but analysis of their function has been hampered by the overlapping nature of their activities. To uncover clues to their function, we generated inducible TF lines using glucocorticoid receptor (GR) fusion techniques in Arabidopsis. These TF-GR lines each express one of 1255 TFs as a fusion with the GR gene. An average 14 lines of T₂ transgenic TF-GR lines were generated for each TF to monitor their function. To evaluate these transcription lines, we induced the TF-GR lines of phytochrome-interacting factor 4, which controls photomorphogenesis, with synthetic glucocorticoid dexamethasone. These phytochrome-interacting factor 4-GR lines showed the phenotype described in a previous report. We performed screening of the other TF-GR lines for TFs involved in light signaling under blue and far-red light conditions and identified 13 novel TF candidates. Among these, we found two lines showing higher anthocyanin accumulation under light conditions and we examined the regulating genes. These results indicate that the TF-GR lines can be used to dissect functionally redundant genes in plants and demonstrate that the TF-GR line collection can be used as an effective tool for functional analysis of TFs.

The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses

The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.

Spatiotemporal development of suberized barriers in cork oak taproots

The longevity and high activity of the cork cambium (or phellogen) from Quercus suber L. (cork oak) are the cornerstones for the sustainable exploitation of a unique raw material. Cork oak is a symbolic model to study cork development and cell wall suberization, yet most genetic and molecular studies on these topics have targeted other model plants. In this study, we explored the potential of taproots as a model system to study phellem development and suberization in cork oak, thereby avoiding the time constraints imposed when studying whole plants. In roots, suberin deposition is found in mature endodermis cells during primary development and in phellem cells during secondary development. By investigating the spatiotemporal characteristics of both endodermis and phellem suberization in young seedling taproots, we demonstrated that secondary growth and phellogen activity are initiated very early in cork oak taproots (approx. 8 days after sowing). We further compared the transcriptomic profile of root segments undergoing primary (PD) and secondary development (SD) and identified multiple candidate genes with predicted roles in cell wall modifications, mainly lignification and suberization, in addition to several regulatory genes, particularly transcription factor- and hormone-related genes. Our results indicate that the molecular regulation of suberization and secondary development in cork oak roots is relatively conserved with other species. The provided morphological characterization creates new opportunities to allow a faster assessment of phellogen activity (as compared with studies using stem tissues) and to tackle fundamental questions regarding its regulation.

Translational profile of developing phellem cells in Arabidopsis thaliana roots

The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP-SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis.

A plant-specific module for homologous recombination repair

Homologous recombination repair (HR) is an error-free DNA damage repair pathway to maintain genome stability and a basis of gene targeting using genome-editing tools. However, the mechanisms of HR in plants are still poorly understood. Through genetic screens for DNA damage response mutants (DDRM) in Arabidopsis, we find that a plant-specific ubiquitin E3 ligase DDRM1 is required for HR. DDRM1 contains an N-terminal BRCT (BRCA1 C-terminal) domain and a C-terminal RING (really interesting new gene) domain and is highly conserved in plants including mosses. The ddrm1 mutant is defective in HR and thus is hypersensitive to DNA-damaging reagents. Biochemical studies reveal that DDRM1 interacts with and ubiquitinates the transcription factor SOG1, a plant-specific master regulator of DNA damage responses. Interestingly, DDRM1-mediated ubiquitination promotes the stability of SOG1. Consistently, genetic data support that SOG1 functions downstream of DDRM1. Our study reveals that DDRM1-SOG1 is a plant-specific module for HR and highlights the importance of ubiquitination in HR.

ORA47 is a transcriptional regulator of a general stress response hub

Transcriptional regulators of the general stress response (GSR) reprogram the expression of selected genes to transduce informational signals into cellular events, ultimately manifested in a plant's ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) binding to the previously established functional GSR motif, termed the rapid stress response element (RSRE). This led to the isolation of octadecanoid-responsive AP2/ERF-domain transcription factor 47 (ORA47), a methyl jasmonate inducible protein. Subsequently, ORA47 transcriptional activity was confirmed using the RSRE-driven luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in the induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of methyl jasmonate led to enhanced levels of ORA47 and CAMTA3 transcripts, as well as the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the present study provides fresh insight into the initial features of the mechanism that transduces informational signals into adaptive responses. This mechanism involves the functional interplay between the JA biosynthesis/signaling cascade and the transcriptional reprogramming that potentiates GSR. Furthermore, these findings offer a window into the role of intraorganellar communication in the establishment of adaptive responses.

