Cell fate in the Arabidopsis root epidermis is determined by competition between WEREWOLF and CAPRICE

The regulatory module MdCPCL-MdILR3L mediates the synthesis of ascorbic acid and anthocyanin in apple

Apple (Malus domestica Borkh.) is one of the most economically valuable fruit crops globally and a key dietary source for various nutrients. However, the levels of ascorbic acid (AsA) and anthocyanin, essential micronutrients for human health, are extremely low in the pulp of commonly cultivated apple varieties. In the present study, the second-generation hybrid strain of Xinjiang red-fleshed apple ('Zihong No. 1' × 'Gala') was used as the test material. The results revealed that AsA content was significantly higher in red-fleshed apple pulp than in non-red-fleshed varieties, and the expression of MdGLDH, a key gene in the D-mannose/L-galactose pathway, correlated strongly with AsA levels. Using the promoter of MdGLDH as bait, an R3-type MYB transcription factor (TF), MdCPC-like, was identified through yeast one-hybrid screening. Further analysis revealed that the overexpression of MdCPCL increased the AsA and anthocyanin levels in both callus and fruits, whereas MdCPCL knockdown led to a reduction in their levels. Moreover, the interaction between MdCPCL and the bHLH TF MdILR3-like was confirmed, forming the MdCPCL-MdILR3L complex. This complex significantly enhanced the transcription of downstream target genes MdGLDH and MdANS, promoting the synthesis of AsA and anthocyanins. This study contributes to further enrich the anabolic pathways of AsA and anthocyanin in apples and provides a theoretical foundation for the quality breeding of red-fleshed apple varieties.

Ectopic expression of AtMYB115 and AtMYB118 induces green tissue formation in non-green organs of Arabidopsis thaliana

BACKGROUND

A dominant mutant, green root-dominant (grt-D), which exhibits a green-root phenotype, was identified using the GAL4-UAS activation tagging system in the Q2610 enhancer trap line of Arabidopsis thaliana (Arabidopsis).

OBJECTIVE

To identify the gene responsible for the grt-D phenotype and investigate whether its ectopic expression induces green petal formation.

METHODS

The gene responsible for the grt-D phenotype was identified via thermal asymmetric interlaced-polymerase chain reaction (PCR). The cloned gene and its homolog were expressed under the control of the Q2610 enhancer for root tip expression and the APETALA3 (AP3) or PISTILLATA (PI) promoter for petal-preferential expression.

RESULTS

The 5 × UAS tag in grt-D was located 111 base pairs upstream of the start codon of AtMYB115. Ectopic expression of AtMYB115 or its closest homolog, AtMYB118, under the Q2610 enhancer recapitulated the grt-D green-root phenotype, indicating functional equivalence between the two genes. To examine their effect on petal development, AtMYB115 and AtMYB118 were expressed under the AP3 and PI promoters. The resulting transgenic lines (AP3 >  > AtMYB115, AP3 >  > AtMYB118, PI >  > AtMYB115, and PI >  > AtMYB118) developed short, pale green petals and sterile stamens. The green petals exhibited reduced expression of STAY-GREEN 1, which encodes Mg-dechelatase, a key enzyme involved in chlorophyll degradation, suggesting that the green-petal phenotype results from impaired chlorophyll breakdown.

CONCLUSION

These findings demonstrate that the ectopic expression of AtMYB115 and AtMYB118 induces green tissue development in non-green organs of Arabidopsis.

MYB30-INTERACTING E3 LIGASE 1 regulates LONELY GUY 5-mediated cytokinin metabolism to promote drought tolerance in cotton

Ubiquitination plays important roles in modulating the abiotic stress tolerance of plants. Drought seriously restricts agricultural production, but how ubiquitination participates in regulating drought tolerance remains largely unknown. Here, we identified a drought-inducible gene, MYB30-INTERACTING E3 LIGASE 1 (GhMIEL1), which encodes a RING E3 ubiquitin ligase in cotton (Gossypium hirsutum). GhMIEL1 was strongly induced by polyethylene glycol (PEG-6000) and the phytohormone abscisic acid. Overexpression and knockdown of GhMIEL1 in cotton substantially enhanced and reduced drought tolerance, respectively. GhMIEL1 interacted with the MYB transcription factor GhMYB66 and could ubiquitinate and degrade it in vitro. GhMYB66 directly bound to the LONELY GUY 5 (GhLOG5) promoter, a gene encoding cytokinin riboside 5'-monophosphate phosphoribohydrolase, to repress its transcription. Overexpression of GhMIEL1 and silencing of GhMYB66 altered the homeostasis of cytokinin of plant roots, increased total root length and number of root tips, and enhanced plant drought tolerance. Conversely, silencing GhLOG5 decreased total root length and number of root tips and reduced plant drought tolerance. Our studies reveal that the GhMIEL1-GhMYB66-GhLOG5 module positively regulates drought tolerance in cotton, which deepens our understanding of plant ubiquitination-mediated drought tolerance and provides insights for improving drought tolerance.

CPK1 activates CNGCs through phosphorylation for Ca2+ signaling to promote root hair growth in Arabidopsis

Cyclic nucleotide-gated channel 5 (CNGC5), CNGC6, and CNGC9 (CNGC5/6/9 for simplicity) control Arabidopsis root hair (RH) growth by mediating the influx of external Ca2+ to establish and maintain a sharp cytosolic Ca2+ gradient at RH tips. However, the underlying mechanisms for the regulation of CNGCs remain unknown. We report here that calcium dependent protein kinase 1 (CPK1) directly activates CNGC5/6/9 to promote Arabidopsis RH growth. The loss-of-function mutants cpk1-1, cpk1-2, cngc5-1 cngc6-2 cngc9-1 (shrh1/short root hair 1), and cpk1 shrh1 show similar RH phenotypes, including shorter RHs, more RH branching, and dramatically attenuated cytosolic Ca2+ gradients at RH tips. The main CPK1-target sites are identified as Ser20, Ser27, and Ser26 for CNGC5/6/9, respectively, and the corresponding alanine substitution mutants fail to rescue RH growth in shrh1 and cpk1-1, while phospho-mimic versions restore the cytosolic Ca2+ gradient at RH apex and rescue the RH phenotypes in the same Arabidopsis mutants. Thus we discover the CPK1-CNGC modules essential for the Ca2+ signaling regulation and RH growth in Arabidopsis.

Regulatory mechanisms of trichome and root hair development in Arabidopsis

In plants, cell fate determination is regulated temporally and spatially via a complex of signals consisting of a large number of genetic interactions. Trichome and root hair formation are excellent models for studying cell fate determination in plants. Nowadays, the mysteries underlying the reprograming of trichome and root hair and how nature programs the development of trichome and root hair is an interesting topic in the scientific field. In this review, we discuss the spatial and temporal regulatory networks and cross-talk between phytohormones and epigenetic modifications in the regulation of trichome and root hair initiation in Arabidopsis. The discussion in this review provides a good model for understanding the regulatory mechanism of cell differentiation processes in plants. Moreover, we summarize recent advances in the modulation of trichome and root hair initiation in plants and compare different regulatory mechanisms to help illuminate key goals for future research.

