The plant homeodomain (PHD) finger is a common zinc-binding domain that existed in all eukaryotic genomes (Bienz, 2006). The PHD finger is usually comprised of 50–80 amino acids and typically has a conserved Cys4-His-Cys3 motif containing insertion sequences with various length and composition in the domain (Aasland et al., 1995; Bienz, 2006). The PHD finger exhibits high sequence similarity to the RING finger (Cys3-His-Cys4 type), which also binds to two zinc atoms (Capili et al., 2001). Previously, some RING fingers were mistaken for PHD fingers, leading to the incorrect conclusion that PHD fingers were also involved in E3 ligase activity (Wei et al., 2015). In general, the three-dimensional structure of the PHD finger shows a globular fold, consisting of an alpha-helix and a two-stranded beta-sheet.

Histone acetyltransferases (HATs) catalyze histone acetylation and play an important role in the positive epigenetic regulation of gene expression in eukaryotes (Zhang et al., 2023). Ever since Arabidopsis HAT3.1 was identified as the first PHD finger protein (Schindler et al., 1993), many PHD finger proteins have been found in fungus, animals, and plants (Martin et al., 2006; Baker et al., 2008; Hu et al., 2018). Most of these proteins are localized in the nucleus (Aasland et al., 1995; Gilbert et al., 2014; Shu et al., 2015), while a few are predicted to be localized in the membrane, including the chloroplast thylakoid membrane (Glyma10g05080.1) and mitochondrial inner membrane (Glyma11g11720.1) (Wu and Wang, 2014). A typical PHD finger protein usually contains one or more PHD finger domains. As an independent structure unit, most PHD finger-containing proteins only have PHD finger domain (Wu and Wang, 2014). However, there are other conserved domains in a certain protein concomitant with PHD finger domain, such as DUF3594 (Domain of Unknown Function 3594), BAH (Bromo Adjacent Homology), and DDT (DNA binding homeobox and different transcription factors) domain (Sun et al., 2017). These various domains individually cooperate with PHD finger domain to play a role in a particular biological event (Wu and Wang, 2014). The Alfin1 group belongs to a plant-specific subfamily of PHD finger proteins. Alfin1 from alfalfa (Medicago sativa) is a salt-induced transcription factor and can efficiently bind to the G-rich elements (GNGGTG/GTGGNG) in the promoter region of MsPRP2, a stress-responsive gene (Bastola et al., 1998). Overexpression of Alfin1 in alfalfa increased the transcript of MsPRP2 in roots and enhanced the tolerance of transgenic plants to salt stress (Winicov et al., 2004). So far, an increasing number of Alfin1-like (AL) proteins have been identified and characterized in various plant species, such as Arabidopsis thaliana (Wei et al., 2015), Brassica rapa (Kayum et al., 2015), and Atriplex hortensis (Tao et al., 2018). Except the conserved PHD finger domain in C-terminal, all AL proteins contain the conserved DUF3594 domain in N-terminal with unknown function. AL proteins containing the DUF3594 domain have not been found in animals, fungi, or prokaryotes (Tao et al., 2018).

PHD finger domains are proved to be involved in protein–DNA and protein–protein interaction (Bastola et al., 1998; Wei et al., 2017). The N-terminal tails of nucleosome core histones (H2A, HAB, H3, and H4) are usually modified by methylation or acetylation, which is called post-translational modification in histone proteins (PTM) (Lee et al., 2010; Yang et al., 2013; Sun et al., 2014). The PHD finger is a methyllysine and methylarginine “reader” domain, which can specifically recognize and bind to methylation marks in histone H3 (Sanchez and Zhou, 2011; Milosevich and Hof, 2016; Miura et al., 2020). Lee et al. (2009) first identified that PHD fingers in ING (inhibitor of growth) homologues AtING and AL proteins are able to bind histone H3 at di- or tri-methylated lysine4 (H3K4me2/me3) in Arabidopsis. Additionally, many PHD finger proteins are proved to be involved in chromatin remodeling and have transcriptional regulation activity (Bienz, 2006; Wei et al., 2015; Milosevich and Hof, 2016; Diego-Martin et al., 2022). Chromatin remodeling processes function in the control of gene expression patterns that modulate development in eukaryotic organisms (López-González et al., 2014). Thus, these “reader” proteins are essential for recruiting chromatin remodeling complexes and transcription factors to target loci and regulating their transcriptional status (López-González et al., 2014; Milosevich and Hof, 2016). In this way, the PHD finger proteins play important roles in translating histone modifications into downstream gene expression patterns.

