The Arabidopsis homeodomain-leucine zipper II gene family: diversity and redundancy

'Organ'ising Floral Organ Development

Flowers are plant structures characteristic of the phylum Angiosperms composed of organs thought to have emerged from homologous structures to leaves in order to specialize in a distinctive function: reproduction. Symmetric shapes, colours, and scents all play important functional roles in flower biology. The evolution of flower symmetry and the morphology of individual flower parts (sepals, petals, stamens, and carpels) has significantly contributed to the diversity of reproductive strategies across flowering plant species. This diversity facilitates attractiveness for pollination, protection of gametes, efficient fertilization, and seed production. Symmetry, the establishment of body axes, and fate determination are tightly linked. The complex genetic networks underlying the establishment of organ, tissue, and cellular identity, as well as the growth regulators acting across the body axes, are steadily being elucidated in the field. In this review, we summarise the wealth of research already at our fingertips to begin weaving together how separate processes involved in specifying organ identity within the flower may interact, providing a functional perspective on how identity determination and axial regulation may be coordinated to inform symmetrical floral organ structures.

The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development

The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.

Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri)

BACKGROUND

The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls.

RESULTS

In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets.

CONCLUSIONS

This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.

Genome-wide characterization and expression profiling of the HD-ZIP gene family in Acoraceae under salinity and cold stress

The Homeodomain-Leucine Zipper (HD-ZIP) transcription factors play a pivotal role in governing various aspects of plant growth, development, and responses to abiotic stress. Despite the well-established importance of HD-ZIPs in many plants, their functions in Acoraceae, the basal lineage of monocots, remain largely unexplored. Using recently published whole-genome data, we identified 137 putative HD-ZIPs in two Acoraceae species, Acorus gramineus and Acorus calamus. These HD-ZIP genes were further classified into four subfamilies (I, II, III, IV) based on phylogenetic and conserved motif analyses, showcasing notable variations in exon-intron patterns among different subfamilies. Two microRNAs, miR165/166, were found to specifically target HD-ZIP III genes with highly conserved binding sites. Most cis-acting elements identified in the promoter regions of Acoraceae HD-ZIPs are involved in modulating light and phytohormone responsiveness. Furthermore, our study revealed an independent duplication event in Ac. calamus and a one-to-multiple correspondence between HD-ZIP genes of Ac. calamus and Ac. gramineus. Expression profiles obtained from qRT-PCR demonstrated that HD-ZIP I genes are strongly induced by salinity stress, while HD-ZIP II members have contrasting stress responses in two species. HD-ZIP III and IV genes show greater sensitivity in stress-bearing roots. Taken together, these findings contribute valuable insights into the roles of HD-ZIP genes in stress adaptation and plant resilience in basal monocots, illuminating their multifaceted roles in plant growth, development, and response to abiotic stress.

HD-Zip II transcription factors control distal stem cell fate in Arabidopsis roots by linking auxin signaling to the FEZ/SOMBRERO pathway

In multicellular organisms, specialized tissues are generated by specific populations of stem cells through cycles of asymmetric cell divisions, where one daughter undergoes differentiation and the other maintains proliferative properties. In Arabidopsis thaliana roots, the columella - a gravity-sensing tissue that protects and defines the position of the stem cell niche - represents a typical example of a tissue whose organization is exclusively determined by the balance between proliferation and differentiation. The columella derives from a single layer of stem cells through a binary cell fate switch that is precisely controlled by multiple, independent regulatory inputs. Here, we show that the HD-Zip II transcription factors (TFs) HAT3, ATHB4 and AHTB2 redundantly regulate columella stem cell fate and patterning in the Arabidopsis root. The HD-Zip II TFs promote columella stem cell proliferation by acting as effectors of the FEZ/SMB circuit and, at the same time, by interfering with auxin signaling to counteract hormone-induced differentiation. Overall, our work shows that HD-Zip II TFs connect two opposing parallel inputs to fine-tune the balance between proliferation and differentiation in columella stem cells.

Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis

BACKGROUND

Homeodomain-leucine zipper (HD-Zip) transcription factors are plant-specific and play important roles in plant defense against environmental stresses. Identification and functional studies have been carried out in model plants such as rice, Arabidopsis thaliana, and poplar, but comprehensive analysis on the HD-Zip family of Salix suchowensis have not been reported.

RESULTS

A total of 55 HD-Zip genes were identified in the willow genome, unevenly distributed on 18 chromosomes except for chromosome 19. And segmental duplication events containing SsHD-Zip were detected on all chromosomes except chromosomes 13 and 19. The SsHD-Zip were classified into 4 subfamilies subfamilies (I-IV) according to the evolutionary analysis, and members of each subfamily shared similar domain structure and gene structure. The combination of GO annotation and promoter analysis showed that SsHD-Zip genes responded to multiple abiotic stresses. Furthermore, the results of qPCR analysis showed that the SsHD-Zip I gene exhibited different degrees of expression under salt stress, PEG treatment and heat treatment. Moreover, there was a synergistic effect between SsHD-Zip I genes under stress conditions based on coregulatory networks analysis.

CONCLUSIONS

In this study, HD-Zip transcription factors were systematically identified and analyzed at the whole genome level. These results preliminarily clarified the structural characteristics and related functions of willow HD-Zip family members, and it was found that SsHox34, SsHox36 and SsHox51 genes were significantly involved in the response to various stresses. Together, these findings laid the foundation for further research on the resistance functions of willow HD-Zip genes.

Pepper homeobox abscisic acid signalling-related transcription factor 1, CaHAT1, plays a positive role in drought response

Abscisic acid (ABA) signalling triggers drought resistance mediated by SNF1-related kinase 2s (SnRK2s), which transmits stress signals through the phosphorylation of several downstream factors. However, these kinases and their downstream targets remain elusive in pepper plants. This study aimed to isolate interacting partners of CaSnRK2.6, a homologue of Arabidopsis SnRK2.6/OST1. Among the candidate proteins, we identified a homeodomain-leucine zipper (HD-Zip) class II protein and named it CaHAT1 (Capsicum annuum homeobox ABA signalling related- transcription factor 1). CaHAT1-silenced pepper and -overexpression (OE) transgenic Arabidopsis plants were generated to investigate the in vivo function of CaHAT1 in drought response. Following the application of drought stress, CaHAT1-silenced pepper plants exhibited drought-sensitive phenotypes with reduced ABA-mediated stomatal closure and lower expression of stress-responsive genes compared with control plants. In contrast, CaHAT1-OE transgenic Arabidopsis plants showed the opposite phenotypes, including increased drought resistance and ABA sensitivity. CaHAT1, particularly its N-terminal consensus sequences, was directly phosphorylated by CaSnRK2.6. Furthermore, CaSnRK2.6 kinase activity and CaSnRK2.6-mediated CaHAT1 phosphorylation levels were enhanced by treatment with ABA and drought stress. Taken together, our results indicated that CaHAT1, which is the target protein of CaSnRK2.6, is a positive regulator of drought stress response. This study advances our understanding of CaHAT1-CaSnRK2.6 mediated defence mechanisms in pepper plants against drought stress.

