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• The patterning of adaxial–abaxial tissues plays a vital role in the morphology of lateral organs, which is maintained by antagonism between the genes that specify adaxial and abaxial tissue identity. The homeo-domain leucine zipper class III (HD-ZIP III) family genes regulate adaxial identity; however, little information is known about the physical interactions or transcriptionally regulated downstream genes of HD-ZIP III. • In this study, we identified a dominant rice mutant, lateral floret 1 (lf1), which has defects in lateral organ polarity. LF1 encodes the HD-ZIP III transcription factor, which expressed in the adaxial area of lateral organs. • LF1 can activate directly the expression of LITTLE ZIPPER family gene OsZPR4 and HD-ZIP II family gene OsHOX1, and OsZPR4 and OsHOX1 respectively interact with LF1 to form a heterodimer to repress the transcriptional activity of LF1. LF1 influences indole-3-acetic acid (IAA) content by directly regulating the expression of OsYUCCA6. Therefore, LF1 forms negative feedback loops between OsZPR4 and OsHOX1 to affect IAA content, leading to the regulation of lateral organs polarity development. • These results reveal the cross-talk among HD-ZIP III, LITTLE ZIPPER, and HD-ZIP II proteins and provide new insights into the molecular mechanisms underlying the polarity development of lateral organs.

Summary Glandular trichomes and cuticles are both specialized structures that cover the epidermis of aerial plant organs. The former are commonly regarded as ‘biofactories’ for producing valuable natural products. The latter are generally considered as natural barriers for defending plants against abiotic and biotic stresses. However, the regulatory network for their formation and relationship remains largely elusive. Here we identify a homeodomain‐leucine zipper (HD‐ZIP) IV transcription factor, AaHD8, directly promoting the expression of AaHD1 for glandular trichome initiation in Artemisia annua. We found that AaHD8 positively regulated leaf cuticle development in A. annua via controlling the expression of cuticle‐related enzyme genes. Furthermore, AaHD8 interacted with a MIXTA‐like protein AaMIXTA1, a positive regulator of trichome initiation and cuticle development, forming a regulatory complex and leading to enhanced transcriptional activity in regulating the expression of AaHD1 and cuticle development genes. Our results reveal a molecular mechanism by which a novel HD‐ZIP IV/MIXTA complex plays a significant role in regulating epidermal development, including glandular trichome initiation and cuticle formation.

The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron–exon structure and by unique codomain architectures. We identified many new genes belonging to previously defined classes (HD-ZIP I to IV, BEL, KNOX, PLINC, WOX). Other newly identified genes allowed us to characterize PHD, DDT, NDX, and LD genes as members of four new evolutionary classes and to define two additional classes, which we named SAWADEE and PINTOX. Our comprehensive analysis allowed us to identify several newly characterized conserved motifs, including novel zinc finger motifs in SAWADEE and DDT. Members of the BEL and KNOX classes were found in Chlorobionta (green plants) and in Rhodophyta. We found representatives of the DDT, WOX, and PINTOX classes only in green plants, including unicellular green algae, moss, and vascular plants. All 14 homeobox gene classes were represented in flowering plants, Selaginella, and moss, suggesting that they had already differentiated in the last common ancestor of moss and vascular plants.

• Plant glandular secretory trichomes (GSTs) produce various specialized metabolites. Increasing GST density represents a strategy to enhance the yield of these chemicals; however, the gene regulatory network that controls GST initiation remains unclear. • In a previous study of Artemisia annua L., we found that a HD-ZIP IV transcription factor, AaHD1, promotes GST initiation by directly regulating AaGSW2. Here, we identified two AaHD1-interacting transcription factors, namely AaMIXTA-like 2 (AaMYB16) and AaMYB5. • Through the generation and characterization of transgenic plants, we found that AaMYB16 is a positive regulator of GST initiation, whereas AaMYB5 has the opposite effect. Notably, neither of them regulates GST formation independently. Rather, they act competitively, by interacting and modulating AaHD1 promoter binding activity. Additionally, the phytohormone jasmonic acid (JA) was shown to be associated with the AaHD1-AaMYB16/AaMYB5 regulatory network through transcriptional regulation via a JASMONATE-ZIM DOMAIN (JAZ) protein repressor. • These results bring new insights into the mechanism of GST initiation through regulatory complexes, which appear to have similar functions in a range of vascular plant taxa.

Wood development is strictly regulated by various phytohormones and auxin plays a central regulatory role in this process. However, how the auxin signaling is transducted in developing secondary xylem during wood formation in tree species remains unclear. Here, we identified an Aux/INDOLE-3-ACETIC ACID 9 (IAA9)-AUXIN RESPONSE FACTOR 5 (ARF5) module in Populus tomentosa as a key mediator of auxin signaling to control early developing xylem development. PtoIAA9, a canonical Aux/IAA gene, is predominantly expressed in vascular cambium and developing secondary xylem and induced by exogenous auxin. Overexpression of PtoIAA9m encoding a stabilized IAA9 protein significantly represses secondary xylem development in transgenic poplar. We further showed that PtoIAA9 interacts with PtoARF5 homologs via the C-terminal III/IV domains. The truncated PtoARF5.1 protein without the III/IV domains rescued defective phenotypes caused by PtoIAA9m. Expression analysis showed that the PtoIAA9-PtoARF5 module regulated the expression of genes associated with secondary vascular development in PtoIAA9m- and PtoARF5.1-overexpressing plants. Furthermore, PtoARF5.1 could bind to the promoters of two Class III homeodomain-leucine zipper (HD-ZIP III) genes, PtoHB7 and PtoHB8, to modulate secondary xylem formation. Taken together, our results suggest that the Aux/IAA9-ARF5 module is required for auxin signaling to regulate wood formation via orchestrating the expression of HD-ZIP III transcription factors in poplar.