Stress-Inducible Overexpression of SlDDF2 Gene Improves Tolerance against Multiple Abiotic Stresses in Tomato Plant

Dehydration-responsive element-binding protein 1 (DREB1)/C-repeat binding factor (CBF) family plays a key role in plant tolerance against different abiotic stresses. In this study, an orthologous gene of the DWARF AND DELAYED FLOWERING (DDF) members in Arabidopsis, SlDDF2, was identified in tomato plants. The SlDDF2 gene expression was analyzed, and a clear induction in response to ABA treatment, cold, salinity, and drought stresses was observed. Furthermore, two transgenic lines (SlDDF2-IOE#6 and SlDDF2-IOE#9) with stress-inducible overexpression of SlDDF2 under Rd29a promoter were generated. Under stress conditions, the gene expression of SlDDF2 was significantly higher in both transgenic lines. The growth performance, as well as physiological parameters, were evaluated in wild-type and transgenic plants. The transgenic lines showed growth retardation phenotypes and had higher chlorophyll content under stress conditions in plants. However, the relative decrease in growth performance (plant height, leaf number, and leaf area) in stressed transgenic lines was lower than that in stressed wild-type plants, compared with nonstressed conditions. The reduction in the relative water content and water loss rate was also lower in the transgenic lines. Compared with wild-type plants, transgenic lines showed enhanced tolerance to different abiotic stresses including water deficit, salinity, and cold. In conclusion, stress-inducible expression of SlDDF2 can be a useful tool to improve tolerance against multiple abiotic stresses in tomato plants.

miR172 Regulates WUS during Somatic Embryogenesis in Arabidopsis via AP2

In plants, the embryogenic transition of somatic cells requires the reprogramming of the cell transcriptome, which is under the control of genetic and epigenetic factors. Correspondingly, the extensive modulation of genes encoding transcription factors and miRNAs has been indicated as controlling the induction of somatic embryogenesis in Arabidopsis and other plants. Among the MIRNAs that have a differential expression during somatic embryogenesis, members of the MIRNA172 gene family have been identified, which implies a role of miR172 in controlling the embryogenic transition in Arabidopsis. In the present study, we found a disturbed expression of both MIRNA172 and candidate miR172-target genes, including AP2, TOE1, TOE2, TOE3, SMZ and SNZ, that negatively affected the embryogenic response of transgenic explants. Next, we examined the role of AP2 in the miR172-mediated mechanism that controls the embryogenic response. We found some evidence that by controlling AP2, miR172 might repress the WUS that has an important function in embryogenic induction. We showed that the mechanism of the miR172-AP2-controlled repression of WUS involves histone acetylation. We observed the upregulation of the WUS transcripts in an embryogenic culture that was overexpressing AP2 and treated with trichostatin A (TSA), which is an inhibitor of HDAC histone deacetylases. The increased expression of the WUS gene in the embryogenic culture of the hdac mutants further confirmed the role of histone acetylation in WUS control during somatic embryogenesis. A chromatin-immunoprecipitation analysis provided evidence about the contribution of HDA6/19-mediated histone deacetylation to AP2-controlled WUS repression during embryogenic induction. The upstream regulatory elements of the miR172-AP2-WUS pathway might involve the miR156-controlled SPL9/SPL10, which control the level of mature miR172 in an embryogenic culture.