Negative feedback regulation of GLABRA1 contributes to epidermal cell patterning in the Arabidopsis root

GLABRA1 (GL1), which encodes an R2R3 MYB transcription factor, is a key regulator of trichome patterning in the aerial organs of Arabidopsis (Arabidopsis thaliana). Although it has been generally assumed that GL1 functions exclusively in shoots and is not expressed in roots, reverse transcription polymerase chain reaction (RT-PCR) analysis has revealed that GL1 is indeed expressed in roots. To investigate whether GL1 plays a role in root epidermal patterning, we analyzed the effects of gl1 mutations in sensitized genetic backgrounds. Our findings show that gl1 mutants enhance the root epidermal phenotype of a weak allele of the werewolf (wer) mutant and suppress the phenotype of the caprice (cpc) mutant. We also demonstrate that the GL1 promoter is active in N-position epidermal cells, and that the GFP-GL1 fusion protein is predominantly localized in the nucleus of N-position cells. Furthermore, we provide evidence that GL1 expression is positively regulated by WER, GLABRA3, ENHANCER OF GLABRA3, and TRANSPARENT TESTA GLABRA1, while negatively regulated by CPC, TRIPTYCHON, and GLABRA2 (GL2). Notably, GL2, which is positively regulated by GL1, moderately represses GL1 expression, and both GL1 and GL2 are positively regulated by WER in N-position cells. These findings suggest that a negative feedback regulation of GL1 expression via GL2 contributes to the fine-tuning of non-hair cell fate determination in Arabidopsis root epidermis.

Abscisic acid-induced transcription factor PsMYB306 negatively regulates tree peony bud dormancy release

Bud dormancy is a crucial strategy for perennial plants to withstand adverse winter conditions. However, the regulatory mechanism of bud dormancy in tree peony (Paeonia suffruticosa) remains largely unknown. Here, we observed dramatically reduced and increased accumulation of abscisic acid (ABA) and bioactive gibberellins (GAs) GA1 and GA3, respectively, during bud endodormancy release of tree peony under prolonged chilling treatment. An Illumina RNA sequencing study was performed to identify potential genes involved in the bud endodormancy regulation in tree peony. Correlation matrix, principal component, and interaction network analyses identified a downregulated MYB transcription factor gene, PsMYB306, the expression of which positively correlated with 9-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (PsNCED3) expression. Protein modeling analysis revealed 4 residues within the R2R3 domain of PsMYB306 to possess DNA binding capability. Transcription of PsMYB306 was increased by ABA treatment. Overexpression of PsMYB306 in petunia (Petunia hybrida) inhibited seed germination and plant growth, concomitant with elevated ABA and decreased GA contents. Silencing of PsMYB306 accelerated cold-triggered tree peony bud burst and influenced the production of ABA and GAs and the expression of their biosynthetic genes. ABA application reduced bud dormancy release and transcription of ENT-KAURENOIC ACID OXIDASE 1 (PsKAO1), GA20-OXIDASE 1 (PsGA20ox1), and GA3-OXIDASE 1 (PsGA3ox1) associated with GA biosynthesis in PsMYB306-silenced buds. In vivo and in vitro binding assays confirmed that PsMYB306 specifically transactivated the promoter of PsNCED3. Silencing of PsNCED3 also promoted bud break and growth. Altogether, our findings suggest that PsMYB306 negatively modulates cold-induced bud endodormancy release by regulating ABA production.

The APETALA2-MYBL2 module represses proanthocyanidin biosynthesis by affecting formation of the MBW complex in seeds of Arabidopsis thaliana

Proanthocyanidins (PAs) are the second most abundant plant phenolic natural products. PA biosynthesis is regulated by the well-documented MYB/bHLH/WD40 (MBW) complex, but how this complex itself is regulated remains ill defined. Here, in situ hybridization and β-glucuronidase staining show that APETALA2 (AP2), a well-defined regulator of flower and seed development, is strongly expressed in the seed coat endothelium, where PAs accumulate. AP2 negatively regulates PA content and expression levels of key PA pathway genes. AP2 activates MYBL2 transcription and interacts with MYBL2, a key suppressor of the PA pathway. AP2 exerts its function by directly binding to the AT-rich motifs near the promoter region of MYBL2. Molecular and biochemical analyses revealed that AP2 forms AP2-MYBL2-TT8/EGL3 complexes, disrupting the MBW complex and thereby repressing expression of ANR, TT12, TT19, and AHA10. Genetic analyses revealed that AP2 functions upstream of MYBL2, TT2, and TT8 in PA regulation. Our work reveals a new role of AP2 as a key regulator of PA biosynthesis in Arabidopsis. Overall, this study sheds new light on the comprehensive regulation network of PA biosynthesis as well as the dual regulatory roles of AP2 in seed development and accumulation of major secondary metabolites in Arabidopsis.

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.

Arabidopsis ABRE-binding factors modulate salinity-induced inhibition of root hair growth by interacting with and suppressing RHD6

Soil salinity causes crop losses worldwide. Root hairs are the primary targets of salt stress, however, the signaling networks involved in the precise regulation of root hair growth and development by salinity are poorly understood. Here, we confirmed that salt stress inhibits the number and length of root hairs in Arabidopsis. We found that the master regulator of root hair development and growth, the RHD6 transcription factor, is involved in this process, as salt treatment largely compromised root hair overaccumulation in RHD6-overexpressing plants. Yeast-two-hybrid and co-immunoprecipitation analyses revealed that RHD6 physically interacts with ABF proteins, the master transcription factors in abscisic acid signaling, which is involved in tolerance to several stresses including salinity. Phenotypic analyses showed that ABF proteins, which function upstream of RHD6, positively modulate the salinity-induced inhibition of root hair development. Further analyses showed that ABF3 suppresses the transcriptional activation activity of RHD6, thereby regulating the expression of genes related to root hair development. Overexpression of ABF3 reduced the root hair-overgrowing phenotype of RHD6-overexpressing plants. Collectively, our results demonstrate an essential signaling module in which ABF proteins directly suppress the transcriptional activation activity of RHD6 to reduce the length and number of root hairs under salt stress conditions.

