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Perspective

Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation

by
An-Qing Shen
1,
Mei-Yan Lv
1,
Yan-Xin Ge
1,
Jin Zhou
1,
Zhen-Zhu Hu
1,
Xu-Qin Ren
1,
Ai-Sheng Xiong
2,* and
Guang-Long Wang
1,*
1
School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China
2
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(7), 1522; https://doi.org/10.3390/agronomy15071522
Submission received: 20 March 2025 / Revised: 13 June 2025 / Accepted: 20 June 2025 / Published: 23 June 2025
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
Browse Figures
Versions Notes

Abstract

Zinc finger-homeodomain (ZF-HD) transcription factors are a unique class that only exist in plants and are essential for plant growth and development, various stress responses, and quality formation and regulation. In recent years, an increasing number of reports regarding this class of transcription factors have been published, identifying their novel functions. In this paper, the evolution, structural characteristics, and subfamily classification of ZF-HD transcription factors are comprehensively introduced and the roles of the ZF-HD in abiotic and biotic stress responses, plant hormone signal transduction, and quality regulation are extensively investigated. In future studies, more efforts should be focused on the in-depth exploration of the mechanisms through which the ZF-HD could act at various stages of plant growth and development. We also determine the current research status and future directions related to the ZF-HD, with the aim of providing a comprehensive knowledge base and research insights for the further exploration of ZF-HD transcription factors in plant molecular biology.

1. Introduction

Plants often face various adverse stresses in their life cycle, including extreme temperature, drought, and salinity, which seriously limit their growth, development, yield, and quality formation [1]. Indeed, plants have evolved a complex network to cope with environmental stimuli and meet their own survival and living needs. A transcription factor (TF) is a key regulatory protein that can bind to the promoters of downstream genes or interact with other proteins to regulate their expression to adapt to various physiological processes [2]. To date, numerous transcription factors with distinct characteristics have been discovered [3]. Zinc finger-homeodomain (ZF-HD) transcription factors, only found in plants, have been shown to play important roles in various conditions [4]. ZF-HD TFs were initially found to be a potential regulator of the C4 phosphoenolpyruvate carboxylase gene [5]. They are a class of plant-specific transcription factors harboring a zinc finger (ZF) structure domain in the N-terminal and a homeodomain (HD) in the C-terminal, respectively [6]. These transcription factors can specifically bind to the promoters of genes or interact with other proteins to regulate the expression of downstream genes, thereby affecting the physiological and developmental processes of plants.
Previous studies on ZF-HD transcription factors in plants have revealed their pivotal role in plant growth, development, and adversity response [7]. Initially, numerous studies focused on their close association with plant growth and development. However, subsequent in-depth research has uncovered that ZF-HD transcription factors also play a crucial role in enhancing plant stress resistance and mediating signal transduction, highlighting their functional versatility. In this study, we introduce the structural characteristics and mechanisms of ZF-HD transcription factors and further summarize their functions, aiming to provide a theoretical foundation for their identification and utilization.

2. The Structural Characteristics of ZF-HD Transcription Factors

The typical domain of ZF-HD transcription factors mainly includes two core parts: the zinc finger domain and homeodomain [8]. These structures enable ZF-HD transcription factors to interact with DNA sequences, thus regulating gene expression and participating in plant growth processes and responses to environmental stresses [9]. The zinc finger (ZF) structure domain, widely distributed in regulatory proteins, consists of two pairs of conserved cysteine and/or histidine residues, coordinating with a zinc ion [10]. Zinc finger structures play diverse roles, primarily in DNA binding and protein interactions, with a minority also engaging in RNA binding and protein folding [11]. These structures can be classified into different subgroups [12] such as C3H, C2H2, PHD, C2C2, LIM, and RING-finger, based on various factors including the type, number, and spatial arrangement of the residues that coordinate with the zinc [13].
In addition to the zinc finger domain, ZF-HD transcription factors also contain a homeodomain (HD), a highly conserved region within the homeobox gene family [14]. The homeodomain, comprising around 60 conserved amino acids, folds into a distinct three-helix structure known as the recognition helix, which can attach to specific DNA sequences, establishing a unique interaction with them [15]. HD-containing proteins are prevalent in both animals and plants, where they play roles in protein–protein interactions and other regulatory functions [13]. According to the size, location, and structure of HD domains and their association with other domains, proteins harboring homeodomains can be categorized into six different families: a finger-like domain associated with an HD (PHD finger), WUSCHEL-related homeobox (WOX), knotted-related homeobox (KNOX), zinc finger motif-related HD (ZF-HD), leucine zipper-related HD (HD-ZIP), and Bell-type HD [16].
In addition to ZF and HD domains, ZF-HD transcription factors may also contain other conserved motifs, which are uniformly distributed among family members and each have their own unique function. These transcription factors are believed to have evolved from the ancestral plant genome and have gradually differentiated into multiple subfamilies with the evolution of plants [17]. The evolutionary history of the ZF-HD gene family in plants can be traced back to approximately 460 to 497 million years ago, a period closely related to the origin and diversification of land plants [18]. Based on conserved motifs and phylogenetic relationships, the ZF-HD gene family is primarily divided into two subfamilies: ZHD and MIF [19]. Notably, many ZF-HD/ZHD genes lack introns, a phenomenon also observed in other types of transcription factors, suggesting that they may have undergone specific selection pressures during evolution [20]. Research indicates that the ZF-HD gene has experienced numerous gene duplications and selection pressures throughout its evolutionary history, leading to the diversification of both its function and structure [21]. Fragmentary duplication, whole-genome duplication, and transposable elements are recognized as the main driving forces for the expansion of the ZF-HD gene family [22].

