Functional analysis of the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis

Genome-wide identification of R2R3-MYB family genes and gene response to stress in ginger

Ginger (Zingiber officinale Roscoe) is an important plant used worldwide for medicine and food. The R2R3-MYB transcription factor (TF) family has essential roles in plant growth, development, and stresses resistance, and the number of genes in the family varies greatly among different types of plants. However, genome-wide discovery of ZoMYBs and gene responses to stresses have not been reported in ginger. Therefore, genome-wide analysis of R2R3-MYB genes in ginger was conducted in this study. Protein phylogenetic relations and conserved motifs and chromosome localization and duplication, structure, and cis-regulatory elements were analyzed. In addition, the expression patterns of selected genes were analyzed under two different stresses. A total of 299 candidate ZoMYB genes were discovered in ginger. Based on groupings of R2R3-MYB genes in the model plant Arabidopsis thaliana (L.) Heynh., ZoMYBs were divided into eight groups. Genes were distributed across 22 chromosomes at uneven densities. In gene duplication analysis, 120 segmental duplications were identified in the ginger genome. Gene expression patterns of 10 ZoMYBs in leaves of ginger under abscisic acid (ABA) and low-temperature stress treatments were different. The results will help to determine the exact roles of ZoMYBs in anti-stress responses in ginger.

A signal R3-type, CAPRICE-like MYB transcription factor from Dendrobium nobile controls trichome and root-hair development in Arabidopsis

The CAPRICE-like MYB transcription factors with R3 MYB motif play a central role in regulating trichome and root-hair development in plants. We identified the homologous gene of ENHANCER OF TRY AND CPC (ETC) in Arabidopsis from Dendrobium nobile Lindl with full cDNA sequence and genomic sequence (CAPRICE-LIKE MYB, DnCPL and DngCPL) respectively. Phylogenic analyses revealed a close relationship of CAPRICE-like MYB TFs between D. nobile and A. thaliana. Promoter analysis indicated that DnCPL is specifically expressed in trichome basal cells of leaf epidermis and root hairs. Overexpression of DnCPL results in the suppression of trichome formation and overproduction of root hairs. In transgenic plants overexpressing DnCPL and DngCPL, trichome formation was inhibited, moreover, no trichomes were observed in tissues of aerial parts, and root-hair differentiation was significantly enhanced by strongly repressing endogenous genes of AtCPC, AtTCL1, and AtTCL2 expression, thereby enhancing AtTRY expression. The DnCPL RNAi plants formed fewer lateral roots with a corresponding change in AtCPC, AtTCL1 and AtTCL2 expression. These results suggest that Dendrobium and Arabidopsis partially use similar transcription factors for epidermal cell differentiation and the CPC-like R3 MYB, DnCPL, may be a key common regulator of plant trichome and root-hair development. The results also provided genes and means of regulation to improve the survival ratio of artificially cultivated Dendrobium with more lateral roots.

Persulfidation of transcription factor MYB10 inhibits anthocyanin synthesis in red-skinned pear

Hydrogen sulfide (H2S) is a gaseous signaling molecule that delays color change during fruit ripening. Whether H2S affects anthocyanin biosynthesis in red-skinned pears (Pyrus L.) remains unclear. Here, we found that H2S substantially inhibits anthocyanin accumulation in red-skinned pears and the expression of several genes encoding transcription factors is affected in response to H2S signaling. For example, PyMYB10 and PyMYB73 were down-regulated, whereas PyMYB114 and PyMYB6 were up-regulated. Bioinformatics analysis showed that PyMYB73 and PyMYB6, each containing an EAR motif, may negatively regulate anthocyanin accumulation. Transient expression analysis showed that PyMYB73 substantially promotes anthocyanin biosynthesis by co-transforming with PyMYB10/PyMYB114 + PybHLH3; however, PyMYB6 inhibited anthocyanin biosynthesis in strawberry (Fragaria vesca) receptacles and pear fruits, and PyMYB73 interacted with PyMYB10 and PyMYB6 but not PyMYB114 or PybHLH3. Further investigation showed that Cys194 and Cys218 of PyMYB10 were modified by persulfidation and that PyMYB10Cys218Ala substantially increased anthocyanin accumulation by a transient transformation system. Co-transformation of PyMYB10Cys218Ala + PyMYB73/PyMYB6 also promoted anthocyanin accumulation in pear fruits. Yeast two-hybrid assays showed that the mutation of PyMYB10 did not affect the interaction between PyMYB10 and PyMYB73, but it inhibited interaction with PyMYB6. Moreover, H2S weakened the interaction between PyMYB10 and PyMYB73 but enhanced the interaction with PyMYB6. Thus, we provided a model in which PyMYB10 undergoes persulfidation at Cys218, enhancing the interaction with PyMYB6 and reducing the interaction with PyMYB73. These subsequently results in lower expression of the anthocyanin biosynthesis-related genes Pyrus dihydroflavonol 4-reductase (PyDFR), Pyrus anthocyanidin synthase (PyANS), Pyrus UDP-glucose: flavonoid 3-glucosyl transferase (PyUFGT) and Pyrus glutathione S-transferase (PyGST), thereby inhibiting anthocyanin accumulation in red-skinned pears. Our findings provided a molecular mechanism for H2S-mediated anthocyanin biosynthesis in red-skinned pears.

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.

Complementation and protein localization analyses of R3 MYBs in an Arabidopsis caprice mutant

Root hairs play vital roles in plant growth since they enable the efficient absorption of water and nutrients from the soil. Recent advances in Arabidopsis research have provided a deeper understanding of the molecular genetic mechanisms underlying root hair differentiation. CAPRICE (CPC) and its four homologs, which belong to the CPC gene family and encode R3 MYB transcription factors, play central roles in root hair differentiation. In this study, to better understand the functional specificity and contribution of these five CPC family genes, we conducted phenotypic and expression analyses of the CPC family proteins in a cpc mutant background. As a result, ENHANCER OF TRY AND CPC1 (ETC1) and ETC3 were found to complement the hairless root phenotype of the cpc mutant, as did CPC, whereas TRIPTYCHON (TRY) and ETC2 did not rescue the cpc phenotype. Protein expression analysis revealed that GFP fluorescence was nearly undetectable in pCPC::TRY:GFP/cpc and pCPC::ETC2:GFP/cpc plants, supporting the incapability of root hair formation in these plants. Interestingly, the fluorescence intensity of the CPC:GFP fusion protein was weaker than that of ETC1:GFP and ETC3:GFP fusion proteins. These results were inconsistent with the result of the phenotypic analysis, in which the three genes promoted root hair formation to almost the same degree in the cpc mutant background. We further discuss the discrepancy between the root hair phenotypes and the expression levels of CPC family proteins.

Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea (Camellia gymnogyna Chang) under red light quality

As the formation of adventitious roots (AR) is an important component of in vitro regeneration of tea plants, the propagation and preservation of Huangshan Bitter tea (Camellia gymnogyna Chang) cuttings have been hindered due to its lower rooting rate. As light is a crucial environmental factor that affects AR formation, this study aimed to investigate the special role of red light (RL) in the formation of AR in Huangshan Bitter tea plants, which has not been well understood. Huangshan Bitter tea plants were induced with white light (control, WL) and red light (660 nm, RL) qualities 36 days after induced treatment (DAI) to investigate dynamic AR formation and development, anatomical observation, hormones content change, and weighted gene co-expression network analysis (WGCNA) of the transcriptome. Results showed that RL promoted the rooting rate and root characteristics compared to WL. Anatomical observations demonstrated that root primordium was induced earlier by RL at the 4 DAI. RL positively affected IAA, ZT and GA₃ content and negatively influenced ABA from the 4 to 16 DAI. RNA-seq and analysis of differential expression genes (DEGs) exhibited extensive variation in gene expression profiles between RL and WL. Meanwhile, the results of WGCNA and correlation analysis identified three highly correlated modules and hub genes mainly participated in 'response to hormone', 'cellular glucan metabolic progress', and 'response to auxin'. Furthermore, the proportion of transcription factors (TFs) such as ethylene response factor (ERF), myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WRKYGQK (WRKY) were the top four in DEGs. These results suggested that the AR-promoting potential of red light was due to complex hormone interactions in tea plants by regulating the expression of related genes. This study provided an important reference to shorten breeding cycles and accelerate superiority in tea plant propagation and preservation.

Uncovering the involvement of DoDELLA1-interacting proteins in development by characterizing the DoDELLA gene family in Dendrobium officinale

BACKGROUND

Gibberellins (GAs) are widely involved in plant growth and development. DELLA proteins are key regulators of plant development and a negative regulatory factor of GA. Dendrobium officinale is a valuable traditional Chinese medicine, but little is known about D. officinale DELLA proteins. Assessing the function of D. officinale DELLA proteins would provide an understanding of their roles in this orchid's development.

RESULTS

In this study, the D. officinale DELLA gene family was identified. The function of DoDELLA1 was analyzed in detail. qRT-PCR analysis showed that the expression levels of all DoDELLA genes were significantly up-regulated in multiple shoots and GA3-treated leaves. DoDELLA1 and DoDELLA3 were significantly up-regulated in response to salt stress but were significantly down-regulated under drought stress. DoDELLA1 was localized in the nucleus. A strong interaction was observed between DoDELLA1 and DoMYB39 or DoMYB308, but a weak interaction with DoWAT1.

CONCLUSIONS

In D. officinale, a developmental regulatory network involves a close link between DELLA and other key proteins in this orchid's life cycle. DELLA plays a crucial role in D. officinale development.

Genome-Scale Identification, Classification, and Expression Profiling of MYB Transcription Factor Genes in Cinnamomum camphora

The camphor tree (Cinnamomum camphora (L.) Presl.) is the representative species of subtropical evergreen broadleaved forests in eastern Asia and an important raw material for essential oil production worldwide. Although MYBs have been comprehensively characterized and their functions have been partially resolved in many plants, it has not been explored in C. camphora. In this study, 121 CcMYBs were identified on 12 chromosomes in the whole genome of C. camphora and found that CcMYBs were mainly expanded by segmental duplication. They were divided into 28 subgroups based on phylogenetic analysis and gene structural characteristics. In the promoter regions, numerous cis-acting elements were related to biological processes. Analysis of RNA sequencing data from seven tissues showed that CcMYBs exhibited different expression profiles, suggesting that they have various roles in camphor tree development. In addition, combined with the correlation analysis of structural genes in the flavonoid synthesis pathway, we identified CcMYBs from three subgroups that might be related to the flavonoid biosynthesis pathway. This study systematically analyzed CcMYBs in C. camphora, which will set the stage for subsequent research on the functions of CcMYBs during their lifetime and provide valuable insights for the genetic improvement of camphor trees.

LbMYB48 positively regulates salt gland development of Limonium bicolor and salt tolerance of plants

Limonium bicolor is a dicotyledonous recretohalophyte with several multicellular salt glands on the leaves. The plant can directly secrete excess salt onto the leaf surface through the salt glands to maintain ion homeostasis under salt stress. Therefore, it is of great significance to study the functions of genes related to salt gland development and salt tolerance. In this study, an R1-type MYB transcription factor gene was screened from L. bicolor, named LbMYB48, and its expression was strongly induced by salt stress. Subcellular localization analysis showed that LbMYB48 was localized in the nucleus. LbMYB48 protein has transcriptional activation activity shown by transcriptional activation experiments. The density of salt glands in the leaves and the salt secretion capacity of LbMYB48-silenced lines were decremented, as demonstrated by the leaf disc method to detect sodium ion secretion. Furthermore, salt stress index experiments revealed that the ability of LbMYB48-silenced lines to resist salt stress was significantly reduced. LbMYB48 regulates salt gland development and salt tolerance in L. bicolor mainly by regulating the expression of epidermal cell development related genes such as LbCPC-like and LbDIS3 and salt stress-related genes (LbSOSs, LbRLKs, and LbGSTs) as demonstrated by RNA-seq analysis of LbMYB48-silenced lines. The heterologous over-expression of LbMYB48 in Arabidopsis thaliana improves salt tolerance of plants by stabilizing ion and osmotic balance and is likely to be involved in the abscisic acid signaling pathway. Therefore, LbMYB48, a transcriptional activator regulates the salt gland development of L. bicolor and salt tolerance of L. bicolor and A. thaliana.

MYB Transcription Factors Becoming Mainstream in Plant Roots

The function of the root system is crucial for plant survival, such as anchoring plants, absorbing nutrients and water from the soil, and adapting to stress. MYB transcription factors constitute one of the largest transcription factor families in plant genomes with structural and functional diversifications. Members of this superfamily in plant development and cell differentiation, specialized metabolism, and biotic and abiotic stress processes are widely recognized, but their roles in plant roots are still not well characterized. Recent advances in functional studies remind us that MYB genes may have potentially key roles in roots. In this review, the current knowledge about the functions of MYB genes in roots was summarized, including promoting cell differentiation, regulating cell division through cell cycle, response to biotic and abiotic stresses (e.g., drought, salt stress, nutrient stress, light, gravity, and fungi), and mediate phytohormone signals. MYB genes from the same subfamily tend to regulate similar biological processes in roots in redundant but precise ways. Given their increasing known functions and wide expression profiles in roots, MYB genes are proposed as key components of the gene regulatory networks associated with distinct biological processes in roots. Further functional studies of MYB genes will provide an important basis for root regulatory mechanisms, enabling a more inclusive green revolution and sustainable agriculture to face the constant changes in climate and environmental conditions.

Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis)

Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.

Evolution and functional diversification of R2R3-MYB transcription factors in plants

R2R3-MYB genes (R2R3-MYBs) form one of the largest transcription factor gene families in the plant kingdom, with substantial structural and functional diversity. However, the evolutionary processes leading to this amazing functional diversity have not yet been clearly established. Recently developed genomic and classical molecular technologies have provided detailed insights into the evolutionary relationships and functions of plant R2R3-MYBs. Here, we review recent genome-level and functional analyses of plant R2R3-MYBs, with an emphasis on their evolution and functional diversification. In land plants, this gene family underwent a large expansion by whole genome duplications and small-scale duplications. Along with this population explosion, a series of functionally conserved or lineage-specific subfamilies/groups arose with roles in three major plant-specific biological processes: development and cell differentiation, specialized metabolism, and biotic and abiotic stresses. The rapid expansion and functional diversification of plant R2R3-MYBs are highly consistent with the increasing complexity of angiosperms. In particular, recently derived R2R3-MYBs with three highly homologous intron patterns (a, b, and c) are disproportionately related to specialized metabolism and have become the predominant subfamilies in land plant genomes. The evolution of plant R2R3-MYBs is an active area of research, and further studies are expected to improve our understanding of the evolution and functional diversification of this gene family.

Ectopic Expression of JcCPL1, 2, and 4 Affects Epidermal Cell Differentiation, Anthocyanin Biosynthesis and Leaf Senescence in Arabidopsis thaliana

The CAPRICE (CPC)-like (CPL) genes belong to a single-repeat R3 MYB family, whose roles in physic nut (Jatropha curcas L.), an important energy plant, remain unclear. In this study, we identified a total of six CPL genes (JcCPL1–6) in physic nut. The JcCPL3, 4, and 6 proteins were localized mainly in the nucleus, while proteins JcCPL1, 2, and 5 were localized in both the nucleus and the cytoplasm. Ectopic overexpression of JcCPL1, 2, and 4 in Arabidopsis thaliana resulted in an increase in root hair number and decrease in trichome number. Consistent with the phenotype of reduced anthocyanin in shoots, the expression levels of anthocyanin biosynthesis genes were down-regulated in the shoots of these three transgenic A. thaliana lines. Moreover, we observed that OeJcCPL1, 2, 4 plants attained earlier leaf senescence, especially at the late developmental stage. Consistent with this, the expression levels of several senescence-associated and photosynthesis-related genes were, respectively, up-regulated and down-regulated in leaves. Taken together, our results indicate functional divergence of the six CPL proteins in physic nut. These findings also provide insight into the underlying roles of CPL transcription factors in leaf senescence.

Identification of six CPC-like genes and their differential expression in leaves of tea plant, Camellia sinensis

Tea is one of the most consumed beverages worldwide, and trichome formation in tea plant leaves impairs their commercial value. In Arabidopsis thaliana leaves, trichome formation is negatively regulated by the CPC family genes, which encode R3-type MYB transcription factors. Here, we identified six CPC-like genes in a tea plant (Camellia sinensis var. sinensis) for the first time. Simulated three-dimensional structure of the MYB domains of all the six CPC-like proteins exhibited negative charge on the surface, as observed on that of the Arabidopsis CPC protein that does not bind to DNA, indicating their similarity with regard to molecular interaction. We further found that the six CPC-like genes were differentially expressed in different developmental stages of tea leaves, and four out of the six genes were upregulated in the youngest 1st leaves, which formed more trichomes than other older leaves. Although it does not establish a causal link, the correlation between differential expression of CPC-like genes and variable trichome formation suggests that the R3-type MYB transcription factors are potential precipitating factors in affecting the value of tea leaf.

In vitro and in vivo activity analysis of poplar CLE dodecapeptides that are most divergent from Arabidopsis counterparts

Intercellular communication mediated by the plant-specific CLAVATA3/ENDOSPERM SURROUNDING REGION (ESR)-related (CLE) family members is one of the fundamental mechanisms coordinating the development of complex bodies of plants. In this work, we chose 8 out of 38 putative CLE dodecapeptides encoded in the genome of P. trichocarpa based on their lowest sequence similarity with Arabidopsis CLE peptides, and investigated how such sequence variations affect their functional characteristics. In group 1, PtCLE16p faithfully retained the AtCLE1-7p activity, while PtCLE49p reversed the root-enhancing effect to an inhibitory one with two extra amino acid substitutions, which might have disrupted the capacity of PtCLE49p to recognize the corresponding receptors. In group 2, PtCLE9p conferred Arabidopsis with retarded root growth and suppressed phloem differentiation in a negative dominant manner just like AtCLE25^G6T did. PtCLE9p enhanced the vegetative growth in both basal and aerial rosettes by regulating the expression of AERIAL ROSETTE 1 (ART1) and FRIGIDA (FRI) as well as the downstream FLOWERING LOCUS C (FLC) genes. In group 3, PtCLE34p and PtCLE5p slightly promoted primary root growth, while PtCLE40p revealed CLV3p-like and TDIF activity in root and hypocotyls, respectively. The remaining PtCLE18p in group 4 dramatically disturbed the expression of WOX5 and promoted the development of root hairs by repressing the expression of GLABRA2 (GL2) gene, which encoded a negative regulator of epidermal cells differentiation towards root hairs. In summary, our data indicated that with significant functional conservation and common signaling machinery existing for CLE families of land plants, unique and diverse activities of CLE peptides have evolved to perform specific functions in different plant species.

Heterologous expression of the Limonium bicolor MYB transcription factor LbTRY in Arabidopsis thaliana increases salt sensitivity by modifying root hair development and osmotic homeostasis

Arabidopsis thaliana TRY is a negative regulator of trichome differentiation that promotes root hair differentiation. Here, we established that LbTRY, from the recretohalophyte Limonium bicolor, is a typical MYB transcription factor that exhibits transcriptional activation activity and locates in nucleus. By in situ hybridization in L. bicolor, LbTRY may be specifically positioned in salt gland of the expanded leaves. LbTRY expression was the highest in mature leaves and lowest under NaCl treatment. For functional assessment, we heterologously expressed LbTRY in wild-type and try29760 mutant Arabidopsis plants. Epidermal differentiation was remarkably affected in the transgenic wild-type line, as was increased root hair development. Complementation of try29760 with LbTRY under both 35S and LbTRY specific promoter restored the wild-type phenotype. qRT-PCR analysis suggested that AtGL3 and AtZFP5 promote root hair cell fate in lines heterologously producing LbTRY. In addition, four genes (AtRHD6, AtRSL1, AtLRL2, and AtLRL3) involved in root hair initiation and elongation were upregulated in the transgenic lines. Furthermore, LbTRY specifically increased the salt sensitivity of the transgenic lines. The transgenic and complementation lines showed poor germination rates and reduced root lengths, whereas the mutant unexpectedly fared the best under a range of NaCl treatments. Under salt stress, the transgenic seedlings accumulated more MDA and Na⁺ and less proline and soluble sugar than try29760. Thus, when heterologously expressed in Arabidopsis, LbTRY participates in hair development, similar to other MYB proteins, and specifically reduces salt tolerance by increasing ion accumulation and reducing osmolytes. The expression of salt-tolerance marker genes (SOS1, SOS2, SOS3 and P5CS1) was significant reduced in the transgenic lines. More will be carried by downregulating expression of TRY homologs in crops to improve salt tolerance.

