Role of the INDETERMINATE DOMAIN Genes in Plants

The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.


Introduction
The Cys2His2 zinc-finger domain (C2H2) transcription factor family is one of the largest in plants. Analysis of 176 zinc finger proteins (ZFPs) from Arabidopsis revealed that 81% (143 ZFPs) were plant-specific (Arabidopsis thaliana, Zea mays, and Solanum tuberosum); only 19% (33 ZFPs) were conserved in other eukaryotes (Protozoa and animals) [1,2]. Extensive duplication has led to an expanded C2H2 family in plants [3]. Its subfamily INDETERMINATE DOMAIN (IDD), a conserved group across plants, contains functional genes that encode putative nuclear proteins with four zinc finger domains [4]. Since the report of the first plant IDD gene, PCP1, which is involved in sucrose uptake via an unknown mechanism in potatoes [5], many IDD genes have been functionally characterized. In general, IDDs form extensive protein interaction networks to ensure precise transcriptional control and thereby tissueand/or cell-fate specification and hormonal signaling to control various aspects of plant growth and development [6][7][8][9].
Here, we provide a new understanding of the biological functions of IDD genes and their working mechanisms. We mainly focus on the role of IDDs in the linkage between sugar metabolism and developmental processes in plants.

Modulation of Sugar Metabolism and Floral Transition
ID1 regulates floral transition in maize [4,16,17]. Structural studies of ID1, along with other IDD proteins revealed the unique DNA-binding properties of two out of four zinc finger motifs [18], indicating that maize ID1 acts as a unique transcriptional regulator in the control of the floral transition. The id1 mutant displays a prolonged vegetative phase without other developmental defects. In support, various genes involved in flowering significantly changed their expression in the id1 mutant, including ZCN8 and ZMM4 [19,20]. The ID1 ortholog in rice, INDETERMINATE1 (OsID1)/Early Heading Date2 (Ehd2), Rice Indeterminate1 (RID1) is also involved in flowering [20][21][22][23]. Ehd2 acts as a floral activator by upregulating Ehd1 and the downstream floral activator genes, Heading date 3a (Hd3a) and Rft1 (Hd3b) genes in a unique regulatory network of photoperiodic flowering [20][21][22][23].
As a source of energy and carbon, sugar is the most important nutrient for growth and development of nearly all living organisms. Sugar metabolism is most likely associated with the floral transition, and IDDs are core members involved in the crosstalk. PCP1, an IDD gene of Solanum tuberosum, was shown to activate the silent endogenous sucrose uptake system in yeast [5]. The yeast strain SUSY7, which lacks an endogenous invertase gene, is unable to grow on sucrose-containing medium, but can be rescued by complementation of PCP1. Moreover, expression of PCP1 also rescues the yeast mutant strains that have defects in sucrose synthase and sucrose transport, although the underlying molecular mechanism remains unclear [5].
Several Arabidopsis IDD members function as transcriptional regulators of floral transition, possibly through the control of sucrose signaling [24]. In Arabidopsis, AtIDD8 has been reported to function in sugar metabolism and contribute to photoperiodic flowering [25]. Expression of Sucrose Transporter genes (SUC2, SUC6, SUC7, and SUC8) and Sucrose Synthase genes (SUS1 and SUS4) are affected by IDD8 activity. IDD8-SUS4 module-regulated sugar metabolism is associated with photoperiod flowering [25,26]. AtIDD8 is further regulated through phosphorylation at two positions, Ser-178 and Ser-182, which is catalyzed by the catalytic α-subunit of Sucrose-non-fermenting1 (Snf1)-related kinase 1 (SnRK1)/AKIN10 [27]. Phosphorylation of AtIDD8 significantly reduced its transcriptional activation activity [27]. Consistently, atidd8 mutants and plants overexpressing AKIN10 display a delayed-flowering phenotype. This pathway can be referred to as a gatekeeping mechanism for plants to regulate floral transition in a malnourished, low sugar level state ( Figure 4).

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As a source of energy and carbon, sugar is the most important nutrient for growth and 87 development of nearly all living organisms. Sugar metabolism is most likely associated with the floral 88 transition, and IDDs are core members involved in the crosstalk. PCP1, an IDD gene of Solanum 89 tuberosum, was shown to activate the silent endogenous sucrose uptake system in yeast [5]. The yeast 90 strain SUSY7, which lacks an endogenous invertase gene, is unable to grow on sucrose-containing 91 medium, but can be rescued by complementation of PCP1. Moreover, expression of PCP1 also rescues 92 the yeast mutant strains that have defects in sucrose synthase and sucrose transport, although the 93 underlying molecular mechanism remains unclear [5].