3. Roles of ZF-HD Transcription Factors in Plants

3.1. Abiotic Stress Response

Due to the fixation characteristics of plants, they are subjected to various abiotic stresses caused by climate change [23]. Abiotic stresses, such as extreme temperatures, drought, heavy metals, nutrient deficiency, and mineral toxicity, can seriously affect the productivity of crops and other plant species [24,25]. ZF-HD transcription factors have a wide range of functions in plants and play a crucial role in coping with environmental stresses, including drought, high temperature, and saline–alkali conditions [26]. These transcription factors help plants adapt to unfavorable growth conditions by altering the expression patterns of specific genes [27].

3.1.1. Temperature

The growth of plants is significantly affected by temperature, as both increases and decreases in temperature may lead to changes in key physiological processes, including photosynthesis, respiration, and water-use efficiency [28]. ZF-HD transcription factors can interact with other proteins or modulate the expression of downstream genes, thereby enhancing plants’ tolerance to both low and high temperatures [29].
High temperatures can lead to metabolic imbalances in plant cells, resulting in protein degeneration and damage to cell membranes [30]. Under heat stress, TaZHD4 and TaZHD28 from wheat were highly expressed at the early treatment stage, suggesting a potential role of these two genes in high temperature acclimation [17]. GHIR_A05G037870.1 in cotton was believed to play roles in heat, cold, salinity stress, and fiber development, whereas Ghir_A13G007510.1 and Ghir_D11G019490.1 might only participate in heat stress tolerance [22]. These results indicated that ZF-HD transcription factors could facilitate plant adaptation to elevated temperatures by influencing physiological processes and initiating the expression of related genes.
Low-temperature stress can affect diverse processes during plant growth and development, such as cell physiology, seed germination, and reproductive development [31]. Low-temperature stress slows down the division of plant cells, affects their expansion and growth, and thus retards the overall growth of plants. Extremely low temperatures may cause the water within cells to freeze, resulting in physical damage to those cells [32]. A previous study indicated that ZFHD1 was involved in the polyamine biosynthesis pathway and might interact with the NAC domain protein to regulate the expression of ADC or/and SAMDC genes in Lilium lancifolium in response to cold stress [33]. Further research revealed that transgenic Arabidopsis plants overexpressing a lily ZFHD gene, LlZFHD4, showed a higher survival rate under cold stress, accompanied by lower water-loss rates, electrolyte leakage amounts, and higher soluble sugar levels, suggesting that LlZFHD4 could improve the osmotic adjustment capacity to cope with low-temperature conditions [34]. In rice, a transcriptome-based comparative analysis revealed that OsZHD8 was a key regulator responsible for different chilling resistances in rice varieties [35]. It was found that the expression levels of some ZF-HD genes in peas, such as the PsZHD10 gene, were upregulated under low-temperature stress, which indicated that ZF-HD genes might be involved in the response of plants to low temperature stress [36]. It is assumed that plants overexpressing ZF-HD transcription factors demonstrate greater cold resistance, providing a theoretical foundation for potential applications in agriculture.

3.1.2. Water Stress

Water is necessary for photosynthesis and nutrient transport in plants. A lack of water reduces the photosynthetic efficiency of plants, subsequently affecting their growth and development [37]. Plants establish multifaceted strategies like drought escape, drought avoidance, and drought tolerance to adapt to the reduced availability of water during drought [38,39]. ZFHD1 could activate several stress-inducible genes, and transgenic plants overexpressing ZFHD1 exhibit a smaller morphological phenotype and a significant improvement in drought stress tolerance, indicating that ZF-HD transcription factors are crucial for regulating the responses of plants to drought [40]. A whole-genome characterization and expression profile analysis of the ZF-HD gene family in cucumber (Cucumis sativus) revealed that the selected CsZF-HD genes were responsive to drought stress, indicating their potential roles in drought stress adaptation [41]. CsZHD9 and CsZHD10 might regulate chlorophyll biosynthesis and stomatal movement, thereby contributing positively to cucumber drought tolerance [7]. The overexpression of PtrVCS2 encoding a zinc finger-homeodomain transcription factor in Populus trichocarpa resulted in lower stomatal apertures, higher water use efficiency, and strong drought-resistance phenotypes [42]. The survival rate of plants infected with TRV2-NtZF-HD21 was dramatically lower compared with control plants, indicating that the NtZF-HD21 gene was a positive regulator of drought tolerance in tobacco [43]. ZF-HD transcription factors may work in conjunction with other transcription factors to enhance plant responses to water stress. The transient expression of the quinoa CqZF-HD14 gene enhanced the accumulation of photosynthetic pigments under drought stress, reinforced the antioxidant system, and thus improved plant performance and drought tolerance. Further studies revealed that CqZF-HD14 could interact with CqNAC79 and CqHIPP34 to further confer the drought tolerance of quinoa seedlings [44]. In bread wheat, leaf rolling during moisture stress conditions was demonstrated to be regulated by the upregulation of a pair of closely linked/duplicate zinc finger homeodomain class transcription factors, TaZHD1 and TaZHD10 [45]. By integrating bulk segregant analysis, fine mapping, and transcriptome analysis, it was found that a gene encoding zinc finger-homeodomain protein 2 (ZHD2), might be involved in drought adaptation in watermelon [46]. These studies suggested that ZF-HD transcription factors may play important roles in enhancing plant adaptability to water stress.