Localization of tomato (Solanum lycopersicum) R3 MYB protein encoded by SlTRY in Arabidopsis roots

CAPRICE (CPC), an R3-type MYB transcription factor, is known to promote root hair differentiation in the root epidermis of Arabidopsis. CPC moves from non-hair cells to adjacent hair-forming cells. In contrast, we have previously shown that there is no movement of the CPC homologs, ENHANCER OF TRY AND CPC 1, 2, and 3 (ETC1, 2, and 3), and TRYPTICHON (TRY) between root epidermal cells. We also identified a tomato homolog of CPC, named Solanum lycopersicumTRYPTICHON (SlTRY).SlTRY-introduced transgenic Arabidopsis produced many root hairs, like CPC-introduced transgenic Arabidopsis. To clarify the cell-to-cell movement ability of the SlTRY protein, in this study, we observed the distribution of GFP fluorescence in CPCp:SlTRY:GFP transgenic Arabidopsis. Unexpectedly, SlTRY moved from non-hair cells to adjacent root hair cells, like CPC, in Arabidopsis root epidermis. SlTRY does not have the cell-to-cell movement sequence (S1) defined in CPC, and the mechanism of movement is still unknown. Further investigation is necessary to elucidate the mechanism of cell-to-cell movement of SlTRY. Our results will help in the further unraveling of the functions of these MYB transcription factors in determining cell fate.

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.

BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa

Comprehensive research in various plants shows that the metabolic pathway of anthocyanin biosynthesis is affected by environmental factors and regulated by microRNAs through post-transcriptional regulation. In seedlings of Brassica rapa Tsuda, the accumulation of anthocyanin is induced by light. However, the roles of BrmiR828 in the light-induced synthesis of anthocyanin in Brassica rapa remain to be explored. Here, a primary transcript of BrmiR828 was identified to be located on the chromosomes of the A03 sub-genome. Five candidate MYB family genes were predicted as targets of BrmiR828 in the database of Brassica rapa (BRAD, V1.1) by using psRNATarget. The transcript abundance of mature BrmiR828 was reduced in seedlings of Brassica rapa Tsuda under blue light irradiation comparing with dark treatment. However, Real-time PCR showed the transcript level of the five candidate targets, Bra004162, Bra022602, Bra001917, Bra029113, and Bra039763 was up-regulated when the seedlings exposed to blue or UV-A light. Trans-acting siRNA gene 4 (BrTAS4) was also identified to have a higher transcript level under blue and UV-A light irradiation than that in dark treatment. RNA ligase mediated 5′amplification of cDNA ends (RLM-5′ RACE) showed that BrmiR828 can splice the mRNA of Bra039763, Bra022602, and BrTAS4 on binding sites. Phylogenetic analysis of candidate BrMYBs targets along with MYBs from Arabidopsis thaliana showed that Bra039763, Bra004162, Bra001917, Bra029113, and Bra022602 are classified to the same group with AtMYB75, AtMYB114, AtMYB90, AtMYB113, and AtMYB82 which are involved in the anthocyanin biosynthetic pathway. As a result, light-induced down-regulation of BrmiR828 can target BrTAS4, BrPAP1 (Bra039763), MYB82 (Bra022602) to negatively regulate their transcript levels leading to the accumulation of MYB transcription factors that positively regulate anthocyanin biosynthesis in light-exposed seedlings of Brassica rapa.

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.

MYB Gene Family in Potato (Solanum tuberosum L.): Genome-Wide Identification of Hormone-Responsive Reveals Their Potential Functions in Growth and Development

As an important nongrain crop, the growth and yield of potato (Solanum tuberosum L.) is often affected by an unfavorable external environment in the process of cultivation. The MYB family is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. Several MYB genes in potato that regulate anthocyanin synthesis and participate in abiotic stress responses have been identified. To identify all Solanum tuberosum L. MYB (StMYB) genes involved in hormone or stress responses to potentially regulate potato growth and development, we identified the MYB gene family at the genome-wide level. In this work, 158 StMYB genes were found in the potato genome. According to the amino acid sequence of the MYB domain and gene structure, the StMYB genes were divided into R2R3-MYB and R1R2R3-MYB families, and the R2R3-MYB family was divided into 20 subgroups (SGs). The expression of 21 StMYB genes from different SGs in roots, stems, leaves, flowers, shoots, stolons, young tubers, and mature tubers was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The expression patterns of StMYB genes in potatoes treated with abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin acid 3 (GA3), NaCl, mannitol, and heat were also measured. We have identified several potential candidate genes that regulate the synthesis of potato flavonoids or participate in hormone or stress responses. This work provides a comprehensive understanding of the MYB family in potato and will lay a foundation for the future investigation of the potential functions of StMYB genes in the growth and development of potato.

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.

Activator-type R2R3-MYB genes induce a repressor-type R2R3-MYB gene to balance anthocyanin and proanthocyanidin accumulation

Anthocyanin and proanthocyanidin (PA) accumulation is regulated by both myeloblastosis (MYB) activators and repressors, but little information is available on hierarchical interactions between the positive and negative regulators. Here, we report on a R2R3-MYB repressor in peach, designated PpMYB18, which acts as a negative regulator of anthocyanin and PA accumulation. PpMYB18 can be activated by both anthocyanin- and PA-related MYB activators, and is expressed both at fruit ripening and juvenile stages when anthocyanins or PAs, respectively, are being synthesized. The PpMYB18 protein competes with MYB activators for binding to basic Helix Loop Helixes (bHLHs), which develops a fine-tuning regulatory loop to balance PA and anthocyanin accumulation. In addition, the bHLH binding motif in the R3 domain and the C1 and C2 repression motifs in the C-terminus of PpMYB18 both confer repressive activity of PpMYB18. Our study also demonstrates a modifying negative feedback loop, which prevents cells from excess accumulation of anthocyanin and PAs, and serves as a model for balancing secondary metabolite accumulation at the transcriptional level.