DNA features beyond the transcription factor binding site specify target recognition by plant MYC2-related bHLH proteins

Transcription factors (TFs) regulate gene expression by binding to cis-regulatory sequences in the promoters of target genes. Recent research is helping to decipher in part the cis-regulatory code in eukaryotes, including plants, but it is not yet fully understood how paralogous TFs select their targets. Here we addressed this question by studying several proteins of the basic helix-loop-helix (bHLH) family of plant TFs, all of which recognize the same DNA motif. We focused on the MYC-related group of bHLHs, that redundantly regulate the jasmonate (JA) signaling pathway, and we observed a high correspondence between DNA-binding profiles in vitro and MYC function in vivo. We demonstrated that A/T-rich modules flanking the MYC-binding motif, conserved from bryophytes to higher plants, are essential for TF recognition. We observed particular DNA-shape features associated with A/T modules, indicating that the DNA shape may contribute to MYC DNA binding. We extended this analysis to 20 additional bHLHs and observed correspondence between in vitro binding and protein function, but it could not be attributed to A/T modules as in MYCs. We conclude that different bHLHs may have their own codes for DNA binding and specific selection of targets that, at least in the case of MYCs, depend on the TF-DNA interplay.

Transcription Factor-Based Genetic Engineering in Microalgae

Sequence-specific DNA-binding transcription factors (TFs) are key components of gene regulatory networks. Advances in high-throughput sequencing have facilitated the rapid acquisition of whole genome assembly and TF repertoires in microalgal species. In this review, we summarize recent advances in gene discovery and functional analyses, especially for transcription factors in microalgal species. Specifically, we provide examples of the genome-scale identification of transcription factors in genome-sequenced microalgal species and showcase their application in the discovery of regulators involved in various cellular functions. Herein, we highlight TF-based genetic engineering as a promising framework for designing microalgal strains for microalgal-based bioproduction.

The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation

Gene expression is reconfigured rapidly during the cell cycle to execute the cellular functions specific to each phase. Studies conducted with synchronized plant cell suspension cultures have identified hundreds of genes with periodic expression patterns across the phases of the cell cycle, but these results may differ from expression occurring in the context of intact organs. Here, we describe the use of fluorescence-activated cell sorting to analyze the gene expression profile of G2/M cells in the growing root. To this end, we isolated cells expressing the early mitosis cell cycle marker CYCLINB1;1-GFP from Arabidopsis root tips. Transcriptome analysis of these cells allowed identification of hundreds of genes whose expression is reduced or enriched in G2/M cells, including many not previously reported from cell suspension cultures. From this dataset, we identified SCL28, a transcription factor belonging to the GRAS family, whose messenger RNA accumulates to the highest levels in G2/M and is regulated by MYB3R transcription factors. Functional analysis indicates that SCL28 promotes progression through G2/M and modulates the selection of cell division planes.

Innovation, conservation, and repurposing of gene function in root cell type development

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.

A Plant Based Modified Biostimulant (Copper Chlorophyllin), Mediates Defense Response in Arabidopsis thaliana under Salinity Stress

To date, managing salinity stress in agriculture relies heavily on development of salt tolerant plant varieties, a time-consuming process particularly challenging for many crops. Plant based biostimulants (PBs) that enhance plant defenses under stress can potentially address this drawback, as they are not crop specific and are easy to apply in the field. Unfortunately, limited knowledge about their modes of action makes it harder to utilize them on a broader scale. Understanding how PBs enhance plant defenses at cellular and molecular levels, is a prerequisite for the development of sustainable management practices utilizing biostimulants to improve crop health. In this study we elucidated the protective mechanism of copper chlorophyllin (Cu-chl), a PB, under salinity stress. Our results indicate that Cu-chl exerts protective effects primarily by decreasing oxidative stress through modulating cellular H₂O₂ levels. Cu-chl treated plants increased tolerance to oxidative stress imposed by an herbicide, methyl viologen dichloride hydrate as well, suggesting a protective role against various sources of reactive oxygen species (ROS). RNA-Seq analysis of Cu-chl treated Arabidopsis thaliana seedlings subjected to salt stress identified genes involved in ROS detoxification, and cellular growth.

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana

Temperature impacts plant immunity and growth but how temperature intersects with endogenous pathways to shape natural variation remains unclear. Here we uncover variation between Arabidopsis thaliana natural accessions in response to two non-stress temperatures (22°C and 16°C) affecting accumulation of the thermoresponsive stress hormone salicylic acid (SA) and plant growth. Analysis of differentially responding A. thaliana accessions shows that pre-existing SA provides a benefit in limiting infection by Pseudomonas syringae pathovar tomato DC3000 bacteria at both temperatures. Several A. thaliana genotypes display a capacity to mitigate negative effects of high SA on growth, indicating within-species plasticity in SA—growth tradeoffs. An association study of temperature x SA variation, followed by physiological and immunity phenotyping of mutant and over-expression lines, identifies the transcription factor bHLH059 as a temperature-responsive SA immunity regulator. Here we reveal previously untapped diversity in plant responses to temperature and a way forward in understanding the genetic architecture of plant adaptation to changing environments.