Jasmonate-regulated root growth inhibition and root hair elongation

The phytohormone jasmonate is an essential endogenous signal in the regulation of multiple plant processes for environmental adaptation, such as primary root growth inhibition and root hair elongation. Perception of environmental stresses promotes the accumulation of jasmonate, which is sensed by the CORONATINE INSENSITIVE1 (COI1)-JASMONATE ZIM-DOMAIN (JAZ) co-receptor, triggering the degradation of JAZ repressors and induction of transcriptional reprogramming. The basic helix-loop-helix (bHLH) subgroup IIIe transcription factors MYC2, MYC3, and MYC4 are the most extensively characterized JAZ-binding factors and together stimulate jasmonate-signaled primary root growth inhibition. Conversely, the bHLH subgroup IIId transcription factors (i.e. bHLH3 and bHLH17) physically associate with JAZ proteins and suppress jasmonate-induced root growth inhibition. For root hair development, JAZ proteins interact with and inhibit ROOT HAIR DEFECTIVE 6 (RHD6) and RHD6 LIKE1 (RSL1) transcription factors to modulate jasmonate-enhanced root hair elongation. Moreover, jasmonate also interacts with other signaling pathways (such as ethylene and auxin) to regulate primary root growth and/or root hair elongation. Here, we review recent progress into jasmonate-mediated primary root growth and root hair development.

The roles of HD-ZIP proteins in plant abiotic stress tolerance

Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.

Structural insights into partner selection for MYB and bHLH transcription factor complexes

MYB and basic helix-loop-helix (bHLH) transcription factors form complexes to regulate diverse metabolic and developmental processes in plants. However, the molecular mechanisms responsible for MYB-bHLH interaction and partner selection remain unclear. Here, we report the crystal structures of three MYB-bHLH complexes (WER-EGL3, CPC-EGL3 and MYB29-MYC3), uncovering two MYB-bHLH interaction modes. WER and CPC are R2R3- and R3-type MYBs, respectively, but interact with EGL3 through their N-terminal R3 domain in a similar mode. A single amino acid of CPC, Met49, is crucial for competition with WER to interact with EGL3. MYB29, a R2R3-type MYB transcription factor, interacts with MYC3 by its C-terminal MYC-interaction motif. The WER-EGL3 and MYB29-MYC3 binding modes are widely applied among MYB-bHLH complexes in Arabidopsis and evolve independently in plants.

The rolB-transgenic Nicotiana tabacum plants exhibit upregulated ARF7 and ARF19 gene expression

Agrobacterium rhizogenes root oncogenic locus B (rolB) is known to induce hairy roots along with triggering several physiological and morphological changes when present as a transgene. However, it is still unknown how this gene triggers these changes within the plant system. In this study, the effect of rolB in-planta, when present as a transgene, was assessed on the gene expression levels of auxin response factors (ARFs)-transcription factors which are key players in auxin-mediated responses. The goal was to uncover Auxin/ARF-driven transcriptional networks potentially active and working selectively, if any, in rolB transgenic background, which might potentially be associated with hairy root development. Hence, the approach involved establishing rolB-transgenic Nicotiana tabacum plants, selecting ARFs (NtARFs) for context-relevance using bioinformatics followed by gene expression profiling. It was observed that out of the chosen NtARFs, NtARF7 and NtARF19 exhibited a consistent pattern of gene upregulation across organ types. In order to understand the significance of these selective gene upregulation, ontology-based transcriptional network maps of the differentially and nondifferentially expressed ARFs were constructed, guided by co-expression databases. The network maps suggested that NtARF7-NtARF19 might have major deterministic, underappreciated roles to play in root development in a rolB-transgenic background-as observed by higher number of "root-related" biological processes present as nodes compared to network maps for similarly constructed other non-differentially expressed ARFs. Based on the inferences drawn, it is hypothesized that rolB, when present as a transgene, might drive hairy root development by selective induction of NtARF7 and NtARF19, suggesting a functional link between the two, leading to the specialized and characteristic rolB-associated traits.

Short Peptides Induce Development of Root Hair Nicotiana tabacum

Root hairs absorb soil nutrients and water, and anchor the plant in the soil. Treatment of tobacco (Nicotiana tabacum) roots with glycine (Gly) amino acid, and glycilglycine (GlyGly) and glycilaspartic acid (GlyAsp) dipeptides (10⁻⁷ M concentration) significantly increased the development of root hairs. In the root, peptide accumulation was tissue-specific, with predominant localization to the root cap, meristem, elongation zone, and absorption zone. Peptides penetrated the epidermal and cortical cell and showed greater localization to the nucleus than to the cytoplasm. Compared with the control, tobacco plants grown in the presence of Gly, GlyGly, and GlyAsp exhibited the activation of WER, CPC, bHLH54, and bHLH66 genes and suppression of GTL1 and GL2 genes during root hair lengthening. Although Gly, GlyGly, and GlyAsp have a similar structure, the mechanism of regulation of root hair growth in each case were different, and these differences are most likely due to the fact that neutral Gly and GlyGly and negatively charged GlyAsp bind to different motives of functionally important proteins. Short peptides site-specifically interact with DNA, and histones. The molecular mechanisms underlying the effect of exogenous peptides on cellular processes remain unclear. Since these compounds acted at low concentrations, gene expression regulation by short peptides is most likely of epigenetic nature.

EIN3 and RSL4 interfere with an MYB-bHLH-WD40 complex to mediate ethylene-induced ectopic root hair formation in Arabidopsis

The alternating cell specifications of root epidermis to form hair cells or nonhair cells in Arabidopsis are determined by the expression level of GL2, which is activated by an MYB-bHLH-WD40 (WER-GL3-TTG1) transcriptional complex. The phytohormone ethylene (ET) has a unique effect of inducing N-position epidermal cells to form root hairs. However, the molecular mechanisms underlying ET-induced ectopic root hair development remain enigmatic. Here, we show that ET promotes ectopic root hair formation through down-regulation of GL2 expression. ET-activated transcription factors EIN3 and its homolog EIL1 mediate this regulation. Molecular and biochemical analyses further revealed that EIN3 physically interacts with TTG1 and interferes with the interaction between TTG1 and GL3, resulting in reduced activation of GL2 by the WER-GL3-TTG1 complex. Furthermore, we found through genetic analysis that the master regulator of root hair elongation, RSL4, which is directly activated by EIN3, also participates in ET-induced ectopic root hair development. RSL4 negatively regulates the expression of GL2, likely through a mechanism similar to that of EIN3. Therefore, our work reveals that EIN3 may inhibit gene expression by affecting the formation of transcription-activating protein complexes and suggests an unexpected mutual inhibition between the hair elongation factor, RSL4, and the hair specification factor, GL2. Overall, this study provides a molecular framework for the integration of ET signaling and intrinsic root hair development pathway in modulating root epidermal cell specification.

The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold

Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity, leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4. Furthermore, we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter. WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.