The Beneficial Root-Colonizing Fungus Mortierella hyalina Promotes the Aerial Growth of Arabidopsis and Activates Calcium-Dependent Responses That Restrict Alternaria brassicae-Induced Disease Development in Roots

The endophytic fungus Mortierella hyalina colonizes the roots of Arabidopsis thaliana and stimulates growth and biomass production of the aerial parts but not of roots. An exudate fraction from the fungus induces rapid and transient cytoplasmic Ca²⁺elevation in the roots. The Ca²⁺ response does not require the well-characterized (co)receptors BAK1, CERK1, and FLS2 for pathogen-associated molecular patterns, and the Ca²⁺ channels GLR-2.4, GLR-2.5, and GLR-3.3 or the vacuolar TWO PORE CHANNEL1, which might be involved in cytoplasmic Ca²⁺ elevation. We isolated an ethyl-methane-sulfonate-induced Arabidopsis mutant that is impaired in this Ca²⁺ response. The roots of the mutant are impaired in M. hyalina-mediated suppression of immune responses after Alternaria brassicae infection, i.e., jasmonate accumulation, generation of reactive oxygen species, as well as the activation of jasmonate-related defense genes. Furthermore, they are more colonized by M. hyalina than wild-type roots. We propose that the mutant gene product is involved in a Ca²⁺-dependent signaling pathway activated by M. hyalina to suppress immune responses in Arabidopsis roots.

Dawn regulates guard cell proteins in Arabidopsis thaliana that function in ATP production from fatty acid beta-oxidation

Based on the nature of the proteins that are altered in abundance, we conclude that guard cells switch their energy source from fatty acid metabolism to chloroplast activity, at the onset of dawn. During stomatal opening at dawn, evidence was recently presented for a breakdown and liquidation of stored triacylglycerols in guard cells to supply ATP for use in stomatal opening. However, proteome changes that happen in the guard cells during dawn were until now poorly understood. Bad accessibility to pure and intact guard cell samples can be considered as the primary reason behind this lack of knowledge. To overcome these technical constraints, epidermal guard cell samples with ruptured pavement cells were isolated at 1 h pre-dawn, 15 min post-dawn and 1 h post-dawn from Arabidopsis thaliana. Proteomic changes were analysed by ultra-performance-liquid-chromatography-mass-spectrometry. With 994 confidently identified proteins, we present the first analysis of the A. thaliana guard cell proteome that is not influenced by side effects of guard cell protoplasting. Data are available via ProteomeXchange with identifier PXD009918. By elucidating the identities of enzymes that change in abundance by the transition from dark to light, we corroborate the hypothesis that respiratory ATP production for stomatal opening results from fatty acid beta-oxidation. Moreover, we identified many proteins that were never reported in the context of guard cell biology. Among them are proteins that might play a role in signalling or circadian rhythm.

Sub-epidermal Expression of ENHANCER OF TRIPTYCHON AND CAPRICE1 and Its Role in Root Hair Formation Upon Pi Starvation

Root hair patterning is best studied in Arabidopsis thaliana. A pattern of root hair and non-root hair files is governed by a gene-regulatory network of activators and inhibitors. Under phosphate starvation conditions, extra root hairs are formed in non-root hair positions. This raises the question, whether and how this environmental stimulus is mediated by the known root hair gene network. In this study, we provide genetic and molecular data on the role of ETC1 in the phosphate starvation induced ectopic root hair formation. We show that the expression in the epidermis is irregular and reduced and that a new expression domain is induced in the sub-epidermis. By expressing ETC1 in the sub-epidermis, we show that this is sufficient to induce extra root hair formation in N-files. This suggests that the phosphate induced expressional switch from epidermal to epidermal plus sub-epidermal expression of ETC1 is one environmental input to the underlying patterning network.

Combined fine mapping, genetic diversity, and transcriptome profiling reveals that the auxin transporter gene ns plays an important role in cucumber fruit spine development

Map-based cloning was used to identify the ns gene, which was involved in the formation of cucumber numerous fruit spines together with other genes under regulation by plant hormone signal transduction. The cucumber (Cucumis sativus) fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation. Here, we identified NUMEROUS SPINES (NS), which regulate fruit spine development by modulating the Auxin signaling pathway. We fine-mapped the ns using a 2513 F₂ population derived from NCG122 (numerous fruit spines line) and NCG121 (few fruit spines line), and showed that NS encoded auxin transporter-like protein 3. Genetic diversity analysis of the NS gene in natural populations revealed that one SNP and one InDel in the coding region of ns are co-segregated with the fruit spine density. The NS protein sequence was highly conserved among plants, but its regulation of fruit spine development in cucumber seems to be a novel function. Transcriptome profiling indicated that the plant hormone signal transduction-related genes were highly enriched in the up-regulated genes in NCG122 versus NCG121. Moreover, expression pattern analysis of the auxin signal pathway-related genes in NCG122 versus NCG121 showed that upstream genes of the pathway (like ns candidate gene Csa2M264590) are down-regulated, while the downstream genes are up-regulated. Quantitative reverse transcription PCR confirmed the differential expression during the fruit spine development. Therefore, reduced expression of ns may promote the fruit spine formation. Our findings provide a valuable framework for dissecting the regulatory mechanism for the fruit spine development.

CLE14 peptide signaling in Arabidopsis root hair cell fate determination

Morphological adjustment is a critical strategy for the survival of plant species in various environments. The CLE (CLAVATA3/EMBRYO SURROUNDING REGION) family of plant polypeptides is known to play important roles in various physiological and developmental processes and the relevant signaling pathways are conserved in diverse land plants. Previously, it has been suggested that overexpression of CLE14 promotes root hair cell differentiation in Arabidopsis roots. To clarify this suggested function of CLE14 peptide on root hair induction, we examined the effect of synthetic CLE14 peptide on Arabidopsis root hair development. Consistent with the results of previous overexpression analyses of CLE14, we demonstrated that application of synthetic CLE14 peptide induced excess root hair formation on CLE14-treated Arabidopsis roots. In addition, CLE14 reduced the expression of the non-hair cell fate determinant gene, GLABRA2. Our results thus indicate that CLE14 can activate the transcriptional regulatory cascade of root hair formation.

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.