3.1.3. Light

Light is a key environmental signal for plant growth and development, and it serves as an important energy source for photosynthesis [47]. Plants require light to promote cell division and expansion, thereby supporting their overall growth. Additionally, light regulates various development processes, including photoperiodicity, phototropism, and morphogenesis. Light stress refers to the adverse conditions plants face when light intensity is either extremely high or low, which can negatively impact photosynthesis, respiration, and overall physiological health [48]. ZF-HD transcription factors aid plants in adapting to diverse light conditions by modulating the expression of genes associated with environmental adaptation. ZFHD10 was identified as a transcription factor that is directly associated with TANDEM ZINC-FINGER PLUS3 (TZP) to control the expression of genes required for hypocotyl elongation in response to low blue light [49,50]. In blueberry, zinc finger-homeodomain protein 1/4/5/9 may bind to the promoter of VcTCP18, a regulator responsive to light conditions, contributing to bud dormancy [51]. The identification of cis-regulatory elements in the promoter region revealed that Box 4, the GT1-motif, and G-box, which respond to light, were enriched in the promoters of MsZF-HD genes, suggesting that ZF-HD transcription factors may be directly involved in light responses [52].

3.1.4. Salt and Alkali Stress

Both salt stress and alkali stress can change the osmotic balance inside and outside plants, resulting in difficulties in absorbing water, ion toxicity, and oxidative damage [53]. ZF-HD transcription factors are capable of sensing internal and external signals induced by salt stress, activating the corresponding signal transduction pathways to initiate the expression of genes that respond to salt stress. In soybean (Glycine max), GmZF-HD1 was recognized as a transcription factor that activates the calmodulin isoform-4 gene (GmCaM-4), an essential player in the response to salt stress stimuli [54]. In sunflowers, both digital expression data and quantitative real-time PCR results showed that the relative expression levels of HaZF6 and HaZF9 rapidly and significantly decrease when exposed to salt stress [55]. HOMEOBOX PROTEIN 24, a zinc finger-homeodomain family transcription factor, is able to directly interact with the promoters of Sugars Will Eventually be Exported Transporter 11/12 to modulate their expression in roots, resulting in improved sucrose supply and root growth for salt-stress resistance [56]. Furthermore, ZF-HD transcription factors can interact with other transcription factors to create a regulatory network that jointly modulates gene expression in response to salt stress. The cooperation between LlZFHD4 and LlNAC2 proteins can enhance the tolerance of plants to salt stress, facilitating their survival in extreme environments [57]. It can thus be seen that the ZFHD gene family has a significant impact on plant responses to salt stress.
Alkaline stress is a significant adversity that plants face in high pH conditions, primarily due to the accumulation of alkaline salts in the soil. In such environments, the availability of water and nutrients for plant absorption decreases, adversely affecting normal physiological functions, including increased oxidative stress and altered nutrient availability [58]. Research conducted by He et al. indicated that the expression levels of all MsZF-HD genes were significantly downregulated under alkaline stress, revealing that the response of these genes may be negatively manipulated by alkaline stress [52]. These findings indicate that ZF-HD may actively participate in regulating plant responses to salt and alkaline stress. In the future, the function of these genes can be further verified, and their characteristics can be used as an important target for salt and alkaline tolerance breeding.

3.1.5. Heavy Metal

Heavy metals are naturally occurring elements; however, due to the acceleration of industrialization and improper waste management, the problem of heavy metal pollution is becoming increasingly serious [59]. Heavy metal stress can lead to inhibited photosynthesis and antioxidant capacity, thereby hindering plant growth and development [60]. Studies have shown that ZF-HD transcription factors play a crucial role in the response of plants to heavy metals. In soybean, the transcription of all the tested GmZF-HD genes was altered in the presence of CdCl2, CoCl2, MnSO4, ZnSO4, and FeSO4 stress treatments, indicating their potential roles in heavy metal stress adaptation [26]. Another study found that ATHB29, a zinc finger-homeodomain transcription factor, could interact with the heavy metal-associated domain in stress-induced HIPP26, suggesting a potential role of ATHB29 in heavy metal stress responses [61]. It is assumed that ZF-HD can regulate the expression of related genes to mitigate the toxicity and accumulation of heavy metals under heavy metal stress.