MYB30 and ETHYLENE INSENSITIVE3 antagonistically modulate root hair growth in Arabidopsis

Root hair (RH) is essential for plant nutrient acquisition and the plant-environment communication. Here we report that transcription factors MYB30 and ETHYLENE INSENSITIVE3 (EIN3) modulate RH growth/elongation in Arabidopsis in an antagonistic way. The MYB30 loss-of-function mutant displays enhanced RH length, whereas the RH elongation in MYB30-overexpressing plants is highly repressed. MYB30 physically interacts with EIN3, a master transcription factor in ethylene signaling. MYB30 directly binds the promoter region of ROOT HAIR DEFECTIVE SIX-LIKE4 (RSL4) and represses its transcription. RSL4 loss-of-function suppresses the enhanced RH growth in myb30 mutant plants. Ethylene enhances MYB30-EIN3 complex formation, and reduces the association between MYB30 and RSL4 promotor via the action of EIN3. MYB30 and EIN3 antagonistically regulate the expression of RSL4 and a subset of core RH genes in a genome-wide way. Taken together, our work revealed a novel transcriptional network that modulates RH growth in plants.

Epidermal cell-patterning genes of the stem parasitic plant Cuscuta campestris are involved in the development of holdfasts

Cuscuta campestris, a stem parasitic plant, commences its parasitic behavior by forming a specialized disk-like adhesive structure called a holdfast, which facilitates tight adhesion to the stem surface of the host plant. The morphology of epidermal cells in the holdfast is similar to that of the leaf trichome and root hairs of dicotyledonous plants. However, the regulatory network underlying the development of the holdfast has not been elucidated to date. In this study, we assessed the roles of epidermal cell-patterning genes in the development of a holdfast. Epidermal cell-patterning genes of C. campestris, including CcWER, CcGL3, CcTTG1, CcGL2, and CcJKD, were expressed slightly before the initiation of the outgrowth of stem epidermal cells. CcJKD-silencing repressed CcJKD, CcWER, CcGL3, CcTTG1, CcGL2; therefore, CcJKD is an upstream regulator of other epidermal cell-patterning genes. Unlike other genes, CcCPC was not upregulated after attachment to the host, and was not repressed by CcJKD-silencing. Protein interaction assays demonstrated that CcJKD interacted with CcTTG1 and CcCPC. Furthermore, CcJKD-silencing repressed the outgrowth of holdfast epidermal cells. Therefore, C. campestris invokes epidermal cell-patterning genes for the outgrowth of holdfast epidermal cells, and their regulatory mechanism is different from those for leaf trichome or root hairs.

Receptor-like Kinases in Root Development: Current Progress and Future Directions

Cell-to-cell and cell-to-environment communications are critical to the growth and development of plants. Cell surface-localized receptor-like kinases (RLKs) are mainly involved in sensing various extracellular signals to initiate their corresponding cellular responses. As important vegetative organs for higher plants to adapt to a terrestrial living situation, roots play a critical role for the survival of plants. It has been demonstrated that RLKs control many biological processes during root growth and development. In this review, we summarize several key regulatory processes during Arabidopsis root development in which RLKs play critical roles. We also put forward a number of relevant questions that are required to be explored in future studies.

Developmental phenotypes of Arabidopsis plants expressing phosphovariants of AtMYB75

The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is a well-established transcriptional activator of genes required for anthocyanin and flavonoid production, and a repressor of lignin and other secondary cell wall biosynthesis genes. MYB75 is itself tightly regulated at the transcriptional, translational and post-translational levels, including protein phosphorylation by Arabidopsis MAP kinases Examination of the behavior of different phosphovariant versions of MYB75 in vitro and in vivo revealed that overexpression of the MYB75^T131E phosphovariant had a particularly marked effect on global changes in gene expression suggesting that phosphorylated MYB75 could be involved in a broader range of functions than previously recognized. Here, we describe a range of distinct developmental phenotypes observed among Arabidopsis lines expressing various phosphovariant forms of MYB75. Expression of either MYB75^T131E or MYB75^T131A phosphovariants, from the endogenous MYB75 promoter, in Arabidopsis myb75^- mutants (Nossen background), resulted in severely impaired germination rates, and developmental arrest at early seedling stages. Arabidopsis plants overexpressing MYB75^T131E from a strong constitutive Cauliflower mosaic virus (CaMV35S) promoter displayed slower development, with delayed bolting, flowering and onset of senescence. Conversely, MYB75^T131A -overexpressing lines flowered and set seed earlier than either Col-0 WT controls or other MYB75-overexpressors (MYB75^WT and MYB75^T131E ). Histochemical analysis of mature stems also revealed ectopic vessel development in plants overexpressing MYB75; this phenotype was particularly prominent in the MYB75^T131E phosphovariant. These data suggest that MYB75 plays a significant role in plant development, and that this aspect of MYB75 function is influenced by its phosphorylation status.

Remodeling of Root Growth Under Combined Arsenic and Hypoxia Stress Is Linked to Nutrient Deprivation

Root architecture responds to environmental stress. Stress-induced metabolic and nutritional changes affect the endogenous root development program. Transcriptional and translational changes realize the switch between stem cell proliferation and cell differentiation, lateral root or root hair formation and root functionality for stress acclimation. The current work explores the effects of stress combination of arsenic toxicity (As) and hypoxia (Hpx) on root development in Arabidopsis thaliana. As revealed previously, combined As and Hpx treatment leads to severe nutritional disorder evident from deregulation of root transcriptome and plant mineral contents. Both As and Hpx were identified to pose stress-specific constraints on root development that lead to unique root growth phenotype under their combination. Besides inhibition of root apical meristem (RAM) activity under all stresses, As induced lateral root growth while root hair density and lengths were strongly increased by Hpx and HpxAs-treatments. A dual stimulation of phosphate (Pi)-starvation response was observed for HpxAs-treated plant roots; however, the response under HpxAs aligned more with Hpx than As. Transcriptional evidence along with biochemical data suggests involvement of PHOSPHATE STARVATION RESPONSE 1; PHR1-dependent systemic signaling. Pi metabolism-related transcripts in close association with cellular iron homeostasis modulate root development under HpxAs. Early redox potential changes in meristematic cells, differential ROS accumulation in root hair zone cell layers and strong deregulation of NADPH oxidases, NADPH-dependent oxidoreductases and peroxidases signify a role of redox and ROS signaling in root architecture remodeling under HpxAs. Differential aquaporin expression suggests transmembrane ROS transport to regulate root hair induction and growth. Reorganization of energy metabolism through NO-dependent alternate oxidase, lactate fermentation, and phosphofructokinase seems crucial under HpxAs. TOR and SnRK-signaling network components were potentially involved in control of sustainable utilization of available energy reserves for root hair growth under combined stress as well as recovery on reaeration. Findings are discussed in context of combined stress-induced signaling in regulation of root development in contrast to As and Hpx alone.

Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of Dryopteris fragrans (L.) Schott

Background: Dryopteris fragrans, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of D. fragrans were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild D. fragrans sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in D. fragrans. Conclusions: This study is the first report of global transcriptomic analysis in different tissues of D. fragrans, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of D. fragrans glandular trichomes.

