SUMMARYMYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. To gain insights into MYB46-mediated transcriptional regulation, we first established an inducible secondary wall thickening system in Arabidopsis by expressing MYB46 under the control of dexamethasone-inducible promoter. Then, we used an ATH1 GeneChip microarray and Illumina digital gene expression system to obtain a series of transcriptome profiles with regard to the induction of secondary wall development. These analyses allowed us to identify a group of transcription factors whose expression coincided with or preceded the induction of secondary wall biosynthetic genes. A transient transcriptional activation assay was used to confirm the hierarchical relationships among the transcription factors in the network. The in vivo assay showed that MYB46 transcriptionally activates downstream target transcription factors, three of which (AtC3H14, MYB52 and MYB63) were shown to be able to activate secondary wall biosynthesis genes. AtC3H14 activated the transcription of all of the secondary wall biosynthesis genes tested, suggesting that AtC3H14 may be another master regulator of secondary wall biosynthesis. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The present study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis, and generated several testable hypotheses.

While many aspects of primary cell wall have been extensively elucidated, our current understanding of secondary wall biosynthesis is limited. Recently, transcription factor MYB46 has been identified as a master regulator of secondary wall biosynthesis in Arabidopsis thaliana. To gain better understanding of this MYB46-mediated transcriptional regulation, we analyzed the promoter region of a direct target gene, AtC3H14, of MYB46 and identified a cis-acting regulatory motif that is recognized by MYB46. This MYB46-responsive cis-regulatory element (M46RE) was further characterized and shown to have an eight-nucleotide core motif, RKTWGGTR. We used electrophoretic mobility shift assay, transient transcriptional activation assay and chromatin immunoprecipitation analysis to show that the M46RE was necessary and sufficient for MYB46-responsive transcription. Genome-wide analysis identified that the frequency of M46RE in the promoters were highly enriched among the genes upregulated by MYB46, especially in the group of genes involved in secondary wall biosynthesis.

These authors contributed equally to this work. SUMMARYCellulose is the most abundant biopolymer on Earth. Three cellulose synthases (CESA4, CESA7 and CESA8) are necessary for cellulose production in the secondary cell walls of Arabidopsis. Little is known about how expression of these CESA genes is regulated. We recently identified a cis-regulatory element (M46RE) that is recognized by MYB46, which is a master switch for secondary wall formation in Arabidopsis. A genome-wide survey of promoter sequences for the presence of M46REs led to the hypothesis that MYB46 may function as a direct regulator of all three secondary wall-associated cellulose synthase genes: CESA4, CESA7 and CESA8. We tested this hypothesis using several lines of experimental evidence. All three CESA genes are highly up-regulated by both constitutive and inducible over-expression of MYB46 in planta. Using a steroid receptor-based inducible activation system, we show that MYB46 directly activates transcription of the three CESA genes. We then used an electrophoretic mobility shift assay and chromatin immunoprecipitation analysis to confirm that MYB46 protein directly binds to the promoters of the three CESA genes both in vitro and in vivo. Furthermore, ectopic up-regulation of MYB46 resulted in a significant increase of crystalline cellulose content in Arabidopsis. Taken together, we have identified MYB46 as a transcription factor that directly regulates all three secondary wall-associated CESA genes. Yeast one-hybrid screening identified additional transcription factors that regulate the CESA genes. However, none of the putative regulators appears to be regulated by MYB46, suggesting the multi-faceted nature of transcriptional regulation of secondary wall cellulose biosynthesis.

Secondary wall formation requires coordinated transcriptional regulation of the genes involved in the biosynthesis of the components of secondary wall. Transcription factor (TF) MYB46 (At5g12870) has been shown to function as a central regulator for secondary wall formation in Arabidopsis thaliana, activating biosynthetic genes as well as the TFs involved in the pathways. Recently, we reported that MYB46 directly regulates secondary wall-associated cellulose synthase (CESA4, CESA7, and CESA8) and a mannan synthase (CSLA9) genes. However, it is not known whether MYB46 directly activates the biosynthetic genes for hemicellulose and lignin, which are the other two major components of secondary wall. Based on the observations that the promoter regions of many of the secondary wall biosynthetic genes contain MYB46-binding cis-regulatory motif(s), we hypothesized that MYB46 directly regulates the genes involved in the biosynthesis of the secondary wall components. In this report, we describe several lines of experimental evidence in support of the hypothesis. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that MYB46 directly binds to the promoters of 13 genes involved in lignin and xylan biosynthesis. We then used steroid receptor-based inducible activation system to confirm that MYB46 directly activates the transcription of the xylan and lignin biosynthetic genes. Furthermore, ectopic up-regulation of MYB46 resulted in a significant increase in xylose and a small increase in lignin content based on acetyl bromide soluble lignin measurements in Arabidopsis. Taken together, we conclude that MYB46 function as a central and direct regulator of the genes involved in the biosynthesis of all three major secondary wall components.