PHD finger proteins function in various biological processes because of high sequence diversity except the eight conserved cysteine/histidine residues (Wei et al., 2015). In plants, diverse functions of PHD finger proteins have been characterized, which are involved in different biological processes, including the regulation of seed dormancy and germination (Ye et al., 2016), vernalization response (Sung and Amasino, 2004; Kim and Sung, 2013), flowering time (Qian et al., 2021), and pollen development (Yang et al., 2019a; Yang et al., 2019b). Furthermore, many genes encoding PHD finger proteins can be induced by environmental stresses and participate in plant abiotic stress responses (Wei et al., 2009; Gao et al., 2018; Alam et al., 2019; Pang et al., 2022). In this review, we aim to summarize and analyze the functions of PHD finger proteins in plants, particularly in plant reproduction development and responses to abiotic stresses. This will provide useful information for studying novel PHD finger proteins and further exploring the molecular mechanisms of these proteins involved in specific biological events.

The processes of plant growth and development play vital roles in plant reproduction and the completion of its life cycle. Previous studies showed that lots of PHD finger proteins are involved in these biological events, such as the regulation of flowering time, pollen development, seed germination, metabolite biosynthesis, and metal transport ( Table 1 ).

Abiotic stresses are major adverse environment factors limiting plant growth, development, and productivity in the whole world (Wang et al., 2019). During the long-time evolution, plants have formed complicated mechanisms to sense, transmit, and respond to these abiotic stress signals in order to survive and reproduce (Gong et al., 2020). The transcriptional regulation of stress-related genes through transcription factors is an important component of plant stress responses (Wang et al., 2019).

A lot of studies reported that many PHD finger genes are stress responsive and play key roles in plant responses to abiotic stresses, such as salt, drought, and freezing stresses ( Table 2 ). Genome-wide PHD/AL genes are identified and analyzed in various plant species, including Arabidopsis (Zhang et al., 2009; Guk et al., 2022), maize (Wang et al., 2015; Zhou et al., 2017), B. rapa (Kayum et al., 2015; Alam et al., 2019), and wheat (Triticum aestivum L.) (Pang et al., 2022) ( Table 3 ). Wang et al. (2015) reported that 67 PHD finger genes are identified in maize, and 15 ZmPHDs are stress-responsive genes detected by promoter cis-element and expression analysis. When subjected to PEG, NaCl, and ABA treatments, ZmPHD14 and ZmPHD19 are strongly induced or repressed in all stress treatments, while the expression levels of other genes are highly regulated only by one or two treatments. Totally, 73 non-redundant PHD finger genes are isolated from the poplar (Populus trichocarpa) genome. Some paralogous genes have high degrees of sequence homology, such as PtPHD29/PtPHD65, PtPHD35/PtPHD23, and PtPHD45/PtPHD18, suggesting that these genes may have redundant functions. In addition, nine genes, for instance PtPHD68, PtPHD31, and PtPHD65, are strongly regulated under drought, salt, or cold stress (Wu et al., 2016b). In moso bamboo (Phyllostachys edulis), 60 PHD finger genes are classified into 11 subfamilies according to phylogenetic analysis. Among them, 16 PePHDs are stress-responsive genes and differentially induced by drought, low temperature, and NaCl and ABA treatments (Gao et al., 2018). 18 of 145 BrPHD genes from B. rapa are responsive to drought and salt stresses (Alam et al., 2019). As plant genome annotations are updated, a larger number of previously omitted protein-coding genes are re-identified and re-annotated (Cheng et al., 2017; Kim et al., 2020). Through genome-wide re-annotation of PHD finger genes in tomato (Solanum lycopersicum), potato (Solanum tuberosum), pepper (Capsicum annuum), rice, and Arabidopsis, 225 of 875 PHD finger genes were newly identified in the five species, of which 57 is in pepper (Guk et al., 2022). Combining gene expression profiling and GO enrichment analysis showed that many pepper PHD finger differentially expressed genes (DEGs) perform some degree of function in response to salt, heat, or mannitol stress (Guk et al., 2022).