A cell surface arabinogalactan-peptide influences root hair cell fate

Root hairs (RHs) develop from specialized epidermal trichoblast cells, whereas epidermal cells that lack RHs are known as atrichoblasts. The mechanism controlling RH cell fate is only partially understood. RH cell fate is regulated by a transcription factor complex that promotes the expression of the homeodomain protein GLABRA 2 (GL2), which blocks RH development by inhibiting ROOT HAIR DEFECTIVE 6 (RHD6). Suppression of GL2 expression activates RHD6, a series of downstream TFs including ROOT HAIR DEFECTIVE 6 LIKE-4 (RSL4) and their target genes, and causes epidermal cells to develop into RHs. Brassinosteroids (BRs) influence RH cell fate. In the absence of BRs, phosphorylated BIN2 (a Type-II GSK3-like kinase) inhibits a protein complex that regulates GL2 expression. Perturbation of the arabinogalactan peptide (AGP21) in Arabidopsis thaliana triggers aberrant RH development, similar to that observed in plants with defective BR signaling. We reveal that an O-glycosylated AGP21 peptide, which is positively regulated by BZR1, a transcription factor activated by BR signaling, affects RH cell fate by altering GL2 expression in a BIN2-dependent manner. Changes in cell surface AGP disrupts BR responses and inhibits the downstream effect of BIN2 on the RH repressor GL2 in root epidermis.

Molecular Basis for a Cell Fate Switch in Response to Impaired Ribosome Biogenesis in the Arabidopsis Root Epidermis

The Arabidopsis (Arabidopsis thaliana) root epidermis consists of a position-dependent pattern of root hair cells and non-hair cells. Underlying this cell type patterning is a network of transcription factors including a central MYB-basic helix-loop-helix-WD40 complex containing WEREWOLF (WER), GLABRA3 (GL3)/ENHANCER OF GLABRA3, and TRANSPARENT TESTA GLABRA1. In this study, we used a genetic enhancer screen to identify apum23-4, a mutant allele of the ribosome biogenesis factor (RBF) gene ARABIDOPSIS PUMILIO23 (APUM23), which caused prospective root hair cells to instead adopt the non-hair cell fate. We discovered that this cell fate switch relied on MYB23, a MYB protein encoded by a WER target gene and acting redundantly with WER. In the apum23-4 mutant, MYB23 exhibited ectopic expression that was WER independent and instead required ANAC082, a recently identified ribosomal stress response mediator. We examined additional RBF mutants that produced ectopic non-hair cells and determined that this cell fate switch is generally linked to defects in ribosome biogenesis. Furthermore, the flagellin peptide flg22 triggers the ANAC082-MYB23-GL2 pathway. Taken together, our study provides a molecular explanation for root epidermal cell fate switch in response to ribosomal defects and, more generally, it demonstrates a novel regulatory connection between stress conditions and cell fate control in plants.

Novel TTG1 Mutants Modify Root-Hair Pattern Formation in Arabidopsis

The patterning of root-hair and non-hair epidermal cells in the Arabidopsis root is governed by a network of transcriptional regulators. The central MYB-bHLH-WD40 (MBW) transcriptional complex includes the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1). To clarify the role of TTG1, we describe the identification and analysis of two new ttg1 mutants. Each of these mutants contains a single nucleotide change in the TTG1 gene, which causes a single amino-acid substitution in the predicted TTG1 protein and alters root-hair pattern formation. Surprisingly, these new ttg1 mutants exhibit decreased root-hair formation, particularly in the caprice (cpc) mutant background, rather than increased root-hair formation as reported for strong ttg1 mutants. We show that the unique phenotype of these mutants is due to differential effects of the altered TTG1 proteins on target gene expression, associated with a weakened ability to interact with its GLABRA3 bHLH partner. These findings demonstrate the crucial role of TTG1 for the appropriate balance of target gene activation to achieve the proper pattern of epidermal cell types during Arabidopsis root development.

Arabidopsis JAZ Proteins Interact with and Suppress RHD6 Transcription Factor to Regulate Jasmonate-Stimulated Root Hair Development

Root hairs arise from trichoblasts and are crucial for plant anchorage, nutrient acquisition, and environmental interactions. The phytohormone jasmonate is known to regulate root hair development in Arabidopsis (Arabidopsis thaliana), but little is known about the molecular mechanism underlying jasmonate modulation in this process. Here, we show that the application of exogenous jasmonate significantly stimulated root hair elongation, but, on the contrary, blocking the perception or signaling of jasmonate resulted in defective root hairs. Jasmonate consistently elevated the expression levels of several crucial genes positively involved in root hair growth. Mechanistic investigation revealed that JASMONATE ZIM-DOMAIN (JAZ) proteins, critical repressors of jasmonate signaling, physically interacted with ROOT HAIR DEFECTIVE 6 (RHD6) and RHD6 LIKE1 (RSL1), two transcription factors that are essential for root hair development. JAZ proteins inhibited the transcriptional function of RHD6 and interfered with the interaction of RHD6 with RSL1. Genetic analysis indicated that jasmonate promoted root hair growth in a RHD6/RSL1-dependent manner. Moreover, overexpression of RHD6 largely rescued the root hair defects of JAZ-accumulating plants. Collectively, our study reveals a key signaling module in which JAZ repressors of the jasmonate pathway directly modulate RHD6 and RSL1 transcription factors to integrate jasmonate signaling and the root hair developmental process.

Overexpression of three related root-cap outermost-cell-specific C2H2-type zinc-finger protein genes suppresses the growth of Arabidopsis in an EAR-motif-dependent manner

The root meristem of Arabidopsis thaliana is protected by the root cap, the size of which is tightly regulated by the balance between the formative cell divisions and the dispersal of the outermost cells. We isolated an enhancer-tagged dominant mutant displaying the short and twisted root by the overexpression of ZINC-FINGER OF ARABIDOPSIS THALIANA1 (ZAT1) encoding an EAR motif-containing zinc-finger protein. The growth inhibition by ZAT1 was shared by ZAT4 and ZAT9, the ZAT1 homologues. The ZAT1 promoter was specifically active in the outermost cells of the root cap, in which ZAT1-GFP was localized when expressed by the ZAT1 promoter. The outermost cell-specific expression pattern of ZAT1 was not altered in the sombrero (smb) or smb bearskin1 (brn1) brn2 accumulating additional root-cap layers. In contrast, ZAT4-GFP and ZAT9- GFP fusion proteins were distributed to the inner root-cap cells in addition to the outermost cells where ZAT4 and ZAT9 promoters were active. Overexpression of ZAT1 induced the ectopic expression of PUTATIVE ASPARTIC PROTEASE3 involved in the programmed cell death. The EAR motif was essential for the growth inhibition by ZAT1. These results suggest that the three related ZATs might regulate the maturation of the outermost cells of the root cap.