Identification and analysis of HD-Zip genes involved in the leaf development of Liriodendron chinense using multidimensional analysis

Homeodomain-leucine zipper (HD-Zip) proteins are plant-specific transcription factors that play important roles in different biological processes, especially leaf development. However, no studies to date have identified the HD-Zip genes in Liriodendron chinense nor characterized their functions. We identified the HD-Zip genes in L. chinense by analysing the phylogeny, chromosome location, structure, conserved motif, cis-regulatory elements, synteny, post-transcriptional regulation and expression patterns of these genes during leaf development. A total of 36 LcHD-Zip genes were identified and divided into four subfamilies (HD-Zip I to IV). Synteny analysis revealed that segmental duplication was the main force driving the expansion of LcHD-Zip genes. These 36 LcHD-Zip genes exhibited 11 different expression patterns. Pattern 1, 2, 3, 4, 6, 7, 8 and 9 genes may play important roles in leaf development, such as leaf initiation, leaf polarity establishment, leaf shape development, phytohormone-mediated leaf growth and leaf epidermal structure formation. Four HD-Zip III genes were targeted by microRNAs (miRNAs), and the miR165/166a-HD-Zip regulatory module formed regulated leaf initiation and leaf polarity establishment. Overall, LcHD-Zip genes play key roles in leaf development of L. chinense. This work provides a foundation for the functional verification of HD-Zip genes identified in this study.

Arabidopsis homeobox-leucine zipper transcription factor BRASSINOSTEROID-RELATED HOMEOBOX 3 regulates leaf greenness by suppressing BR signaling

Brassinosteroid (BR) is a phytohormone that acts as important regulator of plant growth. To identify novel transcription factors that may be involved in unknown mechanisms of BR signaling, we screened the chimeric repressor expressing plants (CRES-T), in which transcription factors were converted into chimeric repressors by the fusion of SRDX plant-specific repression domain, to identify those that affect the expression of BR inducible genes. Here, we identified a homeobox-leucine zipper type transcription factor, BRASSINOSTEROID-RELATED-HOMEOBOX 3 (BHB3), of which a chimeric repressor expressing plants (BHB3-sx) significantly downregulated the expression of BAS1 and SAUR-AC1 that are BR inducible genes. Interestingly, ectopic expression of BHB3 (BHB3-ox) also repressed the BR inducible genes and shorten hypocotyl that would be similar to a BR-deficient phenotype. Interestingly, both BHB3-sx and BHB3-ox showed pale green phenotype, in which the expression of genes related photosynthesis and chlorophyll contents were significantly decreased. We found that BHB3 contains three motifs similar to the conserved EAR-repression domain, suggesting that BHB3 may act as a transcriptional repressor. These results indicate that BHB3 might play an important role not only to the BR signaling but also the regulation of greenings.

AtERF71/HRE2, an Arabidopsis AP2/ERF Transcription Factor Gene, Contains Both Positive and Negative Cis-Regulatory Elements in Its Promoter Region Involved in Hypoxia and Salt Stress Responses

In the signal transduction network, from the perception of stress signals to stress-responsive gene expression, various transcription factors and cis-regulatory elements in stress-responsive promoters coordinate plant adaptation to abiotic stresses. Among the AP2/ERF transcription factor family, group VII ERF (ERF-VII) genes, such as RAP2.12, RAP2.2, RAP2.3, AtERF73/HRE1, and AtERF71/HRE2, are known to be involved in the response to hypoxia in Arabidopsis. Notably, HRE2 has been reported to be involved in responses to hypoxia and osmotic stress. In this study, we dissected HRE2 promoter to identify hypoxia- and salt stress-responsive region(s). The analysis of the promoter deletion series of HRE2 using firefly luciferase and GUS as reporter genes indicated that the −116 to −2 region is responsible for both hypoxia and salt stress responses. Using yeast one-hybrid screening, we isolated HAT22/ABIG1, a member of the HD-Zip II subfamily, which binds to the −116 to −2 region of HRE2 promoter. Interestingly, HAT22/ABIG1 repressed the transcription of HRE2 via the EAR motif located in the N-terminal region of HAT22/ABIG1. HAT22/ABIG1 bound to the 5′-AATGATA-3′ sequence, HD-Zip II-binding-like cis-regulatory element, in the −116 to −2 region of HRE2 promoter. Our findings demonstrate that the −116 to −2 region of HRE2 promoter contains both positive and negative cis-regulatory elements, which may regulate the expression of HRE2 in responses to hypoxia and salt stress and that HAT22/ABIG1 negatively regulates HRE2 transcription by binding to the HD-Zip II-binding-like element in the promoter region.

The Arabidopsis HDZIP class II transcription factor ABA INSENSITIVE TO GROWTH 1 functions in leaf development

Leaf laminar growth and adaxial-abaxial boundary formation are fundamental outcomes of plant development. Boundary and laminar growth coordinate the further patterning and growth of the leaf, directing the differentiation of cell types within the top and bottom domains and promoting initiation of lateral organs along their adaxial or abaxial axis. Leaf adaxial-abaxial polarity specification and laminar outgrowth are regulated by two transcription factors, REVOLUTA (REV) and KANADI (KAN). ABA INSENSITIVE TO GROWTH 1 (ABIG1) encodes a HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP) class II transcription factor and is a direct target of the adaxial-abaxial regulators REV and KAN. To investigate the role of ABIG1 in leaf development and in the establishment of polarity, we examined the phenotypes of both gain-of-function and loss-of-function mutants. Through genetic interaction analysis with REV and KAN mutants, we determined that ABIG1 plays a role in leaf laminar growth as well as in adaxial-abaxial polarity establishment. Genetic and physical interaction assays showed that ABIG1 interacts with the transcriptional TOPLESS corepressor. This study provides new evidence that ABIG1, another HD-ZIP II, facilitates growth through the corepressor TOPLESS.

PtrHAT22, as a higher hierarchy regulator, coordinately regulates secondary cell wall component biosynthesis in Populus trichocarpa

Homeodomain-leucine zipper (HD-Zip) II transcription factors (TFs) have been reported to play vital roles in diverse biological processes of plants. However, it remains unclear whether HD-Zip II TFs regulate secondary cell wall (SCW) in woody plants. In this study, we performed the functional characterization of a Populus trichocarpa HD-Zip II TF, PtrHAT22, which encodes a nuclear localized transcription repressor predominantly expressing in secondary developing tissues. Overexpression of PtrHAT22 showed arrested growths, including reduced heights and diameters above the ground, small leaves, and decreased biomass. Meanwhile, the contents of lignin, cellulose, and thickness of SCW significantly decreased, whilst the content of hemicellulose obviously increased in PtrHAT22 transgenic poplar. The expressions of some wood-associated TFs and structural genes significantly changed accordingly with the alternations of SCW characteristics in PtrHAT22 transgenic poplar. Furthermore, PtrHAT22 directly repressed the promoter activities of PtrMYB20, PtrMYB28, and PtrCOMT2, and bind two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggested that PtrHAT22, as a higher hierarchy TF like PtrWNDs, exerted coordination regulation of poplar SCW component biosynthesis through directly and indirectly regulating structural genes and different hierarchy TFs of SCW formation network.

Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance

Drought is the main limiting factor of maize productivity, therefore improving drought tolerance in maize has potential practical importance. Cloning and functional verification of drought-tolerant genes is of great importance to understand molecular mechanisms under drought stress. Here, we employed a bioinformatic pipeline to identify 42 ZmHDZ drought responsive genes using previously reported maize transcriptomic datasets. The coding sequences, exon-intron structure and domain organization of all the 42 genes were identified. Phylogenetic analysis revealed evolutionary conservation of members of the ZmHDZ genes in maize. Several regulatory elements associated with drought tolerance were identified in the promoter regions of ZmHDZ genes, indicating the implication of these genes in plant response to drought stress. 42 ZmHDZ genes were distributed unevenly on 10 chromosomes, and 24 pairs of gene duplications were the segmental duplication. The expression of several ZmHDZ genes was upregulated under drought stress, and ZmHDZ9 overexpressing transgenic plants exhibited higher SOD and POD activities and higher accumulation of soluble proteins under drought stress which resulted in enhanced developed phenotype and improved resistance. The present study provides evidence for the evolutionary conservation of HD-ZIP transcription factors homologs in maize. The results further provide a comprehensive insight into the roles of ZmHDZ genes in regulating drought stress tolerance in maize.

Osmotic stress represses root growth by modulating the transcriptional regulation of PIN-FORMED3

Osmotic stress influences root system architecture, and polar auxin transport (PAT) is well established to regulate root growth and development. However, how PAT responds to osmotic stress at the molecular level remains poorly understood. In this study, we explored whether and how the auxin efflux carrier PIN-FORMED3 (PIN3) participates in osmotic stress-induced root growth inhibition in Arabidopsis (Arabidopsis thaliana). We observed that osmotic stress induces a HD-ZIP II transcription factor-encoding gene HOMEODOMAIN ARABIDOPSIS THALIANA2 (HAT2) expression in roots. The hat2 loss-of-function mutant is less sensitive to osmotic stress in terms of root meristem growth. Consistent with this phenotype, whereas the auxin response is downregulated in wild-type roots under osmotic stress, the inhibition of auxin response by osmotic stress was alleviated in hat2 roots. Conversely, transgenic lines overexpressing HAT2 (Pro35S::HAT2) had shorter roots and reduced auxin accumulation compared with wild-type plants. PIN3 expression was significantly reduced in the Pro35S::HAT2 lines. We determined that osmotic stress-mediated repression of PIN3 was alleviated in the hat2 mutant because HAT2 normally binds to the promoter of PIN3 and inhibits its expression. Taken together, our data revealed that osmotic stress inhibits root growth via HAT2, which regulates auxin activity by directly repressing PIN3 transcription.

microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family

MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.

Genetic transformation and growth index determination of the Larix olgensis LoHDZ2 transcription factor gene in tobacco

Homeodomain-leucine zippers (HD-Zip) are plant-specific transcription factors that participate in different plant development processes and differentially regulate metabolic processes. LoHDZ2 is an HD-ZipII subfamily transcription factor gene that we identified from a transcriptomic analysis of Larix olgensis. To understand its function, we built a LoHDZ2 expression vector and then inserted it into tobacco by genetic transformation. Transgenic plants were identified at the DNA and RNA levels. Phenotypic index analysis of transgenic tobacco showed dwarfed growth with larger leaves and earlier flowering than the wild type. LoHDZ2 was expressed differently after hormone treatment with IAA, MeJA and 2,4-D. The results suggested that LoHDZ2 may respond to hormones and be involved in regulating growth and metabolism. These results helped us better understand the function of LoHDZ2 and provided a candidate gene for Larix olgensis molecular breeding.

HD-ZIP Gene Family: Potential Roles in Improving Plant Growth and Regulating Stress-Responsive Mechanisms in Plants

Exploring the molecular foundation of the gene-regulatory systems underlying agronomic parameters or/and plant responses to both abiotic and biotic stresses is crucial for crop improvement. Thus, transcription factors, which alone or in combination directly regulated the targeted gene expression levels, are appropriate players for enlightening agronomic parameters through genetic engineering. In this regard, homeodomain leucine zipper (HD-ZIP) genes family concerned with enlightening plant growth and tolerance to environmental stresses are considered key players for crop improvement. This gene family containing HD and LZ domain belongs to the homeobox superfamily. It is further classified into four subfamilies, namely HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. The first HD domain-containing gene was discovered in maize cells almost three decades ago. Since then, with advanced technologies, these genes were functionally characterized for their distinct roles in overall plant growth and development under adverse environmental conditions. This review summarized the different functions of HD-ZIP genes in plant growth and physiological-related activities from germination to fruit development. Additionally, the HD-ZIP genes also respond to various abiotic and biotic environmental stimuli by regulating defense response of plants. This review, therefore, highlighted the various significant aspects of this important gene family based on the recent findings. The practical application of HD-ZIP biomolecules in developing bioengineered plants will not only mitigate the negative effects of environmental stresses but also increase the overall production of crop plants.

A HAT1-DELLA signaling module regulates trichome initiation and leaf growth by achieving gibberellin homeostasis

Trichome initiation and leaf growth are two critical developmental processes in the plant life cycle, which need to be optimized in accordance with developmental stage and immediate surroundings. To a large extent, this optimization is achieved by fine-tuning of hormonal pathways, including the gibberellin (GA) pathway. However, the mechanism by which plants control GA homeostasis to optimize these two developmental processes is unknown. Here, we report that HAT1, a HD-ZIP II transcription factor, negatively regulates GA-mediated trichome initiation and cotyledon expansion. Both protein and transcript levels indicated that HAT1 was induced by GA, while an increased abundance of HAT1, in turn, was found to suppress GA biosynthesis and signaling, thus forming a regulatory negative feedback loop that controls GA homeostasis to fine-tune trichome development and cotyledon expansion. We also found that HAT1 interacts with DELLAs, including GAI and RGA. GAI inhibits both protein stability and the binding activity of HAT1 to its target genes. Overexpression of HAT1 in della5 can completely suppress the enhanced trichome initiation and enlarged cotyledon of della5. Our findings demonstrate that HAT1 functions as a critical repressor to regulate GA-mediated trichome initiation and cotyledon growth; in addition, we describe a novel mechanism by which the plant regulates trichome initiation and cotyledon expansion through a HAT1-DELLA regulatory module under various GA concentrations.

The underground life of homeodomain-leucine zipper transcription factors

Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I-IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.