In cotton (Gossypium hirsutum), GhCHR encoding a protein with three PHD finger and two DC1 (Cys5-His) motifs can be induced by salt stress and is the target of miRNVL5. Overexpression of GhCHR in Arabidopsis enhances the tolerance of salt stress with less Na⁺ accumulation in shoots and better primary root growth, compared with the wild type (Gao et al., 2016). The expression of an M. truncatula gene, MtPHD6, can be induced by osmotic and drought stresses. MtPHD6-overexpressing Arabidopsis plants display lower MDA and ROS contents and higher leaf water content and antioxidant enzyme activities than the wild-type plants under drought stress, leading to the enhanced drought tolerance. Moreover, they found that the transformation of MtPHD6 predominantly upregulates the expression of WRKY, ZINC FINGER, and AP2/EREBP transcription factors (Quan et al., 2019). Plant SIZ proteins encode SUMO (small ubiquitin-related modifier) E3 ligases that play key roles in sumoylation (Jin et al., 2008). AtSIZ1 contains a plant-specific PHD finger domain, while the orthologs in yeast and animals have no PHD finger. The mutation in the PHD finger domain impairs the SUMO conjugate formation and generates the long-hypocotyl phenotype related to sugar and light conditions (Cheong et al., 2009). The PHD finger of AtSIZ1 recognizes H3K4me3, which is important for the suppression of WRKY70 expression and for the interaction with ATX1, a histone lysine methyltransferases. AtSIZ1 without the PHD finger or with mutated PHD finger does not complement the freezing sensitivity and drought tolerance induced by the siz1-2 mutant, whereas AtSIZ1 does, indicating that the PHD finger is necessary for AtSIZ1 function as a transcriptional repressor (Miura et al., 2020). Additionally, the overexpression of AtSIZ1 enhances the tolerance of transgenic plants to freezing and salinity stresses and reduces the inhibition induced by ABA treatment (Miura and Nozawa, 2014).

As a plant-specific subfamily of the PHD finger proteins, ALs normally possess transcriptional suppression activity and play crucial roles in biological processes by inhibiting expression of downstream target genes (Wei et al., 2017). Most AL genes are also significantly induced by abiotic stresses, such as cold, salt, drought, and ABA treatment (Wei et al., 2009; Wei et al., 2015; Tao et al., 2018). Of the 12 AL genes from B. oleracea, 10 are abiotic stress responsive (Kayum et al., 2016). In soybean, Wei et al. (2009) identified six Alfin1-type PHD finger proteins, GmPHD1-6, with the ability of binding to the cis-element “GTGGAG.” GmPHDs have transcriptional suppression activity except GmPHD6. Heterologous expression of GmPHD2 in Arabidopsis inhibits the expression of seven negative regulator genes, such as DREB1C, STRS1, and STRS2. Eight genes are upregulated in transgenic plants, including ABI5, WAK5, GLP, MDAR, TPP, and three peroxidase genes. Expression changes in these stress-responsive genes showed that GmPHD2 enhances salt tolerance though affecting stress signaling and by eliminating ROS in transgenic plants (Wei et al., 2009). Under salt stress, GmPHD5 regulates the crosstalk between the methylated H3K4 and the acetylated H3K14 and may recruit chromatin remodeling factors and transcription factors to modulate the transcription of stress-inducible genes, including GmRD22 and GmGST (Wu et al., 2011). GmPHD6 overexpression improves the tolerance to salt stress in soybean through interacting with LHP1 by the PHD finger domain. The GmPHD6 and LHP1 form a transcriptional activation complex to activate expression of downstream stress responsive genes, such as CYP82C4, CYP75B1, and CCD7, suggesting that the GmPHD6-LHP1 complex plays a key role in salt tolerance (Wei et al., 2017). In Arabidopsis, seven AL genes are identified and functionally characterized. AtAL6 is essential for the formation of root hair during phosphate (Pi) deficiency stress. It binds to H3K4me marks at the Myb-type transcription factor ETC1 through its PHD finger domain, which may facilitate the transcription of downstream Pi-responsive genes (Chandrika et al., 2013). The T-DNA insertion mutants of AtAL7 display enhanced salt tolerance with longer root length, indicating that AtAL7 functions as a negative regulator in response to salt stress (Song et al., 2013). Overexpression of AtAL5 improves the tolerance of transgenic plants to salt, drought, and freezing stresses by repressing the transcription of downstream negative regulatory genes, including SHMT7, TAC1, OFE, FAO, and CAX1 (Wei et al., 2015). In addition, four AhAL genes are isolated from A. hortensis and encode nuclear-localized proteins with the transcription repression activities. AhAL1-transgenic Arabidopsis shows the higher survival rate under salt and drought stresses by reducing MDA content and water loss. Through binding to the promoter regions of target genes, AhAL1 represses the expression of negative regulator genes in ABA signaling, such as DREB1C, GRF7, and five group-A protein phosphatase 2C (PP2C)-encoding genes (ABI1, ABI2, AHG3, HAB1, and HAB2), which then induces the activation of some ABA/stress-responsive genes, including DREB1A, DREB2A, and three genes encoding ABA-responsive element (ABRE)-binding factors (ABF2, ABF3, and ABF4) (Tao et al., 2018). In conclusion, the overexpression of PHD finger genes can improve abiotic stress tolerance of transgenic plants with better growth phenotype. PHD finger genes exert the transcriptional regulatory activity by inhibiting or activating the expression of downstream stress-related genes in plant adaptation to adverse environment.