Structural insights into target DNA recognition by R2R3-MYB transcription factors

As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein, in complex with its target DNA. Structural analysis showed that the third α-helices in both the R2 and R3 repeats of WER fit in the major groove of the DNA, specifically recognizing the DNA motif 5'-AACNGC-3'. In combination with mutagenesis, in vitro binding and in vivo luciferase assays, we showed that K55, N106, K109 and N110 are critical for the function of WER. Although L59 of WER is not involved in DNA binding in the structure, ITC analysis suggested that L59 plays an important role in sensing DNA methylation at the fifth position of cytosine (5mC). Like 5mC, methylation at the sixth position of adenine (6mA) in the AAC element also inhibits the interaction between WER and its target DNA. Our study not only unravels the molecular basis of how WER recognizes its target DNA, but also suggests that 5mC and 6mA modifications may block the interaction between R2R3-MYB transcription factors and their target genes.

Modulatory Role of Reactive Oxygen Species in Root Development in Model Plant of Arabidopsis thaliana

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, have a higher chemical activity than O₂. Although ROS pose potential risks to all organisms via inducing oxidative stress, indispensable role of ROS in individual development cannot be ignored. Among them, the role of ROS in the model plant Arabidopsis thaliana is deeply studied. Mounting evidence suggests that ROS are essential for root and root hair development. In the present review, we provide an updated perspective on the latest research progress pertaining to the role of ROS in the precise regulation of root stem cell maintenance and differentiation, redox regulation of the cell cycle, and root hair initiation during root growth. Among the different types of ROS, O₂ ^•- and H₂O₂ have been extensively investigated, and they exhibit different gradient distributions in the roots. The concentration of O₂ ^•- decreases along a gradient from the meristem to the transition zone and the concentration of H₂O₂ decreases along a gradient from the differentiation zone to the elongation zone. These gradients are regulated by peroxidases, which are modulated by the UPBEAT1 (UPB1) transcription factor. In addition, multiple transcriptional factors, such as APP1, ABO8, PHB3, and RITF1, which are involved in the brassinolide signaling pathway, converge as a ROS signal to regulate root stem cell maintenance. Furthermore, superoxide anions (O₂ ^•-) are generated from the oxidation in mitochondria, ROS produced during plasmid metabolism, H₂O₂ produced in apoplasts, and catalysis of respiratory burst oxidase homolog (RBOH) in the cell membrane. Furthermore, ROS can act as a signal to regulate redox status, which regulates the expression of the cell-cycle components CYC2;3, CYCB1;1, and retinoblastoma-related protein, thereby controlling the cell-cycle progression. In the root maturation zone, the epidermal cells located in the H cell position emerge to form hair cells, and plant hormones, such as auxin and ethylene regulate root hair formation via ROS. Furthermore, ROS accumulation can influence hormone signal transduction and vice versa. Data about the association between nutrient stress and ROS signals in root hair development are scarce. However, the fact that ROBHC/RHD2 or RHD6 is specifically expressed in root hair cells and induced by nutrients, may explain the relationship. Future studies should focus on the regulatory mechanisms underlying root hair development via the interactions of ROS with hormone signals and nutrient components.

Root Epidermal Cell Patterning Is Modulated by a Critical Residue in the WEREWOLF Transcription Factor

The Arabidopsis (Arabidopsis thaliana) root epidermis exhibits a position-dependent pattern of root-hair and nonhair cell types. A highly orchestrated network of gene regulatory interactions, including the R2R3-type MYB transcription factor WEREWOLF (WER), is responsible for generating this cell pattern during root development. In this study, we identified a novel wer mutant from a genetic enhancer screen, designated wer-4, that exhibits an abnormal pattern of root-hair and nonhair cells. We established that wer-4 bears a single-residue substitution (D105N) in the DNA-binding R3 MYB repeat of WER, which differentially affects the transcription of WER target genes, including GLABRA2, CAPRICE, TRIPTYCHON, and ENHANCER OF TRY AND CPC1 This modulation of the gene regulatory network leads to altered levels and distributions of cell fate regulators in the differentiating epidermal cells that ultimately generate the abnormal cell-type pattern. We also created several WER variants with substitutions at the Asp-105 position, and these exhibited a variety of gene expression and cell-type pattern alterations, further supporting the critical role of this residue. These findings provide insight into WER protein function and its importance in generating the proper balance of downstream transcriptional factors in the gene regulatory network that establishes root epidermal cell fate.

Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus

Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.

Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus

Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.

Root hairs enhance Arabidopsis seedling survival upon soil disruption

Root hairs form a substantial portion of the root surface area. Compared with their nutritional function, the physical function of root hairs has been poorly characterised. This study investigates the physical role of root hairs of Arabidopsis thaliana seedlings in interaction of the root with water and soil and in plant survival upon soil disruption. Five transgenic lines with different root hair lengths were used to assess the physical function of root hairs. Upon soil disruption by water falling from a height (mimicking rainfall), long-haired lines showed much higher anchorage rates than short-haired lines. The root-pulling test revealed that a greater amount of soil adhered to long-haired roots than to short-haired roots. When seedlings were pulled out and laid on the soil surface for 15 d, survival rates of long-haired seedlings were higher than those of short-haired seedlings. Moreover, the water holding capacity of roots was much greater among long-haired seedlings than short-haired seedlings. These results suggest that root hairs play a significant role in plant survival upon soil disruption which could be fatal for young seedlings growing on thin soil surface with a short primary root and root hairs as the only soil anchoring system.

Contribution of Root Hair Development to Sulfate Uptake in Arabidopsis

Root hairs often contribute to nutrient uptake from environments, but the contribution varies among nutrients. In Arabidopsis, two high-affinity sulfate transporters, SULTR1;1 and SULTR1;2, are responsible for sulfate uptake by roots. Their increased expression under sulfur deficiency (-S) stimulates sulfate uptake. Inspired by the higher and lower expression, respectively, of SULTR1;1 in mutants with more (werwolf [wer]) and fewer (caprice [cpc]) root hairs, we examined the contribution of root hairs to sulfate uptake. Sulfate uptake rates were similar among plant lines under both sulfur sufficiency (+S) and -S. Under -S, the expression of SULTR1;1 and SULTR1;2 was negatively correlated with the number of root hairs. These results suggest that both -S-induced SULTR expression and sulfate uptake rates were independent of the number of root hairs. In addition, we observed (1) a negative correlation between primary root lengths and number of root hairs and (2) a greater number of root hairs under -S than under +S. These observations suggested that under both +S and -S, sulfate uptake was influenced by the root biomass rather than the number of root hairs.

QUIRKY regulates root epidermal cell patterning through stabilizing SCRAMBLED to control CAPRICE movement in Arabidopsis

SCM, a leucine-rich repeat receptor-like kinase, is required for root epidermal cells to appropriately interpret their location and generate the proper cell-type pattern during Arabidopsis root development. Here, via a screen for scm-like mutants we describe a new allele of the QKY gene. We find that QKY is required for the appropriate spatial expression of several epidermal cell fate regulators in a similar manner as SCM in roots, and that QKY and SCM are necessary for the efficient movement of CPC between epidermal cells. We also show that turnover of SCM is mediated by a vacuolar degradation pathway triggered by ubiquitination, and that QKY prevents this SCM ubiquitination through their physical interaction. These results suggest that QKY stabilizes SCM through interaction, and this complex facilitates CPC movement between the epidermal cells to help establish the cell-type pattern in the Arabidopsis root epidermis.