Temperature has a profound effect on plant innate immune responses but little is known about the mechanisms underlying natural variation in transmission of temperature signals to defence pathways. Much of our understanding of temperature effects on plant immunity and tradeoffs between activated defences and growth has come from analysis of the common Arabidopsis thaliana genetic accession, Col-0. Here we examine A. thaliana genetic variation in response to temperature (within the non-stress range—22 ^oC and 16 ^oC) at the level of accumulation of the thermoresponsive biotic stress hormone salicylic acid (SA), bacterial pathogen resistance, and plant biomass. From analysis of 105 genetically diverse A. thaliana accessions we uncover plasticity in temperature-modulated SA homeostasis and in the relationship between SA levels and plant growth. We find that high SA amounts prior to infection provide a robust benefit of enhancing bacterial resistance. In some accessions this benefit comes without compromised plant growth, suggestive of altered defence–growth tradeoffs. Based on a temperature x SA association study we identify the transcription factor gene, bHLH059, and show that it has features of a temperature-sensitive immunity regulator that are unrelated to PIF4, a known thermosensitive coordinator of immunity and growth.

An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.

The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development

VERNALIZATION2 (VRN2), an angiosperm-specific subunit of the polycomb repressive complex 2 (PRC2), is an oxygen (O₂ )-regulated target of the PCO branch of the PRT6 N-degron pathway of ubiquitin-mediated proteolysis. How this post-translational regulation coordinates VRN2 activity remains to be fully established. Here we use Arabidopsis thaliana ecotypes, mutants and transgenic lines to determine how control of VRN2 stability contributes to its functions during plant development. VRN2 localizes to endogenous hypoxic regions in aerial and root tissues. In the shoot apex, VRN2 differentially modulates flowering time dependent on photoperiod, whilst its presence in lateral root primordia and the root apical meristem negatively regulates root system architecture. Ectopic accumulation of VRN2 does not enhance its effects on flowering, but does potentiate its repressive effects on root growth. In late-flowering vernalization-dependent ecotypes, VRN2 is only active outside meristems when its proteolysis is inhibited in response to cold exposure, as its function requires concomitant cold-triggered increases in other PRC2 subunits and cofactors. We conclude that the O₂ -sensitive N-degron of VRN2 has a dual function, confining VRN2 to meristems and primordia, where it has specific developmental roles, whilst also permitting broad accumulation outside of meristems in response to environmental cues, leading to other functions.

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the Vascular-related NAC Domain 7 (VND7), MYB46, and MYB83 transcription factors, which are proposed to act in interconnected feedforward loops (FFLs). Less is known regarding the molecular mechanisms underlying the terminal transition to xylem cell differentiation. Here, we generate whole-root and single-cell data, which demonstrate that VND7 initiates sharp switching of root cells to xylem cell identity. Based on these data, we identified 4 candidate VND7 downstream target genes capable of generating this switch. Although MYB46 responds to VND7 induction, it is not among these targets. This system provides an important model to study the emergent properties that may give rise to totipotency relative to terminal differentiation and reveals xylem cell subtypes.

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

Optimal plant growth is hampered by deficiency of the essential macronutrient phosphate in most soils. Plant roots can, however, increase their root hair density to efficiently forage the soil for this immobile nutrient. By generating and exploiting a high-resolution single-cell gene expression atlas of Arabidopsis roots, we show an enrichment of TARGET OF MONOPTEROS 5/LONESOME HIGHWAY (TMO5/LHW) target gene responses in root hair cells. The TMO5/LHW heterodimer triggers biosynthesis of mobile cytokinin in vascular cells and increases root hair density during low-phosphate conditions by modifying both the length and cell fate of epidermal cells. Moreover, root hair responses in phosphate-deprived conditions are TMO5- and cytokinin-dependent. Cytokinin signaling links root hair responses in the epidermis to perception of phosphate depletion in vascular cells.