A moso bamboo transcription factor, Phehdz1, positively regulates the drought stress response of transgenic rice

78 HD-Zip family genes in Phyllostachys edulis were analyzed. Overexpression of Phehdz1 can improve the drought tolerance of transgenic rice and affect its secondary metabolism. Many studies suggested homeodomain-leucine zipper (HD-Zip) transcription factors are important regulators of plant growth and development, signal transduction, and responses to environmental stresses. In this study, 78 moso bamboo (Phyllostachys edulis) HD-Zip genes were investigated and classified into four subfamilies (HD-Zip I-IV). Additionally, Phehdz1 (HD-Zip I gene) was isolated and confirmed to be highly expressed in the roots. A quantitative real-time PCR analysis indicated Phehdz1 expression was significantly induced by drought, high salinity, and abscisic acid (ABA). A transient expression assay proved that Phehdz1 was localized in the nucleus of tobacco cells. Moreover, it could bind to the core region encoded by the H-box sequence (CAATAATTG) in yeast. In response to mannitol treatments, the Phehdz1-overexpressing transgenic rice had a higher germination rate and longer shoots than the wild-type controls. Moreover, Phehdz1-overexpressing rice plants had a higher survival rate as well as higher relative water and proline contents, but a lower malondialdehyde content, than the WT plants after a 30% polyethylene glycol 6000 treatment. Accordingly, the overexpression of Phehdz1 enhances the drought tolerance of transgenic rice. Many of the differentially expressed genes identified by a transcriptome analysis are involved in MAPK signal transduction and the biosynthesis of secondary metabolites. Thus, the overexpression of Phehdz1 enhances the drought stress tolerance of transgenic rice, while also potentially modulating the expression of metabolism-related genes.

Emerging Molecular Links Between Plant Photomorphogenesis and Virus Resistance

Photomorphogenesis refers to photoreceptor-mediated morphological changes in plant development that are triggered by light. Multiple photoreceptors and transcription factors (TFs) are involved in the molecular regulation of photomorphogenesis. Likewise, light can also modulate the outcome of plant-virus interactions since both photosynthesis and many viral infection events occur in the chloroplast. Despite the apparent association between photosynthesis and virus infection, little is known about whether there are also interplays between photomorphogenesis and plant virus resistance. Recent research suggests that plant-virus interactions are potentially regulated by several photoreceptors and photomorphogenesis regulators, including phytochromes A and B (PHYA and PHYB), cryptochromes 2 (CRY2), phototropin 2 (PHOT2), the photomorphogenesis repressor constitutive photomorphogenesis 1 (COP1), the NAM, ATAF, and CUC (NAC)-family TF ATAF2, the Aux/IAA protein phytochrome-associated protein 1 (PAP1), the homeodomain-leucine zipper (HD-Zip) TF HAT1, and the core circadian clock component circadian clock associated 1 (CCA1). Particularly, the plant growth promoting brassinosteroid (BR) hormones play critical roles in integrating the regulatory pathways of plant photomorphogenesis and viral defense. Here, we summarize the current understanding of molecular mechanisms linking plant photomorphogenesis and defense against viruses, which represents an emerging interdisciplinary research topic in both molecular plant biology and virology.

The HD-ZIP II Transcription Factors Regulate Plant Architecture through the Auxin Pathway

The homeodomain-leucine zipper (HD-ZIP) family transcription factors play important roles in plant growth and development. However, the underlying mechanisms remain largely unclear. Here we found that ATHB2, encoding a HD-ZIP transcription factor, is an early auxin responsive gene. Phenotypic analyses show that overexpression of ATHB2 impairs plant architecture, including reduced plant height and small leaves, and also reduces auxin response in leaves when grown in soil. Simultaneously, the seedlings with chemical induction of ATHB2 exhibit abnormal root gravitropism, a typical auxin-related phenotype. We further show that the auxin response pattern is altered in roots of the inducible ATHB2 seedlings. Consistently, the transcript levels of some auxin biosynthetic and transport genes are significantly decreased in these transgenic seedlings. Further, protein and promoter sequence analyses in common wheat showed that the HD-ZIP II subfamily transcription factors have highly conserved motifs and most of these encoding gene promoters contain the canonical auxin-responsive elements. Expression analyses confirm that some of these HD-ZIP II genes are indeed regulated by auxin in wheat. Together, our results suggest that the HD-ZIP II subfamily transcription factors regulate plant development possibly through the auxin pathway in plants.

Genome wide identification, characterization and expression analysis of HD-ZIP gene family in Cucumis sativus L. under biotic and various abiotic stresses

Information retrieved from genomic assembly may provide important clues and various molecular aspects in plants. Our research identified 40 CsHDZ genes in the Cucumber genome database. Subsequently; we performed the conserved motif and domain analysis of CsHDZ proteins. The phylogeny of the CsHDZ proteins further divides into 4 subfamilies (HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV) based on the structural similarities and functional diversities. The GO (Gene ontology) analysis of CsHDZ proteins showed that they are responsive to environmental stimuli and involved in numerous growth and developmental processes. The qRT-PCR analysis of 11 CsHDZ genes showed that they are expressed in all the tested tissues of Cucumis sativus. The differential expression pattern of CsHDZ genes unfolded their possible involvement in responding to various abiotic stresses and powdery mildew stress. It has been found that the CsHDZ22 localized in the nucleus which possibly participates in the regulatory mechanisms of various biological and cellular processes. In the light of above-mentioned outcomes, it has been deducted that CsHDZ genes in the Cucumis sativus genome play an important role in mediating the resistance to various abiotic stresses and powdery mildew stress as well as provide significant clues for functional studies.

Light affects tissue patterning of the hypocotyl in the shade-avoidance response

Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.

Shade sensitive plants such as Arabidopsis respond to shade by growing tall in order to maximize their access to sunlight. We find that the REVOLUTA (REV) and KANADI1 (KAN1) transcription factors which are primarily involved in patterning the early leaf, impinge on the regulation of WUSCHEL HOMEOBOX4 (WOX4), another transcription factor involved in vascular development. The regulation of WOX4 leads to an increase of the number of water-conducting xylem cells in response to shade. Consequently, mutations in the genes encoding either REV, KAN1 or WOX4 are impaired in their ability to grow tall in shade. Thus, we have uncovered a connection between basic patterning and adaptive growth.

Genome-wide identification and expression profiling of HD-ZIP gene family in Medicago truncatula

The homeodomain-leucine zipper (HD-ZIP) transcription factors are important regulators in various developmental processes and responses to environmental stimuli. Currently, little information is available for HD-ZIP gene family in Medicago truncatula. Here we perform a genome-wide analysis of HD-ZIP gene family in M. truncatula. Totally 52 M. truncatula HD-ZIPs (MtHDZs) were identified and classified into four distinctive subfamilies (I to IV). Members clustered in the same subfamily shared similar gene structure and protein motifs. Fifty-one MtHDZs were non-evenly distributed on eight chromosomes. Segmental duplication and purifying selection mainly contributed to the expansion and retention of M. truncatula HD-ZIP gene family. Expression profiling using the publicly available microarray data revealed that MtHDZ genes exhibited distinctive tissue-specific patterns and divergent responses to drought and salt stresses. In addition, the expression profile between each paralogous pair diverged differentially. Our results identified potential targets for the genetic improvement of abiotic stress tolerance in Medicago.

Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes

Four MaHDZs are possibly involved in banana fruit ripening by activating the transcription of genes related to ethylene biosynthesis and cell wall degradation, such as MaACO5, MaEXP2, MaEXPA10, MaPG4 and MaPL4. The homeodomain-leucine zipper (HD-ZIP) proteins represent plant-specific transcription factors, which contribute to various plant physiological processes. However, little information is available regarding the association of HD-ZIPs with banana fruit ripening. In this study, we identified a total of 96 HD-ZIP genes in banana genome, which were divided into four different groups consisting of 35, 31, 9 and 21 members in the I, II, III and IV subfamilies, respectively. The expression patterns of MaHDZ genes during fruit ripening showed that MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were significantly up-regulated in the ripening stage and thus suggested to be potential regulators of banana fruit ripening. Furthermore, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 were found to localize exclusively in the nucleus and exhibit transcriptional activation capacities. Importantly, MaHDZI.19, MaHDZI.26, MaHDZII.4 and MaHDZII.7 stimulated the transcription of several ripening-related genes including MaACO5 related to ethylene biosynthesis, MaEXP2, MaEXPA10, MaPG4 and MaPL4 were associated with cell wall degradation, through directly binding to their promoters. Taken together, our findings expand the functions of HD-ZIP transcription factors and identify four MaHDZs likely involved in regulating banana fruit ripening by activating the expression of genes related to ethylene biosynthesis and cell wall modification, which may have potential application in banana molecular breeding.

Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome

When subject to vegetational shading, shade-avoiding plants detect neighbors by perceiving reduced light quantity and altered light quality. The former includes decreases in the ratio of red to far-red wavelengths (low R:FR) and low blue light ratio (LBL) predominantly detected by phytochromes and cryptochromes, respectively. By integrating multiple signals, plants generate a suite of responses, such as elongation of a variety of organs, accelerated flowering, and reduced branching, which are collectively termed the shade-avoidance syndrome (SAS). To trigger the SAS, interactions between photoreceptors and phytochrome-interacting factors are the general switch for activation of downstream signaling pathways. A number of transcription factor families and phytohormones, especially auxin, gibberellins, ethylene, and brassinosteroids, are involved in the SAS processes. In this review, shade signals, the major photoreceptors involved, and the phenotypic characteristics of the shade-intolerant plant Arabidopsis thaliana are described in detail. In addition, integration of the signaling mechanisms that link photoreceptors with multiple hormone signaling pathways is presented and future research directions are discussed.

Small Grain and Dwarf 2, encoding an HD-Zip II family transcription factor, regulates plant development by modulating gibberellin biosynthesis in rice

Homeodomain leucine zipper (HD-Zip) proteins are transcription factors that regulate plant development. Bioactive gibberellin (GA) is a key endogenous hormone that participates in plant growth. However, the relationship between HD-Zip genes and modulation of GA biosynthesis in rice remains elusive. Here, we identified a rice mutant, designated as small grain and dwarf 2 (sgd2), which had reduced height and grain size compared with the wild type. Cytological observations indicated that the defective phenotype was mainly due to decreased cell length. Map-based cloning and complementation tests demonstrated that a 9 bp deletion in a homeodomain leucine zipper (HD-Zip) II family transcription factor was responsible for the sgd2 mutant phenotype. Expression of SGD2 was pronounced in developing panicles, and its protein was localized in nucleus. Luciferase reporter system and transactivation assays in yeast suggested that SGD2 functioned as a transcriptional repressor. High performance liquid chromatography assays showed that the endogenous GA₁ level in the sgd2 mutant was dramatically decreased, and exogenous GA₃ recovered the second leaf sheath to normal length. Results of qRT-PCR showed that the expression levels of genes positively regulating GA-biosynthesis were mostly down-regulated in the mutant. Our data identified the role of an HD-Zip transcription factor that affects rice plant development by modulating gibberellin biosynthesis.

Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

Background

The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas.

Results

In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame.

Conclusions

This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

Overexpressing the HD-Zip class II transcription factor EcHB1 from Eucalyptus camaldulensis increased the leaf photosynthesis and drought tolerance of Eucalyptus

Alteration in the leaf mesophyll anatomy by genetic modification is potentially a promising tool for improving the physiological functions of trees by improving leaf photosynthesis. Homeodomain leucine zipper (HD-Zip) transcription factors are candidates for anatomical alterations of leaves through modification of cell multiplication, differentiation, and expansion. Full-length cDNA encoding a Eucalyptus camaldulensis HD-Zip class II transcription factor (EcHB1) was over-expressed in vivo in the hybrid Eucalyptus GUT5 generated from Eucalyptus grandis and Eucalyptus urophylla. Overexpression of EcHB1 induced significant modification in the mesophyll anatomy of Eucalyptus with enhancements in the number of cells and chloroplasts on a leaf-area basis. The leaf-area-based photosynthesis of Eucalyptus was improved in the EcHB1-overexpression lines, which was due to both enhanced CO₂ diffusion into chloroplasts and increased photosynthetic biochemical functions through increased number of chloroplasts per unit leaf area. Additionally, overexpression of EcHB1 suppressed defoliation and thus improved the growth of Eucalyptus trees under drought stress, which was a result of reduced water loss from trees due to the reduction in leaf area with no changes in stomatal morphology. These results gave us new insights into the role of the HD-Zip II gene.

Overexpressing the HD-Zip class II transcription factor EcHB1 from Eucalyptus camaldulensis increased the leaf photosynthesis and drought tolerance of Eucalyptus

Alteration in the leaf mesophyll anatomy by genetic modification is potentially a promising tool for improving the physiological functions of trees by improving leaf photosynthesis. Homeodomain leucine zipper (HD-Zip) transcription factors are candidates for anatomical alterations of leaves through modification of cell multiplication, differentiation, and expansion. Full-length cDNA encoding a Eucalyptus camaldulensis HD-Zip class II transcription factor (EcHB1) was over-expressed in vivo in the hybrid Eucalyptus GUT5 generated from Eucalyptus grandis and Eucalyptus urophylla. Overexpression of EcHB1 induced significant modification in the mesophyll anatomy of Eucalyptus with enhancements in the number of cells and chloroplasts on a leaf-area basis. The leaf-area-based photosynthesis of Eucalyptus was improved in the EcHB1-overexpression lines, which was due to both enhanced CO₂ diffusion into chloroplasts and increased photosynthetic biochemical functions through increased number of chloroplasts per unit leaf area. Additionally, overexpression of EcHB1 suppressed defoliation and thus improved the growth of Eucalyptus trees under drought stress, which was a result of reduced water loss from trees due to the reduction in leaf area with no changes in stomatal morphology. These results gave us new insights into the role of the HD-Zip II gene.