SCM is a receptor-like kinase that ensures proper root patterning. Here, Song et al. find that SCM promotes the movement of CPC from non-hair cells to neighboring root epidermal cells and identify QKY as an additional facilitator of CPC mobility that acts by preventing vacuolar degradation of SCM.

Receptor-like protein kinases: Key regulators controlling root hair development in Arabidopsis thaliana

Root hairs are tubular outgrowths specifically differentiated from epidermal cells in a differentiation zone. The formation of root hairs greatly increases the surface area of a root and maximizes its ability to absorb water and inorganic nutrients essential for plant growth and development. Root hair development is strictly regulated by intracellular and intercellular signal communications. Cell surface-localized receptor-like protein kinases (RLKs) have been shown to be important components in these cellular processes. In this review, the functions of a number of key RLKs in regulating Arabidopsis root hair development are discussed, especially those involved in root epidermal cell fate determination and root hair tip growth.

Regulation and functional diversification of root hairs

Root hairs result from the polar outgrowth of root epidermis cells in vascular plants. Root hair development processes are regulated by intrinsic genetic programs, which are flexibly modulated by environmental conditions, such as nutrient availability. Basic programs for root hair development were present in early land plants. Subsequently, some plants developed the ability to utilize root hairs for specific functions, in particular, for interactions with other organisms, such as legume-rhizobia and host plants-parasites interactions. In this review, we summarize the molecular regulation of root hair development and the modulation of root hairs under limited nutrient supply and during interactions with other organisms.

The Histone Chaperone NRP1 Interacts with WEREWOLF to Activate GLABRA2 in Arabidopsis Root Hair Development

NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss of function of the Arabidopsis thaliana NAP1 family genes NAP1-RELATED PROTEIN1 (NRP1) and NRP2 causes abnormal root hair formation. Yet, the underlying molecular mechanisms remain unclear. Here, we show that NRP1 interacts with the transcription factor WEREWOLF (WER) in vitro and in vivo and enriches at the GLABRA2 (GL2) promoter in a WER-dependent manner. Crystallographic analysis indicates that NRP1 forms a dimer via its N-terminal α-helix. Mutants of NRP1 that either disrupt the α-helix dimerization or remove the C-terminal acidic tail, impair its binding to histones and WER and concomitantly lead to failure to activate GL2 transcription and to rescue the nrp1-1 nrp2-1 mutant phenotype. Our results further demonstrate that WER-dependent enrichment of NRP1 at the GL2 promoter is involved in local histone eviction and nucleosome loss in vivo. Biochemical competition assays imply that the association between NRP1 and histones may counteract the inhibitory effect of histones on the WER-DNA interaction. Collectively, our study provides important insight into the molecular mechanisms by which histone chaperones are recruited to target chromatin via interaction with a gene-specific transcription factor to moderate chromatin structure for proper root hair development.

A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in Arabidopsis mesophyll protoplasts

BACKGROUND

Binding of transcription factors to their target sequences is a primary step in the regulation of gene expression and largely determines gene regulatory networks. Chromatin immunoprecipitation (ChIP) is an indispensable tool used to investigate the binding of DNA-binding proteins (e.g., transcription factors) to their target sequences in vivo. ChIP assays require specific antibodies that recognize endogenous target transcription factors; however, in most cases, such specific antibodies are unavailable. To overcome this problem, many ChIP assays use transgenic plants that express epitope-tagged transcription factors and immunoprecipitate the protein with a tag-specific antibody. However, generating transgenic plants that stably express epitope-tagged proteins is difficult and time-consuming.

RESULTS

Here, we present a rapid, efficient ChIP protocol using transient expression in Arabidopsis mesophyll protoplasts that can be completed in 4 days. We provide optimized experimental conditions, including the amount of transfected DNA and the number of protoplasts. We also show that the efficiency of our ChIP protocol using protoplasts is comparable to that obtained using transgenic Arabidopsis plants. We propose that our ChIP method can be used to analyze in vivo interactions between tissue-specific transcription factors and their target sequences, to test the effect of genotype on the binding of a transcription factor within a protein complex to its target sequences, and to measure temperature-dependent binding of a transcription factor to its target sequence.

CONCLUSIONS

The rapid and simple nature of our ChIP assay using Arabidopsis mesophyll protoplasts facilitates the investigation of in vivo interactions between transcription factors and their target genes.

Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots

Development of the functional endodermis of Arabidopsis thaliana roots is controlled, in part, by GRAS transcription factors, namely SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE 23 (SCL23). Recently, it has been shown that the SHR-SCR-SCL23 regulatory module is also essential for specification of the endodermis (known as the bundle sheath) in leaves. Nevertheless, compared with what is known about the role of the SHR-SCR-SCL23 regulatory network in roots, the molecular interactions of SHR, SCR, and SCL23 are much less understood in shoots. Here, we show that SHR forms protein complexes with SCL23 to regulate transcription of SCL23 in shoots, similar to the regulation mode of SCR expression. Our results indicate that SHR acts as master regulator to directly activate the expression of SCR and SCL23. In the SHR-SCR-SCL23 network, we found a previously uncharacterized negative feedback loop whereby SCL23 modulates SHR levels. Through molecular, genetic, physiological, and morphological analyses, we also reveal that the SHR-SCR-SCL23 module plays a key role in the formation of the endodermis (known as the starch sheath) in hypocotyls. Taken together, our results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots.

The regulation and plasticity of root hair patterning and morphogenesis

Root hairs are highly specialized cells found in the epidermis of plant roots that play a key role in providing the plant with water and mineral nutrients. Root hairs have been used as a model system for understanding both cell fate determination and the morphogenetic plasticity of cell differentiation. Indeed, many studies have shown that the fate of root epidermal cells, which differentiate into either root hair or non-hair cells, is determined by a complex interplay of intrinsic and extrinsic cues that results in a predictable but highly plastic pattern of epidermal cells that can vary in shape, size and function. Here, we review these studies and discuss recent evidence suggesting that environmental information can be integrated at multiple points in the root hair morphogenetic pathway and affects multifaceted processes at the chromatin, transcriptional and post-transcriptional levels.

Brassinosteroids Regulate Root Growth, Development, and Symbiosis

Brassinosteroids (BRs) are natural plant hormones critical for growth and development. BR deficient or signaling mutants show significantly shortened root phenotypes. However, for a long time, it was thought that these phenotypes were solely caused by reduced cell elongation in the mutant roots. Functions of BRs in regulating root development have been largely neglected. Nonetheless, recent detailed analyses, revealed that BRs are not only involved in root cell elongation but are also involved in many aspects of root development, such as maintenance of meristem size, root hair formation, lateral root initiation, gravitropic response, mycorrhiza formation, and nodulation in legume species. In this review, current findings on the functions of BRs in mediating root growth, development, and symbiosis are discussed.