Transcriptome Analysis Reveals Potential Roles of Abscisic Acid and Polyphenols in Adaptation of Onobrychis viciifolia to Extreme Environmental Conditions in the Qinghai-Tibetan Plateau

A detailed understanding of the molecular mechanisms of plant stress resistance in the face of ever-changing environmental stimuli will be helpful for promoting the growth and production of crop and forage plants. Investigations of plant responses to various single abiotic or biotic factors, or combined stresses, have been extensively reported. However, the molecular mechanisms of plants in responses to environmental stresses under natural conditions are not clearly understood. In this study, we carried out a transcriptome analysis using RNA-sequencing to decipher the underlying molecular mechanisms of Onobrychis viciifolia responding and adapting to the extreme natural environment in the Qinghai-Tibetan Plateau (QTP). The transcriptome data of plant samples collected from two different altitudes revealed a total of 8212 differentially expressed genes (DEGs), including 5387 up-regulated and 2825 down-regulated genes. Detailed analysis of the identified DEGs uncovered that up-regulation of genes potentially leading to changes in hormone homeostasis and signaling, particularly abscisic acid-related ones, and enhanced biosynthesis of polyphenols play vital roles in the adaptive processes of O. viciifolia. Interestingly, several DEGs encoding uridine diphosphate glycosyltransferases, which putatively regulate phytohormone homeostasis to resist environmental stresses, were also discovered. Furthermore, numerous DEGs encoding transcriptional factors, such as members of the myeloblastosis (MYB), homeodomain-leucine zipper (HD-ZIP), WRKY, and nam-ataf1,2-cuc2 (NAC) families, might be involved in the adaptive responses of O. viciifolia to the extreme natural environmental conditions. The DEGs identified in this study represent candidate targets for improving environmental stress resistance of O. viciifolia grown in higher altitudes of the QTP, and can provide deep insights into the molecular mechanisms underlying the responses of this plant species to the extreme natural environmental conditions of the QTP.

Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division

Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the Arabidopsis root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.

RAP2.3 negatively regulates nitric oxide biosynthesis and related responses through a rheostat-like mechanism in Arabidopsis

Nitric oxide (NO) is sensed through a mechanism involving the degradation of group-VII ERF transcription factors (ERFVIIs) that is mediated by the N-degron pathway. However, the mechanisms regulating NO homeostasis and downstream responses remain mostly unknown. To explore the role of ERFVIIs in regulating NO production and signaling, genome-wide transcriptome analyses were performed on single and multiple erfvii mutants of Arabidopsis following exposure to NO. Transgenic plants overexpressing degradable or non-degradable versions of RAP2.3, one of the five ERFVIIs, were also examined. Enhanced RAP2.3 expression attenuated the changes in the transcriptome upon exposure to NO, and thereby acted as a brake for NO-triggered responses that included the activation of jasmonate and ABA signaling. The expression of non-degradable RAP2.3 attenuated NO biosynthesis in shoots but not in roots, and released the NO-triggered inhibition of hypocotyl and root elongation. In the guard cells of stomata, the control of NO accumulation depended on PRT6-triggered degradation of RAP2.3 more than on RAP2.3 levels. RAP2.3 therefore seemed to work as a molecular rheostat controlling NO homeostasis and signaling. Its function as a brake for NO signaling was released upon NO-triggered PRT6-mediated degradation, thus allowing the inhibition of growth, and the potentiation of jasmonate- and ABA-related signaling.

DEAR4, a Member of DREB/CBF Family, Positively Regulates Leaf Senescence and Response to Multiple Stressors in Arabidopsis thaliana