Wheat wounding-responsive HD-Zip IV transcription factor GL7 is predominantly expressed in grain and activates genes encoding defensins

Several classes of transcription factors are involved in the activation of defensins. A new type of the transcription factor responsible for the regulation of wheat grain specific defensins was characterised in this work. HD-Zip class IV transcription factors constitute a family of multidomain proteins. A full-length cDNA of HD-Zip IV, designated TaGL7 was isolated from the developing grain of bread wheat, using a specific DNA sequence as bait in the Y1H screen. 3D models of TaGL7 HD complexed with DNA cis-elements rationalised differences that underlined accommodations of binding and non-binding DNA, while the START-like domain model predicted binding of lipidic molecules inside a concave hydrophobic cavity. The 3'-untranslated region of TaGL7 was used as a probe to isolate the genomic clone of TdGL7 from a BAC library prepared from durum wheat. The spatial and temporal activity of the TdGL7 promoter was tested in transgenic wheat, barley and rice. TdGL7 was expressed mostly in ovary at fertilisation and its promoter was active in a liquid endosperm during cellularisation and later in the endosperm transfer cells, aleurone, and starchy endosperm. The pattern of TdGL7 expression resembled that of genes that encode grain-specific lipid transfer proteins, particularly defensins. In addition, GL7 expression was upregulated by mechanical wounding, similarly to defensin genes. Co-bombardment of cultured wheat cells with TdGL7 driven by constitutive promoter and seven grain or root specific defensin promoters fused to GUS gene, revealed activation of four promoters. The data confirmed the previously proposed role of HD-Zip IV transcription factors in the regulation of genes that encode lipid transfer proteins involved in lipid transport and defence. The TdGL7 promoter could be used to engineer cereal grains with enhanced resistance to insects and fungal infections.

Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume

The homeodomain-leucine zipper (HD-Zip) gene family, a group of plant-specific transcriptional factors (TFs), participates in regulating growth, development, and environmental responses. However, the characteristics and biological functions of HD-Zip genes in Prunus mume, which blooms in late winter or early spring, have not been reported. In this study, 32 HD-Zip genes, named PmHB1-PmHB32 based on their chromosomal positions, were identified in the genome of P. mume. These genes are distributed among seven chromosomes and are phylogenetically clustered into four major groups. Gene structure and motif composition were mostly conserved in each group. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolution of the genes, which maintained the function of this family. MicroRNA target site prediction indicated that the genes of the HD-Zip III subfamily may be regulated by miR165/166. Expression pattern analysis showed that the 32 genes were differentially expressed across five different tissues (leaf, flower bud, stem, fruit, and root) and at different stages of stem and leaf-bud development, suggesting that 10 of the genes may play important roles in stem development. Protein-protein interaction predictions showed that the subfamily III genes may regulate vascular development and shoot apical meristem (SAM) maintenance. Promoter analysis showed that the HD-Zip III genes might be involved in responses to light, hormones, and abiotic stressors and stem development. Taken together, our results provide an overview of the HD-Zip family in P. mume and lay the foundation for the molecular breeding of woody ornamental plants.

AtHB2, a class II HD-ZIP protein, negatively regulates the expression of CsANS, which encodes a key enzyme in Camellia sinensis catechin biosynthesis

Tea (Camellia sinensis) is an important cash crop that is beneficial to human health because of its remarkable content of catechins. The biosynthesis of catechins follows the flavonoid pathway, which is highly branched. Among the enzymes involved in catechin biosynthesis, ANTHOCYANIDIN SYNTHASE (CsANS) functions at a branch point and play a critical role. Our previous work has showed that the gene encoding CsANS is regulated by light signals; however, the molecular mechanism behind remains unclear. Here, we cloned a full-length CsANS promoter and found that it contained a cis-element recognized by Arabidopsis thaliana HOMEOBOX2 (AtHB2). AtHB2 constitutes one of the class II HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP) proteins, which accumulate in the dark and mediate the shade avoidance response in most angiosperms. To analyze the transcription of CsANS in vivo, β-glucuronidase and luciferase reporter genes driven by the obtained promoter were introduced into A. thaliana and Nicotiana attenuata, respectively. In both expression systems there were indications that the A. thaliana PRODUCTION OF ANTHOCYANIN PIGMENT1 (AtPAP1), a MYB transcription factor of flavonoid biosynthesis, increased the activity of the CsANS promoter, while AtHB2 could significantly undermine the effect of AtPAP1. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that AtHB2 interacted with the A. thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1). A yeast three-hybrid assay further suggested that AtHB2 represses the expression of CsANS and regulates its response to light signals through competitive interactions with AtTTG1. These results show that HD-ZIP II proteins participate in light regulation of flavonoid biosynthesis.

Regulation of anthocyanin accumulation via MYB75/HAT1/TPL-mediated transcriptional repression

Anthocyanin is part of secondary metabolites, which is induced by environmental stimuli and developmental signals, such as high light and sucrose. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex in plants. But the evidence of how plants maintain anthocyanin in response to signals is lacking. Here we perform molecular and genetic evidence to display that HAT1 plays a new breaker of anthocyanin accumulation via post-translational regulations of MBW protein complex. Loss of function of HAT1 in the Arabidopsis seedlings exhibits increased anthocyanin accumulation, whereas overexpression of HAT1 significantly repressed anthocyanin accumulation. We found that HAT1 interacted with MYB75 and thereby interfered with MBW protein complex. Overexpression of HAT1 suppresses abundant anthocyanin phenotype of pap1-D plant. HAT1 is characterized as a transcriptional repressor possessing an N-terminal EAR motif, which determines to interact with TOPLESS corepressor. Repression activity of HAT1 in regulation of gene expression and anthocyanin accumulation can be abolished by deletion or mutation of the EAR motif 1. Chromatin immunoprecipitation assays revealed that MYB75 formed a transcriptional repressor complex with HAT1-TPL by histone H3 deacetylation in target genes. We proposed that HAT1 restrained anthocyanin accumulation by inhibiting the activities of MBW protein complex through blocking the formation of MBW protein complex and recruiting the TPL corepressor to epigenetically modulate the anthocyanin late biosynthetic genes (LBGs).

Anthocyanins, a class of flavonoids distributed ubiquitously in the plant kingdom, are induced by environmental stimuli and developmental signals, such as high light and sucrose. It is well established that anthocyanin accumulation is regulated by the MYB-bHLH-WD40 (MBW) protein complex in plants. But little is known about the regulation of MBW protein complex by other factors. Here, we show that an HD-ZIP II transcription factor HAT1 negatively regulates anthocyanin accumulation via post-translational regulation of MBW protein complex. Loss of function of HAT1 in the Arabidopsis seedlings exhibits increased anthocyanin accumulation, whereas overexpression of HAT1 significantly repressed anthocyanin accumulation. We reveal that HAT1 interacted with MYB75 and thereby sequestered MBW protein complex. Overexpression of HAT1 in pap1-D mutant suppresses abundant anthocyanin phenotype of the pap1-D mutant. HAT1 identified was as a transcriptional repressor possessing an N-terminal EAR motif, which determines the interaction with TOPLESS corepressor. The deletion or mutation of the EAR motif 1 of HAT1 partially eliminates the repression activity of HAT1 in regulation of gene expression and anthocyanin accumulation. Our results illustrate a new repressor HAT1 which helps plants fine-tune anthocyanin accumulation.