Summary Drought stress seriously impacts on plant development and productivity. Improvement of drought tolerance without yield penalty is a great challenge in crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain‐leucine zipper transcription factor gene, OsTF1L (Oryza sativa transcription factor 1‐like), is a key regulator of drought tolerance mechanisms. Overexpression of the OsTF1L in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both effective photosynthesis and a reduction in the water loss rate under drought conditions. Importantly, the OsTF1L overexpressing plants showed a higher drought tolerance at the reproductive stage of growth with a higher grain yield than nontransgenic controls under field‐drought conditions. Genomewide analysis of OsTF1L overexpression plants revealed up‐regulation of drought‐inducible, stomatal movement and lignin biosynthetic genes. Overexpression of OsTF1L promoted accumulation of lignin in shoots, whereas the RNAi lines showed opposite patterns of lignin accumulation. OsTF1L is mainly expressed in outer cell layers including the epidermis, and the vasculature of the shoots, which coincides with areas of lignification. In addition, OsTF1L overexpression enhances stomatal closure under drought conditions resulted in drought tolerance. More importantly, OsTF1L directly bound to the promoters of lignin biosynthesis and drought‐related genes involving poxN/PRX38, Nodulin protein, DHHC4, CASPL5B1 and AAA‐type ATPase. Collectively, our results provide a new insight into the role of OsTF1L in enhancing drought tolerance through lignin biosynthesis and stomatal closure in rice.

A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial–abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets.

• Fruit spine is an important trait in cucumber, affecting not only commercial quality, but also fruit smoothness, transportation and storage. Spine size is determined by a multi-cellular base. However, the molecular mechanism underlying the regulation of cucumber spine base remains largely unknown. Here, we report map-based cloning and characterization of a spine base size 1 (SBS1) gene, encoding a C2H2 zinc-finger transcription factor. • Near-isogenic lines of cucumber were used to map, identify and quantify cucumber spine base size 1 (CsSBS1). Yeast-hybrid, bimolecular fluorescence complementation (BiFC), co-immunoprecipitation (Co-IP) and RNA-sequencing assays were used to explore the molecular mechanism of CsSBS1 in regulating spine base size development. • CsSBS1 was specifically expressed in cucumber ovaries with particularly high expression in fruit spines. Overexpression of CsSBS1 resulted in large fruit spine base, while RNA-interference silencing of CsSBS1 inhibited the expansion of fruit spine base. Sequence analysis of natural cucumber accessions revealed that CsSBS1 was lost in small spine base accessions, resulting from a 4895 bp fragment deletion in CsSBS1 locus. CsSBS1 can form a trimeric complex with two positive regulators CsTTG1 and CsGL1 to regulate spine base development through ethylene signaling. • A novel regulator network is proposed that the CsGL1/CsSBS1/CsTTG1 complex plays a significant role in regulating spine base formation and size, which offers a strategy for cucumber breeders to develop smooth fruit.

The homeodomain-leucine zipper (HD-Zip) class of transcription factors is unique to plants. HD-Zip proteins bind to DNA exclusively as dimers recognizing dyad symmetric sequences and act as positive or negative regulators of gene expression. On the basis of sequence homology in the HD-Zip DNA-binding domain, HD-Zip proteins have been grouped into four families (HD-Zip I–IV). Each HD-Zip family can be further divided into subfamilies containing paralogous genes that have arisen through genome duplication. Remarkably, all the members of the HD-Zip IIγ and -δ clades are regulated by light quality changes that induce in the majority of the angiosperms the shade-avoidance response, a process regulated at multiple levels by auxin. Intriguingly, it has recently emerged that, apart from their function in shade avoidance, the HD-Zip IIγ and -δ transcription factors control several auxin-regulated developmental processes, including apical embryo patterning, lateral organ polarity, and gynoecium development, in a white-light environment. This review presents recent advances in our understanding of HD-Zip II protein function in plant development, with particular emphasis on the impact of loss-of-function HD-Zip II mutations on auxin distribution and response. The review also describes evidence demonstrating that HD-Zip IIγ and -δ genes are directly and positively regulated by HD-Zip III transcription factors, primary determinants of apical shoot development, known to control the expression of several auxin biosynthesis, transport, and response genes. Finally, the interplay between HD-Zip II and III transcription factors in embryo apical patterning and organ polarity is discussed.

Summary Wood production is dependent on the activity of the vascular cambium, which develops from the fascicular and interfascicular cambia. However, little is known about the mechanisms controlling how the vascular cambium is developed in woody species. Here, we show that PtrHB4, belonging to the Populus HD‐ZIP III family, plays a critical role in the process of vascular cambium development. PtrHB4 was specifically expressed in shoot tip and stem vascular tissue at an early developmental stage. Repression of PtrHB4 caused defects in the development of the secondary vascular system due to failures in interfascicular cambium formation. By contrast, overexpression of PtrHB4 induced cambium activity and xylem differentiation during secondary vascular development. Transcriptional analysis of PtrHB4 repressed plants indicated that auxin response and cell proliferation were affected in the formation of the interfascicular cambium. Taken together, these results suggest that PtrHB4 is required for interfascicular cambium formation to develop the vascular cambium in woody species.