3.2. Biotic Stress

Plants encounter various biotic stresses during growth, which significantly impact their health and development. These biotic stresses are primarily induced by other organisms, including pathogens, pests, and competition among plants [62].
Pathogens, including bacteria, fungi, and viruses, are capable of causing plant diseases and weakening plant health [63]. Infection by these pathogens consumes plant nutrients, which in turn impairs the plants’ ability to effectively carry out photosynthesis. This leads to disruptions in the synthesis and distribution of photosynthetic products [64]. Additionally, infection by various pathogens can reduce seed germination rates and adversely affect the subsequent growth processes in plants [65]. Studies have demonstrated that ZF-HD genes are closely associated with the plant defense mechanism. They play a crucial role in enhancing plant resistance to pathogens by regulating genes related to photosynthesis, disease resistance, and diverse stress responses. Their genetic structure enables a rapid response to environmental changes, particularly in the presence of pathogens. It was reported that some CsZF-HD genes in cucumber are differentially expressed in response to the inoculation of powdery mildew and downy mildew, indicating that ZF-HD genes may play key roles in modulating plant defense against pathogen infection [41]. When infected by pathogens, GmZF-HD1 and GmZF-HD2 proteins in soybean can activate the promoter of the GmCaM4 gene to regulate its expression to cope with pathogen stimulation [66]. In cassava, expression profiling has indicated that some ZF-HD genes are induced in response to the infection of Xanthomonas phaseoli pv. manihotis (Xpm), demonstrating their involvement in defense mechanisms. Furthermore, the MeZHD7 gene from cassava conferred improved resistance against cassava bacterial blight caused by Xpm [13]. Transgenic plants harboring higher ZHD5 levels exhibit a remarkable increase in resistance to fungal and bacterial pathogens, suggesting a positive role of ZHD5 in disease resistance [67]. During the early process of cucumber mosaic virus (CMV) infection, an increase in the transcript of HB27, a homeodomain transcription factor, was observed in Arabidopsis plants. In HB27-overexpressing lines, infected plants exhibit slight symptoms, accumulating a lower virus titer compared with control plants, whereas knockout HB27 mutants do the opposite [68]. These results show that ZF-HD transcription factors can stimulate plant stress resistance signals and help plants resist stress when they are infected by diseases.
Plant pests are numerous and diverse, inflicting damage on plants by feeding on their different tissues or spreading pathogens [69]. The feeding behavior of pests not only causes direct physical harm to plants but also triggers a series of complex physiological and molecular responses [70]. During this process, ZF-HD transcription factors play a crucial role in plant responses to pest attacks. ZF-HD genes typically exhibit a specific expression pattern in plants, which is influenced by environmental factors. When insect pests are present, the expression of the ZF-HD genes is upregulated or decreased to cope with external biological stress. In Gossypium hirsutum, Ghir_A13G007510.1—a ZF-HD gene—displays a marked decrease compared with controls after the infection of nematode (Rotylenchus reniformis) [22].

3.3. Plant Hormone Signaling Pathway

Plant growth hormones such as auxin, cytokinin, gibberellin, abscisic acid, and ethylene are crucial signal molecules for regulating plant growth and development [71,72]. Studies indicate that ZF-HD transcription factors play a significant role in the biosynthesis and signal transduction pathways of these growth hormones. In addition, ZF-HD transcription factors have been shown to regulate the physiological processes mediated by plant hormones.
Auxin, a key plant hormone, primarily regulates plant growth and morphogenesis [73]. ZF-HD transcription factors have been shown to interact with the auxin signaling pathway. For instance, INDOLE-3-BUTYRIC ACID RESPONSE 1 (IBR1) is a gene encoding an enzyme involved in the indole-3-butyric acid-to-indole-3-acetic acid conversion. HOMEOBOX PROTEIN 24 (HB24), a ZF-HD family member, could directly bind to the promoter of IBR1 and regulate its expression to affect auxin levels and root hair growth [74]. It was found that TANDEM ZINC-FINGER PLUS3 (TZP) could upregulate the expression of auxin-related genes, and it could interact with a member of the ZFHD transcription factor family, ZFHD10, to affect the transcription of downstream genes [49].
Abscisic acid (ABA) is a crucial plant hormone that plays a significant role in plant responses to abiotic stress. It regulates the opening and closing of stomata and influences the growth and development of plants, enhancing their capacity to withstand adverse conditions [75]. ABA facilitates plant adaptation to unfavorable environments by modulating the expression of a series of genes [76]. Studies have demonstrated that ZF-HD genes can be induced in the presence of ABA. The upregulation of certain ZF-HD genes under abiotic conditions may improve plants’ stress resistance by influencing the ABA signaling pathway. For example, in tiger lily, studies have identified that ZFHD4 is integral to the ABA signaling pathway, regulating plant responses to cold, salinity, and water stress [34]. In wheat, TaZFHD1 is a hormone-responsive transcription factor and might be involved in jasmonic acid- and ABA-mediated signaling pathways, which possibly suggests a role in biotic and abiotic responses [77]. The overexpression of VvZF-HD11, a transcription factor in response to ABA signaling, could improve the antioxidant enzyme activity of grape leaves, reduce the oxidative damage of cell membranes, and promote the expression of genes related to high-temperature stress, thereby enhancing the high-temperature resistance of grapes [78]. Some ZF-HD proteins can specifically bind to the promoter regions of genes or interact with crucial components associated with ABA responses. ZFHD1 could specifically bind to the 62 bp promoter region of EARLY RESPONSIVE TO DEHYDRATION STRESS 1 (ERD1) gene, a member involved in ABA responses, conferring a smaller morphological phenotype and significant improvement tolerance to drought stress [40]. Transgenic plants harboring tiger lily LlNAC2, noticeably induced by ABA treatment, exhibited ABA hypersensitivity and improved tolerance to cold, drought, and salt stresses. LlNAC2 was verified to physically interact with LlDREB1 and zinc finger-homeodomain ZFHD4, suggesting a potential role of ZFHD4 in ABA-mediated responses [57].
A cytokinin is a major plant hormone involved in regulating cell division, differentiation, and growth [79]. Cytokinins influence the transcriptional activity of downstream genes by regulating the expression of a series of transcription factors. ZF-HD transcription factors can be involved in cytokinin biosynthesis and signal transduction, thereby affecting cell division as well as plant growth and development. Transgenic plants harboring ZHD5, induced by cytokinins, displayed enhanced shoot regeneration and exhibited several distinct cytokinin-associated phenotypes [67]. In tomato, two ZF-HD genes, SlHB25 and SlHB31, were shown to be essential for connecting cytokinin signaling with stomatal formation [80].
Besides the hormones mentioned above, ZF-HD also participates in physiological and biochemical processes mediated by other plant hormones. Transgenic lines overexpressing a zinc finger homeobox transcription factor, BRASSINOSTEORID-RELATED HOMEOBOX 2 (BHB2), displayed an increased expression of brassinosteroid (BR) biosynthesis genes and elongated hypocotyl, indicating that BHB2 is a positive regulator of BR response [81]. In barley, most HvZF-HD genes were dramatically induced in the presence of GA3 and MeJA treatments, revealing that HvZF-HD genes play vital roles in plant growth and development, as well as stress defense responses [9]. In apple, six MdZF-HD genes (MdZHD1/2/6/7/10/11) may take part in the regulation of the ethylene-induced ripening process of postharvest apple fruit [82].