Genome-wide identification and characterization of HD-ZIP genes in potato

HD-ZIP (Homeodomain leucine zipper) transcription factors play an important regulatory role in stress resistance in plants. The purpose of this study was to analyze the characteristics of the HD-ZIP genes/proteins and to study their expression profiles under high and low temperature conditions in potato (Solanum tuberosum L.). A strict homology search was used to find 43 HD-ZIP genes located on potato chromosomes 1-12. Exons/introns, protein features and conserved motifs were analyzed, and six segment duplications were identified from 43 HD-ZIP genes. Then, we analyzed the data from the PGSC (Potato Genome Sequencing Consortium) database regarding the expression of 43 HD-ZIP genes that were induced by biotic and abiotic stresses and phytohormone treatments and conducted an expression analysis for these genes across all potato life stages. Additionally, the expression levels of 13 HD-ZIP genes were analyzed under high temperature (37 °C) and low temperature (4 °C) conditions. The results showed that the transcript levels of all 13 genes changed, which indicated that these genes respond to heat and cold in plants. Especially for StHOX20, the expression significantly upregulated in roots at 37 °C and 4 °C. Our findings laid the foundation and provided clues for understanding the biological functions of HD-ZIP family genes.

The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways

Cells in organ primordia undergo active proliferation at an early stage to generate sufficient number, before exiting proliferation and entering differentiation. However, how the actively proliferating cells are developmentally reprogrammed to acquire differentiation potential during organ maturation is unclear. Here, we induced a microRNA-resistant form of TCP4 at various developmental stages of Arabidopsis leaf primordium that lacked the activity of TCP4 and its homologues and followed its effect on growth kinematics. By combining this with spatio-temporal gene expression analysis, we show that TCP4 commits leaf cells within the transition zone to exit proliferation and enter differentiation. A 24-hour pulse of TCP4 activity was sufficient to impart irreversible differentiation competence to the actively dividing cells. A combination of biochemical and genetic analyses revealed that TCP4 imparts differentiation competence by promoting auxin response as well as by directly activating HAT2, a HD-ZIP II transcription factor-encoding gene that also acts downstream to auxin response. Our study offers a molecular link between the two major organ maturation factors, CIN-like TCPs and HD-ZIP II transcription factors and explains how TCP activity restricts the cell number and final size in a leaf.

Cells in a young organ primordium proliferate to generate sufficient number, before they exit division cycle and enter differentiation programme at later stages. While factors that drive cell cycle progression have been identified and studied in detail in diverse eukaryotic species, developmental factors that promote exit from division and entry into differentiation are less known, especially in the plant kingdom. Here, we show that the class II TCP proteins, notably TCP4, irreversibly reprogram the mitotic cells to exit division and acquire differentiation competence by auxin response as well as direct activation of HAT2 transcription. Our work offers a molecular link between class II TCP and HD-ZIP II genes during the cell differentiation and leaf maturation.

Multiple Links between HD-Zip Proteins and Hormone Networks

HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.

Arabidopsis HD-Zip II proteins regulate the exit from proliferation during leaf development in canopy shade

The shade avoidance response is mainly evident as increased plant elongation at the expense of leaf and root expansion. Despite the advances in understanding the mechanisms underlying shade-induced hypocotyl elongation, little is known about the responses to simulated shade in organs other than the hypocotyl. In Arabidopsis, there is evidence that shade rapidly and transiently reduces the frequency of cell division in young first and second leaf primordia through a non-cell-autonomous mechanism. However, the effects of canopy shade on leaf development are likely to be complex and need to be further investigated. Using combined methods of genetics, cell biology, and molecular biology, we uncovered an effect of prolonged canopy shade on leaf development. We show that persistent shade determines early exit from proliferation in the first and second leaves of Arabidopsis. Furthermore, we demonstrate that the early exit from proliferation in the first and second leaves under simulated shade depends at least in part on the action of the Homeodomain-leucine zipper II (HD-Zip II) transcription factors ARABIDOPSIS THALIANA HOMEOBOX2 (ATHB2) and ATHB4. Finally, we provide evidence that the ATHB2 and ATHB4 proteins work in concert. Together the data contribute new insights on the mechanisms controlling leaf development under canopy shade.

Multiple Pathways in the Control of the Shade Avoidance Response

To detect the presence of neighboring vegetation, shade-avoiding plants have evolved the ability to perceive and integrate multiple signals. Among them, changes in light quality and quantity are central to elicit and regulate the shade avoidance response. Here, we describe recent progresses in the comprehension of the signaling mechanisms underlying the shade avoidance response, focusing on Arabidopsis, because most of our knowledge derives from studies conducted on this model plant. Shade avoidance is an adaptive response that results in phenotypes with a high relative fitness in individual plants growing within dense vegetation. However, it affects the growth, development, and yield of crops, and the design of new strategies aimed at attenuating shade avoidance at defined developmental stages and/or in specific organs in high-density crop plantings is a major challenge for the future. For this reason, in this review, we also report on recent advances in the molecular description of the shade avoidance response in crops, such as maize and tomato, and discuss their similarities and differences with Arabidopsis.

Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land

Plant transition to land required several regulatory adaptations. The mechanisms behind these changes remain unknown. Since the evolution of transcription factors (TFs) families accompanied this transition, we studied the HOMEODOMAIN LEUCINE ZIPPER (HDZ) TF family known to control key developmental and environmental responses. We performed a phylogenetic and bioinformatics analysis of HDZ genes using transcriptomic and genomic datasets from a wide range of Viridiplantae species. We found evidence for the existence of HDZ genes in chlorophytes and early-divergent charophytes identifying several HDZ members belonging to the four known classes (I-IV). Furthermore, we inferred a progressive incorporation of auxiliary motifs. Interestingly, most of the structural features were already present in ancient lineages. Our phylogenetic analysis inferred that the origin of classes I, III, and IV is monophyletic in land plants in respect to charophytes. However, class IIHDZ genes have two conserved lineages in charophytes and mosses that differ in the CPSCE motif. Our results indicate that the HDZ family was already present in green algae. Later, the HDZ family expanded accompanying critical plant traits. Once on land, the HDZ family experienced multiple duplication events that promoted fundamental neo- and subfunctionalizations for terrestrial life.

Transcription factor HAT1 is a substrate of SnRK2.3 kinase and negatively regulates ABA synthesis and signaling in Arabidopsis responding to drought

Drought is a major threat to plant growth and crop productivity. The phytohormone abscisic acid (ABA) plays a critical role in plant response to drought stress. Although ABA signaling-mediated drought tolerance has been widely investigated in Arabidopsis thaliana, the feedback mechanism and components negatively regulating this pathway are less well understood. Here we identified a member of Arabidopsis HD-ZIP transcription factors HAT1 which can interacts with and be phosphorylated by SnRK2s. hat1hat3, loss-of-function mutant of HAT1 and its homolog HAT3, was hypersensitive to ABA in primary root inhibition, ABA-responsive genes expression, and displayed enhanced drought tolerance, whereas HAT1 overexpressing lines were hyposensitive to ABA and less tolerant to drought stress, suggesting that HAT1 functions as a negative regulator in ABA signaling-mediated drought response. Furthermore, expression levels of ABA biosynthesis genes ABA3 and NCED3 were repressed by HAT1 directly binding to their promoters, resulting in the ABA level was increased in hat1hat3 and reduced in HAT1OX lines. Further evidence showed that both protein stability and binding activity of HAT1 was repressed by SnRK2.3 phosphorylation. Overexpressing SnRK2.3 in HAT1OX transgenic plant made a reduced HAT1 protein level and suppressed the HAT1OX phenotypes in ABA and drought response. Our results thus establish a new negative regulation mechanism of HAT1 which helps plants fine-tune their drought responses.