Leaf senescence is a programmed developmental process regulated by various endogenous and exogenous factors. Here we report the characterization of the senescence-regulating role of DEAR4 (AT4G36900) from the DREB1/CBF (dehydration-responsive element binding protein 1/C-repeat binding factor) family in Arabidopsis. The expression of DEAR4 is associated with leaf senescence and can be induced by ABA, JA, darkness, drought and salt stress. Transgenic plants over-expressing DEAR4 showed a dramatically enhanced leaf senescence phenotype under normal and dark conditions while the dear4 knock-down mutant displayed delayed senescence. DEAR4 over-expressing plants showed decreased seed germination rate under ABA and salt stress conditions as well as decreased drought tolerance, indicating that DEAR4 was involved in both senescence and stress response processes. Furthermore, we found that DEAR4 protein displayed transcriptional repressor activities in yeast cells. DEAR4 could directly repress the expression of a subset of COLD-REGULATED (COR) and RESPONSIVE TO DEHYDRATION (RD) genes which have been shown to be involved in leaf longevity and stress response. Also we found that DERA4 could induce the production of Reactive oxygen species (ROS), the common signal of senescence and stress responses, which gives us the clue that DEAR4 may play an integrative role in senescence and stress response via regulating ROS production.

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks

Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA-sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user-friendly platform that can process raw RNA-sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree-based pipeline, rtp-star. We obtained time-course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp-star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild-type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell-type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non-bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.

Silencing against the conserved NAC domain of the potato StNAC103 reveals new NAC candidates to repress the suberin associated waxes in phellem

Both suberin and its associated waxes contribute to the formation of apoplastic barriers that protect plants from the environment. Some transcription factors have emerged as regulators of the suberization process. The potato StNAC103 gene was reported as a repressor of suberin polyester and suberin-associated waxes deposition because its RNAi-mediated downregulation (StNAC103-RNAi) over-accumulated suberin and associated waxes in the tuber phellem concomitantly with the induction of representative biosynthetic genes. Here, to explore if other genes of the large NAC gene family participate to this repressive function, we extended the silencing to other NAC members by targeting the conserved NAC domain of StNAC103 (StNAC103-RNAi-c). Transcript profile of the StNAC103-RNAi-c phellem indicated that StNAC101 gene was an additional potential target. In comparison with StNAC103-RNAi, the silencing with StNAC103-RNAi-c construct resulted in a similar effect in suberin but yielded an increased load of associated waxes in tuber phellem, mainly alkanes and feruloyl esters. Globally, the chemical effects in both silenced lines are supported by the transcript accumulation profile of genes involved in the biosynthesis, transport and regulation of apoplastic lipids. In contrast, the genes of polyamine biosynthesis were downregulated. Altogether these results point out to StNAC101 as a candidate to repress the suberin-associated waxes.

Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed

Maintaining the right balance between plasticity and robustness in biological systems is important to allow adaptation while maintaining essential functions. Developmental plasticity of plant root systems has been the subject of intensive research, but the mechanisms underpinning robustness remain unclear. Here, we show that potassium deficiency inhibits lateral root organogenesis by delaying early stages in the formation of lateral root primordia. However, the severity of the symptoms arising from this perturbation varies within a natural population of Arabidopsis and is associated with the genetic variation in CLSY1, a key component of the RNA-directed DNA-methylation machinery. Mechanistically, CLSY1 mediates the transcriptional repression of a negative regulator of root branching, IAA27, and promotes lateral root development when the auxin-dependent proteolysis pathway fails. Our study identifies DNA-methylation-mediated transcriptional repression as a backup system for post-translational protein degradation which ensures robust development and performance of plants in a challenging environment.

Developmental plasticity of plant root systems has been intensively studied, but the mechanisms underpinning robustness remain unclear. Here, the authors show that DNA-methylation-mediated transcriptional repression serves as a backup system to control lateral root development when auxin signalling is perturbed.

Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO₃^-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO₃^- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO₃^- treatments. NO₃^--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO₃^- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

The Tomato Genome Encodes SPCH, MUTE, and FAMA Candidates That Can Replace the Endogenous Functions of Their Arabidopsis Orthologs

Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.

Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis

Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In Arabidopsis thaliana, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of ATG8 genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that regulate ATG8 gene expression in Arabidopsis, using the promoters of 4 ATG8 genes. We identified a total of 225 TFs from 35 families that bind these promoters. The TF-ATG8 promoter interactions revealed a wide array of diverse TF families for different promoters, as well as enrichment for families of TFs that bound to specific fragments. These TFs are not only involved in plant developmental processes but also in the response to environmental stresses. TGA9 (TGACG (TGA) motif-binding protein 9)/AT1G08320 was confirmed as a positive regulator of autophagy. TGA9 overexpression activated autophagy under both control and stress conditions and transcriptionally up-regulated expression of ATG8B, ATG8E and additional ATG genes via binding to their promoters. Our results provide a comprehensive resource of TFs that regulate ATG8 gene expression and lay a foundation for understanding the transcriptional regulation of plant autophagy.Abbreviations: ABRC: Arabidopsis biological resource center; AP2-EREBP: APETALA2/Ethylene-responsive element binding protein; ARF: auxin response factor; ATF4: activating transcription factor 4; ATG: autophagy-related; ChIP: chromatin immunoprecipitation; DAP-seq: DNA affinity purification sequencing; FOXO: forkhead box O; GFP: green fluorescent protein; GO: gene ontologies; HB: homeobox; LD: long-day; LUC: firefly luciferase; MAP1LC3: microtubule associated protein 1 light chain 3; MDC: monodansylcadaverine; 3-MA: 3-methyladenine; OE: overexpressing; PCD: programmed cell death; qPCR: quantitative polymerase chain reaction; REN: renilla luciferase; RT: room temperature; SD: standard deviation; TF: transcription factor; TFEB: transcription factor EB; TGA: TGACG motif; TOR: target of rapamycin; TSS: transcription start site; WT: wild-type; Y1H: yeast one-hybrid.

Nitric oxide responses in Arabidopsis hypocotyls are mediated by diverse phytohormone pathways

Plants are often exposed to high levels of nitric oxide (NO) that affects development and stress-triggered responses. However, the way in which plants sense NO is still largely unknown. Here we combine the analysis of early changes in the transcriptome of plants exposed to a short acute pulse of exogenous NO with the identification of transcription factors (TFs) involved in NO sensing. The NO-responsive transcriptome was enriched in hormone homeostasis- and signaling-related genes. To assess events involved in NO sensing in hypocotyls, we used a functional sensing assay based on the NO-induced inhibition of hypocotyl elongation in etiolated seedlings. Hormone-related mutants and the TRANSPLANTA collection of transgenic lines conditionally expressing Arabidopsis TFs were screened for NO-triggered hypocotyl shortening. These approaches allowed the identification of hormone-related TFs, ethylene perception and signaling, strigolactone biosynthesis and signaling, and salicylate production and accumulation that are essential for or modulate hypocotyl NO sensing. Moreover, NO inhibits hypocotyl elongation through the positive and negative regulation of some abscisic acid (ABA) receptors and transcripts encoding brassinosteroid signaling components thereby also implicating these hormones in NO sensing.

Expression of the Intracellular COPT3-Mediated Cu Transport Is Temporally Regulated by the TCP16 Transcription Factor

Copper is an essential element in plants. When scarce, copper is acquired from extracellular environment or remobilized from intracellular sites, through members of the high affinity copper transporters family COPT located at the plasma membrane and internal membrane, respectively. Here, we show that COPT3 is an intracellular copper transporter, located at a compartment of the secretory pathway, that is mainly expressed in pollen grains and vascular bundles. Contrary to the COPT1 plasma membrane member, the expression of the internal COPT3 membrane transporter was higher at 12 h than at 0 h of a neutral photoperiod day under copper deficiency. The screening of a library of conditionally overexpressed transcription factors implicated members of the TCP family in the COPT3 differential temporal expression pattern. Particularly, in vitro, TCP16 was found to bind to the COPT3 promoter and down-regulated its expression. Accordingly, TCP16 was mainly expressed at 0 h under copper deficiency and induced at 12 h by copper excess. Moreover, TCP16 overexpression resulted in increased sensitivity to copper deficiency, whereas the tcp16 mutant was sensitive to copper excess. Both copper content and the expression of particular copper status markers were altered in plants with modified levels of TCP16. Consistent with TCP16 affecting pollen development, the lack of COPT3 function led to altered pollen morphology. Furthermore, analysis of copt3 and COPT3 overexpressing plants revealed that COPT3 function exerted a negative effect on TCP16 expression. Taken together, these results suggest a differential daily regulation of copper uptake depending on the external and internal copper pools, in which TCP16 inhibits copper remobilization at dawn through repression of intracellular transporters.