3.4. Plant Growth and Development

3.4.1. Root

The ZF-HD transcription factor plays an important role in plant growth and development. It is involved in regulating key processes such as rooting, flowering, and fruit development, thereby facilitating the smooth progression of plants through various growth stages [83,84]. ZF-HD transcription factors contribute to the formation of essential root structures, including the development of primary roots and the generation of root hair. For example, a zinc finger-homeodomain family transcription factor, HB24, could increase the transcription of IBR1 to promote IBA-to-IAA conversion, thereby contributing to root hair elongation [74]. In addition, transgenic plants overexpressing HB24 showed longer primary roots than the wild-type, whereas the hb24 loss-of-function mutant did the opposite. These changes in phenotype were mainly due to the sugar supply mediated by the HB24–Sugars Will Eventually be Exported Transporter 11 (SWEET11) module in the root [56].

3.4.2. Stem and Leaf

The ZF-HD transcription factor functions as a transcriptional activator or inhibitor, directly regulating gene expression associated with stem and leaf growth [85]. The overexpression of PtrVCS2, encoding a ZF-HD transcription factor in Populus trichocarpa, led to a higher proportion of smaller stem vessels and lower stomatal apertures by regulating the expression of multiple genes associated with stomatal opening and closing and cell wall biosynthesis [42]. In rice, OsZHD1 and OsZHD2 were highly distributed in the stem. A mutant with OsZHD1 and OsZHD2 loss-of-function showed reduced plant height and caused smaller reproductive organs, suggesting a potential role in regulating plant height [8]. ZFHD10 takes part in plant adaptive responses to diverse light conditions, hypocotyl elongation, and flowering by interacting with a nuclear-localized protein [50]. In A. thaliana, GRF3 is able to bind to the promoter of HOMEOBOX PROTEIN 33 (HB33), a ZF-HD member, and induce its transcription. An increase in HB33 levels contributes to variations in the number and size of leaf cells. Furthermore, the long-term expression of HB33 during leaf development can extend leaf longevity. These findings highlight the role of ZF-HD in leaf development and its integration with the GRF pathway [86]. Increased levels of OsZHD1 result in the increased number and abnormal arrangement of bulliform cells in leaves, and thus contribute to the formation of abaxially curled and drooping leaves [87]. Similarly, in bread wheat, two ZF-HD genes—TaZHD1 and TaZHD10—have been shown to be responsible for leaf rolling, in addition to other functions [45]. These findings reveal that ZF-HD transcription factors make a difference in stem and leaf development by predominantly regulating cell proliferation, expansion, and arrangement.

3.4.3. Flowering and Fruit

Transcription factors, including the ZF-HD gene family, play a vital role in flower development. These genes can influence the development of petals and the formation of flower organs, subsequently affecting plant reproductive success. In tomato, SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds, suggesting a potential role of SlZHD genes in flower development [88]. The mRNA abundance of the ZF-HD transcription factors HB31, HB33, and HB34, accumulate at relatively low levels in the root, leaf, and vegetative tissue, and show the highest levels in floral tissue, especially in young flowers. Further studies have revealed that these genes could affect floral organ development and impact silique length [89]. Similarly, the double mutant oszhd1oszhd2 exhibits smaller reproductive organs, and a shorter, narrower, and thinner grain size [8]. The involvement of ZF-HD in fruit development has also been observed in some studies [90,91].