A non-DNA-binding activity for the ATHB4 transcription factor in the control of vegetation proximity

In plants, perception of vegetation proximity by phytochrome photoreceptors activates a transcriptional network that implements a set of responses to adapt to plant competition, including elongation of stems or hypocotyls. In Arabidopsis thaliana, the homeodomain-leucine zipper (HD-Zip) transcription factor ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4) regulates this and other responses, such as leaf polarity. To better understand the shade regulatory transcriptional network, we have carried out structure-function analyses of ATHB4 by overexpressing a series of truncated and mutated forms and analyzing three different responses: hypocotyl response to shade, transcriptional activity and leaf polarity. Our results indicated that ATHB4 has two physically separated molecular activities: that performed by HD-Zip, which is involved in binding to DNA-regulatory elements, and that performed by the ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR-associated amphiphilic repression (EAR)-containing N-terminal region, which is involved in protein-protein interaction. Whereas both activities are required to regulate leaf polarity, DNA-binding activity is not required for the regulation of the seedling responses to plant proximity, which indicates that ATHB4 works as a transcriptional cofactor in the regulation of this response. These findings suggest that transcription factors might employ alternative mechanisms of action to regulate different developmental processes.

Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.)

BACKGROUND

The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs.

RESULTS

A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize. VvHDZs in the same subfamily have similar protein motifs and intron/exon structures. An evaluation of duplication events suggests several HD-Zip genes arose before the divergence of the grape and Arabidopsis lineages. The 33 members of HD-Zip were differentially expressed in ovules of the stenospermic grape, Thompson Seedless and of the seeded grape, Pinot noir. Most have higher expressions during ovule abortion in Thompson Seedless. In addition, transcripts of the HD-Zip family were also detected in somatic embryogenesis of Thompson Seedless and in different vegetative organs of Thompson Seedless at varying levels. Additionally, VvHDZ28 is located in the nucleus and had transcriptional activity consistent with the typical features of the HD-Zip family. Our results provide a foundation for future grape HD-Zip gene function research.

CONCLUSIONS

The identification and expression profiles of the HD-Zip transcription factors in grape, reveal their diverse roles during ovule abortion and organ development. Our results lay a foundation for functional analysis of grape HDZ genes.

ATHB17 enhances stress tolerance by coordinating photosynthesis associated nuclear gene and ATSIG5 expression in response to abiotic stress

Photosynthesis is sensitive to environmental stress and must be efficiently modulated in response to abiotic stress. However, the underlying mechanisms are not well understood. Here we report that ARABIDOPSIS THALIANA HOMEOBOX 17 (ATHB17), an Arabidopsis HD-Zip transcription factor, regulated the expression of a number of photosynthesis associated nuclear genes (PhANGs) involved in the light reaction and ATSIG5 in response to abiotic stress. ATHB17 was responsive to ABA and multiple stress treatments. ATHB17-overexpressing plants displayed enhanced stress tolerance, whereas its knockout mutant was more sensitive compared to the wild type. Through RNA-seq and quantitative real-time reverse transcription PCR (qRT-PCR) analysis, we found that ATHB17 did not affect the expression of many known stress-responsive marker genes. Interestingly, we found that ATHB17 down-regulated many PhANGs and could directly modulate the expression of several PhANGs by binding to their promoters. Moreover, we identified ATSIG5, encoding a plastid sigma factor, as one of the target genes of ATHB17. Loss of ATSIG5 reduced salt tolerance while overexpression of ATSIG5 enhanced salt tolerance, similar to that of ATHB17. ATHB17 can positively modulate the expression of many plastid encoded genes (PEGs) through regulation of ATSIG5. Taken together, our results suggest that ATHB17 may play an important role in protecting plants by adjusting expression of PhANGs and PEGs in response to abiotic stresses.

The shady side of leaf development: the role of the REVOLUTA/KANADI1 module in leaf patterning and auxin-mediated growth promotion

Leaves are present in all land plants and are specialized organs for light harvesting. They arise at the flanks of the shoot apical meristem (SAM), and develop into lamina structures that exhibit adaxial/abaxial (upper/lower side of the leaf) polarity. At the molecular level, an intricate regulatory network determines ad-/abaxial polarity in Arabidopsis thaliana leaves, where the Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) proteins are key mediators. The HD-ZIPIII REVOLUTA (REV) is expressed in the adaxial domain of lateral organs, whereas KAN1 is involved in abaxial differentiation. The REV/KAN1 module directly and antagonistically regulates the expression of several genes involved in shade-induced growth and auxin biosynthetic enzymes.

Regulatory function of homeodomain-leucine zipper (HD-ZIP) family proteins during embryogenesis

Homeodomain-leucine zipper proteins (HD-ZIPs) form a plant-specific family of transcription factors functioning as homo- or heterodimers. Certain members of all four classes of this family are involved in embryogenesis, the focus of this review. They support auxin biosynthesis, transport and response, which are in turn essential for the apical-basal patterning of the embryo, radicle formation and outgrowth of the cotyledons. They transcriptionally regulate meristem regulators to maintain the shoot apical meristem once it is initiated. Some members are specific to the protoderm, the outermost layer of the embryo, and play a role in shoot apical meristem function. Within classes, homeodomain-leucine zippers tend to act redundantly during embryo development, and there are many examples of regulation within and between classes of homeodomain-leucine zippers. This indicates a complex network of regulation that awaits future experiments to uncover.

The Arabidopsis transcription factor ABIG1 relays ABA signaled growth inhibition and drought induced senescence

Drought inhibits plant growth and can also induce premature senescence. Here we identify a transcription factor, ABA INSENSITIVE GROWTH 1 (ABIG1) required for abscisic acid (ABA) mediated growth inhibition, but not for stomatal closure. ABIG1 mRNA levels are increased both in response to drought and in response to ABA treatment. When treated with ABA, abig1 mutants remain greener and produce more leaves than comparable wild-type plants. When challenged with drought, abig1 mutants have fewer yellow, senesced leaves than wild-type. Induction of ABIG1 transcription mimics ABA treatment and regulates a set of genes implicated in stress responses. We propose a model in which drought acts through ABA to increase ABIG1 transcription which in turn restricts new shoot growth and promotes leaf senescence. The results have implications for plant breeding: the existence of a mutant that is both ABA resistant and drought resistant points to new strategies for isolating drought resistant genetic varieties.

Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity

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.

Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes

The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium). Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.