Extended C termini of CPC-LIKE MYB proteins confer functional diversity in Arabidopsis epidermal cell differentiation

The CAPRICE (CPC) gene encodes a R3-type MYB transcription factor that promotes differentiation of root hair cells in Arabidopsis thaliana Here, we have compared the functions of five CPC-homologous genes for epidermal cell differentiation using CPC promoter-driven transgenic plants. Our results show that TRIPTYCHON (TRY) and ENHANCER OF TRY AND CPC2 (ETC2) were less effective in root hair cell differentiation and were unstable in root epidermal cells when compared with CPC, ETC1 or CPC LIKE MYB3 (CPL3). The deletion of the extended C-terminal domain of TRY and ETC2 enhanced protein stability and conferred the ability to induce root hair cell differentiation on them. Treatment with MG132, a proteasome inhibitor, also led to the accumulation of TRY, indicating that TRY proteolysis is mediated by the proteasome-dependent pathway. Our results indicate that the CPC family includes relatively stable (CPC, ETC1 and CPL3) and unstable (TRY and ETC2) proteins that might be degraded by the proteasome. Our findings provide new insights into the regulatory mechanism of CPC family proteins that mediate root hair cell differentiation and should be useful in understanding epidermal development.

Trichome patterning control involves TTG1 interaction with SPL transcription factors

Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.

Regulation of plant secondary metabolism and associated specialized cell development by MYBs and bHLHs

Plants are unrivaled in the natural world in both the number and complexity of secondary metabolites they produce, and the ubiquitous phenylpropanoids and the lineage-specific glucosinolates represent two such large and chemically diverse groups. Advances in genome-enabled biochemistry and metabolomic technologies have greatly increased the understanding of their metabolic networks in diverse plant species. There also has been some progress in elucidating the gene regulatory networks that are key to their synthesis, accumulation and function. This review highlights what is currently known about the gene regulatory networks and the stable sub-networks of transcription factors at their cores that regulate the production of these plant secondary metabolites and the differentiation of specialized cell types that are equally important to their defensive function. Remarkably, some of these core components are evolutionarily conserved between secondary metabolism and specialized cell development and across distantly related plant species. These findings suggest that the more ancient gene regulatory networks for the differentiation of fundamental cell types may have been recruited and remodeled for the generation of the vast majority of plant secondary metabolites and their specialized tissues.

ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon

Genes encoding ROOT HAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix loop helix proteins are expressed in future root hair cells of the Arabidopsis thaliana root meristem where they positively regulate root hair cell development. Here we show that there are three RSL class I protein coding genes in the Brachypodium distachyon genome, BdRSL1, BdRSL2 and BdRSL3, and each is expressed in developing root hair cells after the asymmetric cell division that forms root hair cells and hairless epidermal cells. Expression of BdRSL class I genes is sufficient for root hair cell development: ectopic overexpression of any of the three RSL class I genes induces the development of root hairs in every cell of the root epidermis. Expression of BdRSL class I genes in root hairless Arabidopsis thaliana root hair defective 6 (Atrhd6) Atrsl1 double mutants, devoid of RSL class I function, restores root hair development indicating that the function of these proteins has been conserved. However, neither AtRSL nor BdRSL class I genes is sufficient for root hair development in A. thaliana. These data demonstrate that the spatial pattern of class I RSL activity can account for the pattern of root hair cell differentiation in B. distachyon. However, the spatial pattern of class I RSL activity cannot account for the spatial pattern of root hair cells in A. thaliana. Taken together these data indicate that that the functions of RSL class I proteins have been conserved among most angiosperms-monocots and eudicots-despite the dramatically different patterns of root hair cell development.

Combinatorial control of plant gene expression

Combinatorial gene regulation provides a mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with finely tuned temporal and spatial patterns. This is achieved by transcription factors assembling into complexes in a combinatorial fashion, exponentially increasing the number of genes that they can target. Such an arrangement also increases the specificity and affinity for the cis-regulatory sequences required for accurate target gene expression. Superimposed on this transcription factor combinatorial arrangement is the increasing realization that histone modification marks expand the regulatory information, which is interpreted by histone readers and writers that are part of the regulatory apparatus. Here, we review the progress in these areas from the perspective of plant combinatorial gene regulation, providing examples of different regulatory solutions and comparing them to other metazoans. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis)

MYB proteins comprise a large family of plant transcription factors that play regulatory roles in different biological processes such as plant development, metabolism, and defense responses. To gain insight into this gene superfamily and to elucidate its roles in stress resistance, we performed a comprehensive genome-wide identification, characterization, and expression analysis of MYB genes in Chinese cabbage (Brassica rapa ssp. pekinensis). We identified 475 Chinese cabbage MYB genes, among which most were from R2R3-MYB (256 genes) and MYB-related (202) subfamilies. Analysis of sequence characteristics, phylogenetic classification, and protein motif structures confirmed the existence of several categories (1R, 2R, 3R, 4R, and 5R) of Chinese cabbage MYB genes, which is comparable with MYB genes of other crops. An extensive in silico functional analysis, based on established functional properties of MYB genes from different crop species, revealed 11 and four functional clades within the Chinese cabbage R2R3-MYB and MYB-related subfamilies, respectively. In this study, we reported a MYB-like group within the MYB-related subfamily contains 77 MYB genes. Expression analysis using low temperature-treated whole-genome microarray data revealed variable transcript abundance of 1R/2R/3R/4R/5R-MYB genes in 11 clusters between two inbred lines of Chinese cabbage, Chiifu and Kenshin, which differ in cold tolerance. In further validation tests, we used qRT-PCR to examine the cold-responsive expression patterns of 27 BrMYB genes; surprisingly, the MYB-related genes were induced more highly than the R2R3-MYB genes. In addition, we identified 10 genes with corresponsive expression patterns from a set of salt-, drought-, ABA-, JA-, and SA-induced R2R3-MYB genes. We identified 11 R2R3-MYBs functioning in resistance against biotic stress, including 10 against Fusarium oxysporum f.sp. conglutinans and one against Pectobacterium carotovoram subsp. caratovorum. Furthermore, based on organ-specific expression data, we identified nine R2R3-MYBs that were constitutively expressed in male reproductive tissue, which may provide an important key for studying male sterility in Chinese cabbage. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MYB genes in stress resistance in addition to their growth regulatory functions, ultimately providing the basis for functional characterization and exploitation of the candidate MYB genes for genetic engineering of Chinese cabbage.

Ternary WD40 Repeat-Containing Protein Complexes: Evolution, Composition and Roles in Plant Immunity

Plants, like mammals, rely on their innate immune system to perceive and discriminate among the majority of their microbial pathogens. Unlike mammals, plants respond to this molecular dialog by unleashing a complex chemical arsenal of defense metabolites to resist or evade pathogen infection. In basal or non-host resistance, plants utilize signal transduction pathways to detect "non-self," "damaged-self," and "altered-self"- associated molecular patterns and translate these "danger" signals into largely inducible chemical defenses. The WD40 repeat (WDR)-containing proteins Gβ and TTG1 are constituents of two independent ternary protein complexes functioning at opposite ends of a plant immune signaling pathway. They are also encoded by single-copy genes that are ubiquitous in higher plants, implying the limited diversity and functional conservation of their respective complexes. In this review, we summarize what is currently known about the evolutionary history of these WDR-containing ternary complexes, their repertoire and combinatorial interactions, and their downstream effectors and pathways in plant defense.