3.5. Regulation of Plant Quality

3.5.1. Appearance

The appearance quality of plants usually refers to the characteristics of plants in terms of their shape, color, and texture. ZF-HD transcription factors play an important regulatory role in plant morphological development. Transgenic lines overexpressing EgrZHD5, a ZF-HD transcription factor in Eucalyptus grandis, show reduced plant height, thinner stems, and thicker xylem cell walls [92]. Similarly, the moss gene PpZF-HD1 has been shown to function in plant architecture formation by altering the gene expression of downstream targets [93]. Fruit ripening and associated softening are major determinants contributing to fruit quality. In apple, MdZF-HD11 is able to directly bind to the promoter of Mdβ-GAL18, encoding a pectin-degradation enzyme associated with cell wall metabolism, and upregulate its transcription. The overexpression of MdZF-HD11 results in increased ethylene release, reduced fruit firmness, and accelerated fruit ripening and softening [91]. The color change of plants is closely related to the synthesis of pigments such as chlorophylls, carotenoids, anthocyanins, and betalains. A zinc finger-homeodomain transcription factor from tomato, SlZHD17, is able to regulate chlorophyll and carotenoid accumulation by directly binding to the promoters of SlPOR-B, SlTKN2, and SlSGR1 in the chlorophyll pathway, and the SlPSY1 and SlZISO genes in the carotenoid metabolic pathway [90]. SmZHD12 is able to induce the promoters of SmCHS, SmANS, SmDFR, and SmF3H to promote the accumulation of anthocyanins in eggplant [94]. Similarly, the transcript levels of some GhZHD genes are higher at the early stages of cotton fiber development and then gradually decrease, which correlates well with the accumulation of proanthocyanidins in brown cotton fibers. It is speculated that some GhZHD genes may be involved in proanthocyanidin accumulation [95]. These findings reveal that ZF-HD transcription factors can regulate genes related to pigment synthesis, affecting color formation in plants, and thus enhancing their attractiveness (Figure 1). This regulation mechanism has important application potential in improving the color of horticultural plants.

3.5.2. Nutrient Accumulation

Nutrient accumulation within plants not only endows plants with stress resistance but also benefits human health. The nutritional quality of plants directly affects their growth rate, flowering, fruiting, and other life processes [96]. A proper supply of nutrition can promote the healthy growth of plants, improve their stress resistance, and enhance their resistance to pests and diseases. ZF-HD transcription factors regulate the metabolic pathways of plants, thereby impacting the synthesis of nutrients. SWEET11 is a positive regulator for sucrose accumulation in roots, whereas HB24 can interact with the promoter of SWEET11 to induce sucrose distribution [56]. ZF-HD transcription factors can influence the accumulation of secondary metabolites in plants at different growth stages. Additionally, ZF-HD transcription factors play a crucial role in the fruit development process by regulating cell wall organization and fruit ripening and softening. As mentioned above, ZF-HD can directly act on relevant genes to regulate their expression, widely participating in metabolic processes such as flavonoids and anthocyanins in plant fruits [90,94]. The gene EfCGT1, encoding C-glycosyltransferase in Euryale ferox, plays a central role in the biosynthesis of flavonoid C-glycosides (FCGs), and its activity is negatively regulated by the EfZHD17-EfZHD19 transcriptional regulatory module, suggesting an important role of EfZHD17 and EfZHD19 in FCG accumulation [97]. These findings indicate that ZF-HD transcription factors are involved not only in plant stress responses, growth, and development, but also in the synthesis and regulation of quality-related metabolites (Table 1).

4. The Regulatory Mechanisms of ZF-HD Transcription Factors

The structure of ZF-HD proteins determines their function and regulatory mechanisms. The HD domain at the C-terminal can form three α-helices, connected by a loop and a turn, which typically interact with the major groove of DNA to activate or repress gene expression, whereas the N-terminal ZF domain can promote DNA, RNA, protein, and DNA–RNA interactions, playing a vital role in transcriptional and translational regulation [98]. ZF-HD proteins exert their function mainly via direct transcriptional regulation. They bind directly to the promoters of target genes to activate or repress their transcription. For example, in Arabidopsis, four ZF-HD protein genes were screened and confirmed to bind to the promoter element of the ABF2 gene, which is a crucial regulator for ABA-responsive gene expression [67]. The ZF-HD protein may interact with other types of transcription factors, forming complex regulatory modules that collectively fine-tune stress responses and secondary metabolic pathways. CqZF-HD14 is able to interact with CqNAC79 and CqHIPP34 to confer drought tolerance by enhancing photosynthetic pigment accumulation and intensifying the antioxidant system under drought stress [44]. A ZF-HD transcription factor in Prunus persica, PpZFHD1, could interact with an OVATE family protein, PpOFP1, affecting plant responses to salt stress and improving salt tolerance in tomato and yeast [99]. In addition, ZF-HD activity and function can also be altered in the presence of interplay with other proteins. Research has found that the mini zinc finger protein (MIF1) can act as a negative regulatory factor for ZHD5, affecting its localization and function by forming nonfunctional heterodimers [100].
Some CsZF-HD proteins may produce a marked effect through post-transcriptional regulation in response to organ development and external stimuli. Notably, the predicted endogenous target mimic of csn-miR2673a may indirectly manipulate CsZF-HD transcription by recruiting relevant miRNAs when exposed to salicylic acid treatment [101]. It was reported that ZF-HD TFs, especially HB34, negatively modulate the level of miR157 and positively controlled SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157 [89].
Translational modifications, such as phosphorylation and ubiquitination modifications, can also affect the stability and activity of ZF-HD transcription factors. In the presence of salt stress, a plant U-box type E3 ubiquitin ligase 30 (PUB30) can directly target HB24 and mediate the degradation of HB24 via the ubiquitin–proteasome pathway [56].