WEREWOLF and ENHANCER of GLABRA3 are interdependent regulators of the spatial expression pattern of GLABRA2 in Arabidopsis

In multicellular organisms, cell fates are specified through differential regulation of transcription. Epidermal cell fates in the Arabidopsis thaliana root are precisely specified by several transcription factors, with the GLABRA2 (GL2) homeodomain protein acting at the farthest downstream in this process. To better understand the regulation of GL2 expression, we ectopically expressed WEREWOLF (WER) and ENHANCER OF GLABRA3 (EGL3) in various tissues and examined GL2 expression. Here we show that WER expressed ubiquitously in the root induced GL2 expression only in the root epidermis, whereas co-expression of WER and EGL3 induced GL2 expression in the corresponding tissues. We also found that GL3 accumulated in the nucleus at the early meristematic region and EGL3 accumulated later in the nucleus of epidermal cells. We further found that ectopic expression of WER and EGL3 in ground tissues inhibited GL2 expression in the epidermis. Our results suggest that the co-expression of WER and EGL3 is sufficient for driving GL2 and CPC expression.

Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast

The control of growth and development of all living organisms is a complex and dynamic process that requires the harmonious expression of numerous genes. Gene expression is mainly controlled by the activity of sequence-specific DNA binding proteins called transcription factors (TFs). Amongst the various classes of eukaryotic TFs, the MYB superfamily is one of the largest and most diverse, and it has considerably expanded in the plant kingdom. R2R3-MYBs have been extensively studied over the last 15 years. However, DNA-binding specificity has been characterized for only a small subset of these proteins. Therefore, one of the remaining challenges is the exhaustive characterization of the DNA-binding specificity of all R2R3-MYB proteins. In this study, we have developed a library of Arabidopsis thaliana R2R3-MYB open reading frames, whose DNA-binding activities were assayed in vivo (yeast one-hybrid experiments) with a pool of selected cis-regulatory elements. Altogether 1904 interactions were assayed leading to the discovery of specific patterns of interactions between the various R2R3-MYB subgroups and their DNA target sequences and to the identification of key features that govern these interactions. The present work provides a comprehensive in vivo analysis of R2R3-MYB binding activities that should help in predicting new DNA motifs and identifying new putative target genes for each member of this very large family of TFs. In a broader perspective, the generated data will help to better understand how TF interact with their target DNA sequences.

ANGUSTIFOLIA mediates one of the multiple SCRAMBLED signaling pathways regulating cell growth pattern in Arabidopsis thaliana

In Arabidopsis thaliana, an atypical leucine-rich repeat receptor-like kinase, SCRAMBLED (SCM), is required for multiple developmental processes including root epidermal cell fate determination, silique dehiscence, inflorescence growth, ovule morphogenesis, and tissue morphology. Previous work suggested that SCM regulates these multiple pathways using distinct mechanisms via interactions with specific downstream factors. ANGUSTIFOLIA (AN) is known to regulate cell and tissue morphogenesis by influencing cortical microtubule arrangement, and recently, the AN protein was reported to interact with the SCM protein. Therefore, we examined whether AN might be responsible for mediating some of the SCM-dependent phenotypes. We discovered that both scm and an mutant lines cause an abnormal spiral or twisting growth of roots, but only the scm mutant affected root epidermal patterning. The siliques of the an and scm mutants also exhibited spiral growth, as previously reported, but only the scm mutant altered silique dehiscence. Interestingly, we discovered that the spiral growth of roots and siliques of the scm mutant is rescued by a truncated SCM protein that lacks its kinase domain, and that a juxtamembrane domain of SCM was sufficient for AN binding in the yeast two-hybrid analysis. These results suggest that the AN protein is one of the critical downstream factors of SCM pathways specifically responsible for mediating its effects on cell/tissue morphogenesis through cortical microtubule arrangement.

Intercellular protein movement: deciphering the language of development

Development in multicellular organisms requires the coordinated production of a large number of specialized cell types through sophisticated signaling mechanisms. Non-cell-autonomous signals are one of the key mechanisms by which organisms coordinate development. In plants, intercellular movement of transcription factors and other mobile signals, such as hormones and peptides, is essential for normal development. Through a combination of different approaches, a large number of non-cell-autonomous signals that control plant development have been identified. We review some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development. We also review current models for how mobile signals move via plasmodesmata and how movement is inhibited. Finally, we consider challenges in and new tools for studying protein movement.

The phenylpropanoid pathway is controlled at different branches by a set of R2R3-MYB C2 repressors in grapevine

Because of the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatiotemporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and basic helix-loop-helix protein families. We characterized four grapevine (Vitis vinifera) R2R3-MYB proteins from the C2 repressor motif clade, all of which harbor the ethylene response factor-associated amphiphilic repression domain but differ in the presence of an additional TLLLFR repression motif found in the strong flavonoid repressor Arabidopsis (Arabidopsis thaliana) AtMYBL2. Constitutive expression of VvMYB4a and VvMYB4b in petunia (Petunia hybrida) repressed general phenylpropanoid biosynthetic genes and selectively reduced the amount of small-weight phenolic compounds. Conversely, transgenic petunia lines expressing VvMYBC2-L1 and VvMYBC2-L3 showed a severe reduction in petal anthocyanins and seed proanthocyanidins together with a higher pH of crude petal extracts. The distinct function of these regulators was further confirmed by transient expression in tobacco (Nicotiana benthamiana) leaves and grapevine plantlets. Finally, VvMYBC2-L3 was ectopically expressed in grapevine hairy roots, showing a reduction in proanthocyanidin content together with the down-regulation of structural and regulatory genes of the flavonoid pathway as revealed by a transcriptomic analysis. The physiological role of these repressors was inferred by combining the results of the functional analyses and their expression patterns in grapevine during development and in response to ultraviolet B radiation. Our results indicate that VvMYB4a and VvMYB4b may play a key role in negatively regulating the synthesis of small-weight phenolic compounds, whereas VvMYBC2-L1 and VvMYBC2-L3 may additionally fine tune flavonoid levels, balancing the inductive effects of transcriptional activators.

Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes

Flavonoids are widely known for the colors they confer to plant tissues, their contribution to plant fitness and health benefits, and impact on food quality. As convenient biological markers, flavonoids have been instrumental in major genetic and epigenetic discoveries. We review recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis, with a special focus on the MBW (MYB-bHLH-WDR) protein complexes. These proteins are well conserved in higher plants. They participate in different types of controls ranging from fine-tuned transcriptional regulation by environmental factors to the initiation of the flavonoid biosynthesis pathway by positive regulatory feedback. The MBW protein complexes provide interesting models for investigating developmentally or environmentally controlled transcriptional regulatory networks.