Genetic control of root growth: from genes to networks

BACKGROUND

Roots are essential organs for higher plants. They provide the plant with nutrients and water, anchor the plant in the soil, and can serve as energy storage organs. One remarkable feature of roots is that they are able to adjust their growth to changing environments. This adjustment is possible through mechanisms that modulate a diverse set of root traits such as growth rate, diameter, growth direction and lateral root formation. The basis of these traits and their modulation are at the cellular level, where a multitude of genes and gene networks precisely regulate development in time and space and tune it to environmental conditions.

SCOPE

This review first describes the root system and then presents fundamental work that has shed light on the basic regulatory principles of root growth and development. It then considers emerging complexities and how they have been addressed using systems-biology approaches, and then describes and argues for a systems-genetics approach. For reasons of simplicity and conciseness, this review is mostly limited to work from the model plant Arabidopsis thaliana, in which much of the research in root growth regulation at the molecular level has been conducted.

CONCLUSIONS

While forward genetic approaches have identified key regulators and genetic pathways, systems-biology approaches have been successful in shedding light on complex biological processes, for instance molecular mechanisms involving the quantitative interaction of several molecular components, or the interaction of large numbers of genes. However, there are significant limitations in many of these methods for capturing dynamic processes, as well as relating these processes to genotypic and phenotypic variation. The emerging field of systems genetics promises to overcome some of these limitations by linking genotypes to complex phenotypic and molecular data using approaches from different fields, such as genetics, genomics, systems biology and phenomics.

GLABRA2 Directly Suppresses Basic Helix-Loop-Helix Transcription Factor Genes with Diverse Functions in Root Hair Development

The Arabidopsis thaliana GLABRA2 (GL2) gene encodes a transcription factor involved in the cell differentiation of various epidermal tissues. During root hair pattern formation, GL2 suppresses root hair development in non-hair cells, acting as a node between the gene regulatory networks for cell fate determination and cell differentiation. Despite the importance of GL2 function, its molecular basis remains obscure because the GL2 target genes leading to the network for cell differentiation are unknown. We identified five basic helix-loop-helix (bHLH) transcription factor genes (ROOT HAIR DEFECTIVE6 [RHD6], RHD6-LIKE1 [RSL1], RSL2, Lj-RHL1-LIKE1 [LRL1], and LRL2) as GL2 direct targets using transcriptional and posttranslational induction systems. Chromatin immunoprecipitation analysis confirmed GL2 binding to upstream regions of these genes in planta. Reporter gene analyses showed that these genes are expressed in various stages of root hair development and are suppressed by GL2 in non-hair cells. GL2 promoter-driven GFP fusions of LRL1 and LRL2, but not those of the other bHLH proteins, conferred root hair development on non-hair cells. These results indicate that GL2 directly suppresses bHLH genes with diverse functions in root hair development.

The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion

R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.

TRANSPARENT TESTA GLABRA1 and GLABRA1 Compete for Binding to GLABRA3 in Arabidopsis

The MBW (for R2R3MYB, basic helix-loop-helix [bHLH], and WD40) genes comprise an evolutionarily conserved gene cassette that regulates several traits such as (pro)anthocyanin and anthocyanin biosynthesis and epidermal cell differentiation in plants. Trichome differentiation in Arabidopsis (Arabidopsis thaliana) is governed by GLABRA1 (GL1; R2R3MYB), GL3 (bHLH), and transparent TESTA GLABRA1 (TTG1; WD40). They are thought to form a trimeric complex that acts as a transcriptional activation complex. We provide evidence that these three MBW proteins form either GL1 GL3 or GL3 TTG1 dimers. The formation of each dimer is counteracted by the respective third protein in yeast three-hybrid assays, pulldown experiments (luminescence-based mammalian interactome), and fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer studies. We further show that two target promoters, Triptychon (TRY) and CAPRICE (CPC), are differentially regulated: GL1 represses the activation of the TRY promoter by GL3 and TTG1, and TTG1 suppresses the activation of the CPC promoter by GL1 and GL3. Our data suggest that the transcriptional activation by the MBW complex involves alternative complex formation and that the two dimers can differentially regulate downstream genes.

The R3-MYB gene GhCPC negatively regulates cotton fiber elongation

Cotton (Gossypium spp.) fibers are single-cell trichomes that arise from the outer epidermal layer of seed coat. Here, we isolated a R3-MYB gene GhCPC, identified by cDNA microarray analysis. The only conserved R3 motif and different expression between TM-1 and fuzzless-lintless mutants suggested that it might be a negative regulator in fiber development. Transgenic evidence showed that GhCPC overexpression not only delayed fiber initiation but also led to significant decreases in fiber length. Interestingly, Yeast two-hybrid analysis revealed an interaction complex, in which GhCPC and GhTTG1/4 separately interacted with GhMYC1. In transgenic plants, Q-PCR analysis showed that GhHOX3 (GL2) and GhRDL1 were significantly down regulated in -1-5 DPA ovules and fibers. In addition, Yeast one-hybrid analysis demonstrated that GhMYC1 could bind to the E-box cis-elements and the promoter of GhHOX3. These results suggested that GhHOX3 (GL2) might be downstream gene of the regulatory complex. Also, overexpression of GhCPC in tobacco led to differential loss of pigmentation. Taken together, the results suggested that GhCPC might negatively regulate cotton fiber initiation and early elongation by a potential CPC-MYC1-TTG1/4 complex. Although the fibers were shorter in transgenic cotton lines than in the wild type, no significant difference was detected in stem or leaf trichomes, even in cotton mutants (five naked seed or fuzzless), suggesting that fiber and trichome development might be regulated by two sets of genes sharing a similar model.

R2R3-MYB gene pairs in Populus: evolution and contribution to secondary wall formation and flowering time

In plants, the R2R3-MYB gene family contains many pairs of paralogous genes, which play the diverse roles in developmental processes and environmental responses. The paper reports the characterization of 81 pairs of Populus R2R3-MYB genes. Chromosome placement, phylogenetic, and motif structure analyses showed that these gene pairs resulted from multiple types of gene duplications and had five different gene fates. Tissue expression patterns revealed that most duplicated genes were specifically expressed in the tissues examined. qRT-PCR confirmed that nine pairs were highly expressed in xylem, of which three pairs (PdMYB10/128, PdMYB90/167, and PdMYB92/125) were further functionally characterized. The six PdMYBs were localized to the nucleus and had transcriptional activities in yeast. The heterologous expression of PdMYB10 and 128 in Arabidopsis increased stem fibre cell-wall thickness and delayed flowering. In contrast, overexpression of PdMYB90, 167, 92, and 125 in Arabidopsis decreased stem fibre and vessel cell-wall thickness and promoted flowering. Cellulose, xylose, and lignin contents were changed in overexpression plants. The expression levels of several genes involved in secondary wall formation and flowering were affected by the overexpression of the six PdMYBs in Arabidopsis. This study addresses the diversity of gene duplications in Populus R2R3-MYBs and the roles of these six genes in secondary wall formation and flowering control.

Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum

The R2R3MYB proteins comprise one of the largest families of transcription factors and play regulatory roles in developmental processes and defense responses in plants. However, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of these genes in tomato (Solanum lycopersicum L.), a reference species for Solanaceae plants, and the model plant for fruit development. In this study, a total of 121 R2R3MYB genes were identified in the tomato genome released recently and further classified into 29 subgroups based on the phylogenetic analysis of the complete protein sequences. Phylogenetic comparison of the members of this superfamily among tomato, Arabidopsis, grape, rice, poplar, soybean, cucumber and apple revealed that the putative functions of some tomato R2R3MYB proteins were clustered into the Arabidopsis functional clades. The chromosome distribution pattern revealed that tomato R2R3MYB genes were enriched on several chromosomes and 52 % of the family members were tandemly duplicated genes. Tissue specificity or different expression levels of SlR2R3MYBs in different tissues suggested differential regulation of tissue development as well as metabolic regulation. The transcript abundance level analysis during abiotic conditions identified a group of R2R3MYB genes that responded to one or more treatments suggesting that the SlR2R3MYBs played major roles in the plant response to abiotic conditions and involved in signal transduction pathways. This study not only provides a solid foundation for further functional dissection of tomato R2R3MYB family genes, but may also be profitable for, in the future, the improvement of tomato stress tolerance and fruit quality.

Root hairs

Roots hairs are cylindrical extensions of root epidermal cells that are important for acquisition of nutrients, microbe interactions, and plant anchorage. The molecular mechanisms involved in the specification, differentiation, and physiology of root hairs in Arabidopsis are reviewed here. Root hair specification in Arabidopsis is determined by position-dependent signaling and molecular feedback loops causing differential accumulation of a WD-bHLH-Myb transcriptional complex. The initiation of root hairs is dependent on the RHD6 bHLH gene family and auxin to define the site of outgrowth. Root hair elongation relies on polarized cell expansion at the growing tip, which involves multiple integrated processes including cell secretion, endomembrane trafficking, cytoskeletal organization, and cell wall modifications. The study of root hair biology in Arabidopsis has provided a model cell type for insights into many aspects of plant development and cell biology.

Non-cell-autonomous regulation of root hair patterning genes by WRKY75 in Arabidopsis

In Arabidopsis (Arabidopsis thaliana), root hairs are formed in cell files over the cleft of underlying cortex cells. This pattern is established by a well-known gene regulatory network of transcription factors. In this study, we show that WRKY75 suppresses root hair development in nonroot hair files and that it represses the expression of TRIPTYCHON and CAPRICE. The WRKY75 protein binds to the CAPRICE promoter in a yeast one-hybrid assay. Binding to the promoter fragment requires an intact WRKY protein-binding motif, the W box. A comparison of the spatial expression of WRKY75 and the localization of the WRKY75 protein revealed that WRKY75 is expressed in the pericycle and vascular tissue and that the WRKY75 RNA or protein moves into the epidermis.

A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots

Plants require sophisticated regulatory mechanisms to ensure the degree of anthocyanin pigmentation is appropriate to myriad developmental and environmental signals. Central to this process are the activity of MYB-bHLH-WD repeat (MBW) complexes that regulate the transcription of anthocyanin genes. In this study, the gene regulatory network that regulates anthocyanin synthesis in petunia (Petunia hybrida) has been characterized. Genetic and molecular evidence show that the R2R3-MYB, MYB27, is an anthocyanin repressor that functions as part of the MBW complex and represses transcription through its C-terminal EAR motif. MYB27 targets both the anthocyanin pathway genes and basic-helix-loop-helix (bHLH) ANTHOCYANIN1 (AN1), itself an essential component of the MBW activation complex for pigmentation. Other features of the regulatory network identified include inhibition of AN1 activity by the competitive R3-MYB repressor MYBx and the activation of AN1, MYB27, and MYBx by the MBW activation complex, providing for both reinforcement and feedback regulation. We also demonstrate the intercellular movement of the WDR protein (AN11) and R3-repressor (MYBx), which may facilitate anthocyanin pigment pattern formation. The fundamental features of this regulatory network in the Asterid model of petunia are similar to those in the Rosid model of Arabidopsis thaliana and are thus likely to be widespread in the Eudicots.

Regulation of root hair cell differentiation by R3 MYB transcription factors in tomato and Arabidopsis

CAPRICE (CPC) encodes a small protein with an R3 MYB motif and regulates root hair and trichome cell differentiation in Arabidopsis thaliana. Six additional CPC-like MYB proteins including TRIPTYCHON (TRY), ENHANCER OF TRY AND CPC1 (ETC1), ENHANCER OF TRY AND CPC2 (ETC2), ENHANCER OF TRY AND CPC3/CPC-LIKE MYB3 (ETC3/CPL3), TRICHOMELESS1 (TCL1), and TRICHOMELESS2/CPC-LIKE MYB4 (TCL2/CPL4) also have the ability to regulate root hair and/or trichome cell differentiation in Arabidopsis. In this review, we describe our latest findings on how CPC-like MYB transcription factors regulate root hair cell differentiation. Recently, we identified the tomato SlTRY gene as an ortholog of the Arabidopsis TRY gene. Transgenic Arabidopsis plants harboring SlTRY produced more root hairs, a phenotype similar to that of 35S::CPC transgenic plants. CPC is also known to be involved in anthocyanin biosynthesis. Anthocyanin accumulation was repressed in the SlTRY transgenic plants, suggesting that SlTRY can also influence anthocyanin biosynthesis. We concluded that tomato and Arabidopsis partially use similar transcription factors for root hair cell differentiation, and that a CPC-like R3 MYB may be a key common regulator of plant root-hair development.

Phosphatidic acid interacts with a MYB transcription factor and regulates its nuclear localization and function in Arabidopsis

Phosphatidic acid (PA) has emerged as a class of cellular mediators involved in various cellular and physiological processes, but little is known about its mechanism of action. Here we show that PA interacts with werewolf (WER), a R2R3 MYB transcription factor involved in root hair formation. The PA-interacting region is confined to the end of the R2 subdomain. The ablation of the PA binding motif has no effect on WER binding to DNA, but abolishes its nuclear localization and its function in regulating epidermal cell fate. Inhibition of PA production by phospholipase Dζ also suppresses WER's nuclear localization, root hair formation, and elongation. These results suggest a role for PA in promoting protein nuclear localization.