5. Prospects

Although preliminary progress has been made in research on the plant ZF-HD transcription factor family, studies on this family remain limited overall. To date, most findings are confined to classical model plants such as Arabidopsis, tomato, and rice. Knowledge of ZF-HD family members in other crucial crop species is almost entirely lacking, and their roles in potential key agronomic traits remain largely untapped. Furthermore, existing research has predominantly focused on the family’s functions in specific organ developmental stages or responses to single abiotic stresses. Their roles in processes such as seed germination, the regulation of vegetative growth, the synthesis of secondary metabolites, and intricate interaction networks with plant hormone signaling pathways have scarcely been systematically explored. The complex issues of potential functional redundancy or specificity among ZF-HD members are also urgently in need of clarification.
Although their importance is widely recognized, the specific molecular mechanisms of action for members of the ZF-HD family remain poorly characterized and largely elusive compared to other large transcription factor families (such as MYB, bHLH, and NAC). How do differences among individual members in protein structure, expression patterns, DNA-binding specificity/preference, and protein–protein interaction networks lead to their regulation of distinct biological processes? During crop domestication and breeding, how does natural variation in ZF-HD genes affect their function and important agronomic traits? How do they regulate their downstream direct target genes? This necessitates the use of in vitro and in vivo techniques to systematically identify the cognate target DNA sequences (motifs) precisely bound by different ZF-HD members under specific physiological/stress conditions. How do ZF-HD proteins integrate multiple signaling pathways? Do they form heterodimers or higher-order complexes with transcription factors from other families, thereby altering their respective DNA-binding specificity or transcriptional regulatory activity? Beyond transcriptional regulation, are there more examples of post-transcriptional and post-translational regulation to enrich our understanding of their mechanisms of action? Do modifications such as phosphorylation, ubiquitination, acetylation, and glycosylation participate in regulating ZF-HD protein activity, stability, subcellular localization, and functional execution?
Research on the plant ZF-HD family is currently at a critical turning point, shifting from model plants to important crops, and from isolated functions to systematic network exploration. Future studies should aim to comprehensively decipher the core functional mechanisms of the ZF-HD family in regulating crop growth, development, and environmental adaptability. This can be achieved by deeply integrating molecular genetics approaches with modern bioinformatics, structural biology, and smart phenotyping technologies.

6. Summary

In summary, ZF-HD transcription factors play a significant role in plant biotic and abiotic stress responses, hormone signaling pathways, and the regulation of growth and development (Figure 2). They are widely involved in plant gene regulation and the improvement of genetic traits. Although the functions of ZF-HD transcription factors in plants are somewhat understood, many areas remain unexplored. Most research has focused on a limited number of model plants, leaving a scarcity of functional studies in other species. The complexity of their regulatory networks requires further analysis, particularly their dynamic interactions with other factors across various environmental conditions and developmental stages. Future research should comprehensively explore the functions and regulatory mechanisms of ZF-HD transcription factors in plants using multi-omics analysis and molecular biology techniques. Such studies could facilitate the application of findings in plant genetic improvement and agricultural practices, ultimately contributing to the cultivation of new crop varieties with enhanced growth characteristics and environmental adaptability.

Author Contributions

Conceptualization, A.-S.X. and G.-L.W.; acquisition of data, A.-Q.S. and G.-L.W.; writing—original draft preparation, A.-Q.S., M.-Y.L. and Y.-X.G.; writing—review and editing, M.-Y.L., Y.-X.G., J.Z., Z.-Z.H., A.-S.X. and G.-L.W.; analysis of data, J.Z., Z.-Z.H. and X.-Q.R.; supervision, X.-Q.R. and A.-S.X.; funding acquisition, A.-S.X. and G.-L.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (32372681), the New Century Excellent Talent of the Ministry of Education (NCET-11-0670), and the Jiangsu Natural Science Foundation for Distinguished Young Scholars (BK20130027).

Data Availability Statement

No new data were created or analyzed in this study. Data sharing is not applicable to this article.

Conflicts of Interest

The authors declare no conflicting interest regarding the publication of this work.