Proteins containing the PHD finger domain are widespread in plants and are one of the important transcription regulator families. Recently, many PHD finger proteins are identified in diverse plant species and proved to be involved in various biological processes. In this review, we mainly focused on the roles of PHD finger proteins in plant reproduction development, such as floral transition, tapetum development, and male meiosis ( Figure 1 ), and responses to abiotic stresses, including salinity, drought stress, and low temperature ( Figure 2 ). Moreover, acting as key transcriptional regulators, some PHD finger proteins also function in metal transport and biosynthesis pathways, which are important for the normal growth of plants. In summary, after being exposed to external stimuli, PHD finger proteins can bind to specific regions of downstream target gene promoters through the PHD finger to exert its transcriptional regulatory activity, activate or inhibit the expression of responsive genes related to plant growth and development and stress response, and finally achieve the role of regulating plant development and stress tolerance ( Figure 3 ).

The PHD finger is the “reader” domain of epigenetic modification and directly binds to the methylated histone H3, which plays key roles in chromatin remodeling and transcription regulation of target genes (Sung and Amasino, 2004; Wu et al., 2011; López-González et al., 2014; Wang et al., 2016; Miura et al., 2020). Furthermore, PHD finger proteins can interact with other proteins through the PHD finger domain to regulate specific biological processes. For example, the interaction of OsMS1 with TIP2 and OsMADS15 is necessary for the tapetum development and pollen wall formation, both of which play crucial roles in the production pf mature pollen grains (Yang et al., 2019a). In order to verify the functional importance of the PHD finger, the target gene with or without the PHD finger domain is transferred into the corresponding mutant plants to observe whether the abnormal phenotypes can be restored. For instance, under the control of the AtSIZ1 promoter, the recombinant vector containing AtSIZ1 gene with or without the PHD finger is transferred to the siz1-2 mutant. The expression of Pro_SIZ1::SIZ1:GFP could be able to complement the defective phenotypes of the siz1-2 mutant, while Pro_SIZ1::SIZ1(ΔPHD):GFP does not, demonstrating that the PHD finger is critical for AtSIZ1 in plant response to cold stress, drought stress, and ABA treatment (Miura et al., 2020).

With the development of transcriptome-wide sequencing and the updating of genome-wide annotation, more and more PHD finger genes will be excavated or be re-annotated in plant species; however, further studies still need to focus on the exact functions of PHD finger proteins. For instance, many PHD finger genes are proved to be stress responsive, but their biological functions in plant responses to abiotic stresses remain to be confirmed. By using PHD finger gene-specific overexpression and mutant lines is helpful for analyzing their functions. In addition, it is worth noting that a PHD finger protein may have multiple roles participated in different biological events, such as AtAL6 (Chandrika et al., 2013; Molitor et al., 2014) and AtSIZ1 (Jin et al., 2008; Miura et al., 2020). Last but not the least, the signaling transduction pathways by which many PHD finger proteins perform specific biological functions are still unclear. At present, the research on some PHD finger proteins is limited to the identification of biological functions. The molecular mechanism of its specific biological function has not been studied deeply. Many studies have screened differentially expressed genes through transcriptome sequencing, so as to obtain downstream functional genes modulated by a PHD finger protein. The upstream regulators of this protein expression and their functions have been less studied. Identifying the upstream and downstream interaction factors of PHD finger proteins is essential to better understand their molecular mechanisms in a biological process. The yeast two-hybrid assay and other protein interaction methods are useful for analyzing and verifying proteins interacted with PHD finger proteins. To sum up, the in-depth research on the biological functions of PHD finger proteins and the construction of their molecular regulatory networks will enrich and improve our understanding of the roles of PHD finger proteins in various biological events. Meanwhile, this will also provide a valuable scientific basis for the study of new PHD finger proteins. In addition, the PHD finger protein encoding genes may be used as novel candidate genes to modify the plant genome for enhancing the tolerance of transgenic plants to adverse environment or improving their growth and development, ultimately leading to the plant biomass increase.

WQ: Writing – original draft. ZC: Writing – review & editing. PW: Writing – review & editing. YM: Writing – review & editing. DB: Writing – review & editing. XL: Writing – original draft.