The timing of the onset and release of dormancy impacts the survival, productivity and spatial distribution of temperate horticultural and forestry perennials and is mediated by at least three main regulatory programs involving signal perception and processing by phytochromes (PHYs) and PHY-interacting transcription factors (PIFs). PIF4 functions as a key regulator of plant growth in response to both external and internal signals. In poplar, the expression of PIF4 and PIF3-LIKE1 is upregulated in response to short days, while PHYA and PHYB are not regulated at the transcriptional level. Integration of light and environmental signals is achieved by gating the expression and transcriptional activity of PIF4. During this annual cycle, auxin promotes the degradation of Aux/IAA transcriptional repressors through the SKP–Cullin-F–boxTIR1 complex, relieving the repression of auxin-responsive genes by allowing auxin response factors (ARFs) to activate the transcription of auxin-responsive genes involved in growth responses. Analyses of transcriptome changes during dormancy transitions have identified MADS-box transcription factors associated with endodormancy induction. Previous studies show that poplar dormancy-associated MADS-box (DAM) genes PtMADS7 and PtMADS21 are differentially regulated during the growth-dormancy cycle. Endodormancy may be regulated by internal factors, which are specifically localized in buds. PtMADS7/PtMADS21 may function as an internal regulator in poplar. The control of flowering time shares certain regulatory hierarchies with control of the dormancy/growth cycle. However, the particularities of different stages of the dormancy/growth cycle warrant comprehensive approaches to identify the causative genes for the entire cycle. A growing body of knowledge also indicates epigenetic regulation plays a role in these processes in perennial horticultural and forestry plants. The increased knowledge contributes to better understanding of the dormancy process and consequently to precise manipulation of dormancy-related horticultural traits, such as flowering time.

Formation of secondary wall requires coordinated transcriptional regulation of the genes involved in the biosynthesis of major secondary wall components (e.g. cellulose, hemicellulose, and lignin). even though many aspects of plant biology

SUMMARYAtC3H14 (At1 g66810) is a plant-specific tandem CCCH zinc-finger (TZF) protein that belongs to the 68-member CCCH family in Arabidopsis thaliana. In animals, TZFs have been shown to bind and recruit target mRNAs to the cytoplasmic foci where mRNA decay enzymes are active. However, it is not known whether plant TZF proteins such as AtC3H14 function. So far, no mRNA targets of plant TZFs have been identified. We have obtained several lines of experimental evidence in support of our hypothesis that AtC3H14 is involved in post-transcriptional regulation of its target genes. Nucleic acid binding assays using [ 35 S]-labeled AtC3H14 protein showed that AtC3H14 could bind to ssDNA, dsDNA, and ribohomopolymers, suggesting its RNA-binding activity. RNA immunoprecipitation (RIP) assay identified several putative target RNAs of AtC3H14, including a polygalacturonase, a well-known cell wall modifying gene. RNA electrophoretic mobility shift assays (RNA-EMSA) were used to confirm the RIP results and demonstrate that the TZF domain of AtC3H14 is required for the target RNA binding. Microarray analysis of 35S::AtC3H14 plants revealed that many of the cell wall elongation and/or modification-associated genes were differentially expressed, which is consistent with the cell elongation defect phenotype and the changes in the cell wall monosaccharide composition. In addition, yeast activation assay showed that AtC3H14 also function as a transcriptional activator, which is consistent with the previous finding that AtC3H14 activate the secondary wall biosynthesis genes. Taken together, we conclude that AtC3H14 may play a key role in both transcriptional and post-transcriptional regulation.

Mannans are hemicellulosic polysaccharides that have a structural role and serve as storage reserves during plant growth and development. Previous studies led to the conclusion that mannan synthase enzymes in several plant species are encoded by members of the cellulose synthase-like A (CSLA) gene family. Arabidopsis has nine members of the CSLA gene family. Earlier work has shown that CSLA9 is responsible for the majority of glucomannan synthesis in both primary and secondary cell walls of Arabidopsis inflorescence stems. Little is known about how expression of the CLSA9 gene is regulated. Sequence analysis of the CSLA9 promoter region revealed the presence of multiple copies of a cis-regulatory motif (M46RE) recognized by transcription factor MYB46, leading to the hypothesis that MYB46 (At5g12870) is a direct regulator of the mannan synthase CLSA9. We obtained several lines of experimental evidence in support of this hypothesis. First, the expression of CSLA9 was substantially upregulated by MYB46 overexpression. Second, electrophoretic mobility shift assay (EMSA) was used to demonstrate the direct binding of MYB46 to the promoter of CSLA9 in vitro. This interaction was further confirmed in vivo by a chromatin immunoprecipitation assay. Finally, over-expression of MYB46 resulted in a significant increase in mannan content. Considering the multifaceted nature of MYB46-mediated transcriptional regulation of secondary wall biosynthesis, we reasoned that additional transcription factors are involved in the CSLA9 regulation. This hypothesis was tested by carrying out yeast-one hybrid screening, which identified ANAC041 and bZIP1 as direct regulators of CSLA9. Transcriptional activation assays and EMSA were used to confirm the yeast-one hybrid results. Taken together, we report that transcription factors ANAC041, bZIP1 and MYB46 directly regulate the expression of CSLA9.