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Figure 1. The roles of zinc finger-homeodomain transcription factors in color formation and their regulatory network in plants.
Figure 1. The roles of zinc finger-homeodomain transcription factors in color formation and their regulatory network in plants.
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Figure 2. The functions of zinc finger-homeodomain (ZF-HD) transcription factors in plant growth and development, quality formation, biotic and abiotic stress responses, and hormone signal transduction.
Figure 2. The functions of zinc finger-homeodomain (ZF-HD) transcription factors in plant growth and development, quality formation, biotic and abiotic stress responses, and hormone signal transduction.
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Table 1. ZF-HD transcription factors that mediate plant stress responses, growth and development, and quality formation.
Table 1. ZF-HD transcription factors that mediate plant stress responses, growth and development, and quality formation.
GeneSpeciesFunctionReference
TaZHD4Triticum aestivumHigh-temperature acclimation[17]
TaZHD28Triticum aestivumHigh-temperature acclimation[17]
GHIR_A05G037870.1Gossypium hirsutumResponses to heat, cold, and salinity stress/Fiber development[22]
Ghir_A13G007510.1Gossypium hirsutumHeat-stress tolerance/Response to nematode infection[22]
Ghir_D11G019490.1Gossypium hirsutumHeat-stress tolerance[22]
ZFHD1Lilium lancifoliumCold-stress resistance[33]
LlZFHD4Lilium lancifoliumResponses to cold, salt, and water stress[34,57]
OsZHD8Oryza sativaChilling-stress resistance[35]
PsZHD10Pisum sativumResponse to low temperature[36]
ZFHD1Arabidopsis thalianaDrought-stress tolerance[40]
CsZF-HDsCucumis sativusResponse to drought stress[41]
CsZHD9Cucumis sativusDrought-stress tolerance[7]
CsZHD10Cucumis sativusDrought-stress tolerance[7]
PtrVCS2Populus trichocarpaDrought-stress resistance[42]
NtZF-HD21Nicotiana tabacumDrought-stress tolerance[43]
CqZF-HD14Chenopodium quinoaDrought-stress tolerance[44]
TaZHD1Triticum aestivumResponse to moisture stress/Leaf rolling[45]
TaZHD10Triticum aestivumResponse to moisture stress/Leaf rolling[45]
ZHD2Citrullus lanatusDrought adaptation[46]
ZFHD10Arabidopsis thalianaResponse to low blue light/Hypocotyl elongation/Flowering[49,50]
VcZF-HD1/4/5/9Vaccinium spp.Bud Dormancy[51]
MsZF-HDsMedicago sativaLight response[52]
GmZF-HD1Glycine maxResponse to salt stress and pathogens[54,66]
GmZF-HD2Glycine maxResponse to pathogens[66]
HB24Arabidopsis thalianaSalt-stress resistance/Sucrose supply/Auxin metabolism/Root hair elongation[56,74]
ATHB29Arabidopsis thalianaResponse to heavy metal stress[61]
MeZHD7Manihot esculentaResistance against bacterial blight[13]
ZHD5Arabidopsis thalianaResistance to pathogens/Shoot regeneration[67]
HB27Arabidopsis thalianaTolerance to cucumber mosaic virus[68]
VvZF-HD11Vitis viniferaResistance to high temperatures[78]
SlHB25Solanum lycopersicumStomatal formation[80]
SlHB31Solanum lycopersicumStomatal formation[80]
BHB2Arabidopsis thalianaHypocotyl elongation[81]
MdZF-HD1/2/6/7/10Malus domesticaEthylene-induced fruit ripening[82]
MdZF-HD11Malus domesticaFruit ripening and softening[82,91]
OsZHD1Oryza sativaCell proliferation/Plant height/Grain size formation/Leaf rolling[8,87]
OsZHD2Oryza sativaCell proliferation/Plant height/Grain size formation[8]
HB33Arabidopsis thalianaLeaf development/Flower development[86,89]
SlZHDSolanum lycopersicumFlower development[88]
HB31Arabidopsis thalianaFlower development[89]
HB34Arabidopsis thalianaFlower development[89]
SlZHD17Solanum lycopersicumChlorophyll and carotenoid metabolism[90]
EgrZHD5Eucalyptus grandisPlant height/Stem thickness[92]
PpZF-HD1Physcomitrella patensPlant architecture formation[93]
SmZHD12Solanum melongenaAnthocyanin biosynthesis[94]
GhZHDsGossypium hirsutumProanthocyanidin accumulation[95]
EfZHD17Euryale feroxFlavonoid C-glycoside accumulation[97]
EfZHD19Euryale feroxFlavonoid C-glycoside accumulation[97]
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Shen, A.-Q.; Lv, M.-Y.; Ge, Y.-X.; Zhou, J.; Hu, Z.-Z.; Ren, X.-Q.; Xiong, A.-S.; Wang, G.-L. Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation. Agronomy 2025, 15, 1522. https://doi.org/10.3390/agronomy15071522

AMA Style

Shen A-Q, Lv M-Y, Ge Y-X, Zhou J, Hu Z-Z, Ren X-Q, Xiong A-S, Wang G-L. Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation. Agronomy. 2025; 15(7):1522. https://doi.org/10.3390/agronomy15071522

Chicago/Turabian Style

Shen, An-Qing, Mei-Yan Lv, Yan-Xin Ge, Jin Zhou, Zhen-Zhu Hu, Xu-Qin Ren, Ai-Sheng Xiong, and Guang-Long Wang. 2025. "Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation" Agronomy 15, no. 7: 1522. https://doi.org/10.3390/agronomy15071522

APA Style

Shen, A.-Q., Lv, M.-Y., Ge, Y.-X., Zhou, J., Hu, Z.-Z., Ren, X.-Q., Xiong, A.-S., & Wang, G.-L. (2025). Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation. Agronomy, 15(7), 1522. https://doi.org/10.3390/agronomy15071522

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