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Several Arabidopsis IDD members function as transcriptional regulators of floral transition, 95 possibly through the control of sucrose signaling [24]. In Arabidopsis, AtIDD8 has been reported to 96 function in sugar metabolism and contribute to photoperiodic flowering [25]. Expression of Sucrose

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Under sugar deprived conditions, AKIN10, the α catalytic subunit of SnRK1 kinase, blocks IDD8 At the pre-flowering stage, maize id1 mutant leaves have a significantly lower ratio of sucrose formation from starch [28]. Variations in sucrose and starch levels in id1 suggest an ID1 role in promoting carbohydrate export to the shoot apex upon flowering [28]. Another study reported the involvement of the sugar signaling molecule trehalose 6-phosphate (T6P) in developmental growth, including flowering [29]. Phloem-specific induction of the Arabidopsis florigen FLOWERING LOCUS T (FT) can rescue lines that have a late-flowering phenotype because of reduced expression of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) [30,31]. These results indicate that sugar status linked to T6P signaling is vital for flowering [31]. In rice, OsIDD1 and OsIDD6 overexpression rescue the late-flowering phenotype of rice Ehd2, illustrating that IDD family genes might have a functional redundancy in sugar metabolism and the control of flowering time [32]. These reports suggest that multiple IDD genes modulate sugar metabolism, and some of them have a direct or indirect link with flowering regulation ( Figure 5).
activity. IDD8 is phosphorylated at ser-178 and ser-182 positions to decrease its transcriptional 110 activation activity, and thus, consequently, SUS4 expression. Additionally, endogenous sugar levels 111 give feedback regulation to control the expression of SUS4. AKIN10 also has a role in the negative 112 regulation of FLOWERING LOCUS C (FLC), which acts to suppress FLOWERING LOCUS T (FT), a 113 floral activator in Arabidopsis.

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At the pre-flowering stage, maize id1 mutant leaves have a significantly lower ratio of sucrose 115 formation from starch [28]. Variations in sucrose and starch levels in id1 suggest an ID1 role in 116 promoting carbohydrate export to the shoot apex upon flowering [28]. Another study reported the 117 involvement of the sugar signaling molecule trehalose 6-phosphate (T6P) in developmental growth, 118 including flowering [29]. Phloem-specific induction of the Arabidopsis florigen FLOWERING LOCUS 119 T (FT) can rescue lines that have a late-flowering phenotype because of reduced expression of 120 TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) [30,31]. These results indicate that sugar status redundancy in sugar metabolism and the control of flowering time [32]. These reports suggest that

Starch Accumulation and Cold Response
Abiotic stress, including salinity, drought, and cold, adversely affects plant growth and development. Cold stress is a significant environmental challenge, and plants have evolved various strategies to ensure plant fitness [33]. In Arabidopsis, two splice variants of AtIDD14 (AtIDD14α and β) directly regulate starch metabolism in response to cold via regulation of Qua-quine starch (QQS) expression. QQS represses starch accumulation [34]. The functional AtIDD14 form (AtIDD14α) binds to the QQS promoter and activates its expression, promoting starch degradation. The non-functional AtIDD14β form, which is produced mainly under cold conditions (4 • C), lacks a functional DNA-binding domain, but can form a heterodimer complex with AtIDD14α. Thus, the AtIDD14β isoform acts as a competitive inhibitor to repress DNA binding activity of AtIDD14α. Therefore, QQS is repressed by cold stress via the self-regulatory module provided by cold-induced alternative splicing. Competitive inhibition of AtIDD14α activity by AtIDD14β would serve as a cold adaptation strategy, helping plants maintain an appropriate level of starch accumulation during the dark period; this might be required to tolerate low temperatures during the light period [35].
In rice, an IDD gene encoding the ROC1 protein binds the CBF1 promoter directly to regulate cold tolerance [36]. Transcription activator CBF1 contains an AP2 domain, and it controls many cold-responsive genes [37]. In rice, MYB15 also controls the expression of CBF1 gene in cold stress. These results indicate that there might be some complex system that helps CBF1 regulate cold stress response, along with ROC1 and MYB15 [36,[38][39][40]. The function of IDD in low temperature is remarkable. However, which endogenous signal activates ROC1 or AtIDD14 is less understood. Previous papers have shown that cold stress induces the alternative intracellular auxin gradient via auxin transporter gene (YUC, PIN) to regulate plant growth and development. Auxin and other phytohormones-responsive genes also respond to cold stress [41]. On the other hand, both AtIDD14 and ROC1 are reported to be involved in auxin signaling [6,36]. This suggests that auxin might induce IDD activity under cold-stress conditions.

Regulation of Seed Development
Seed development and maturation is a crucial process in the life cycle of a plant. IDDs are involved in the regulation of seed development. In maize, duplicated genes ZmIDDveg9/NAKED ENDOSPERM (NKD1) and ZmIDD9/NKD2 are involved in seed maturation, cell differentiation, thick walls, and accumulation of anthocyanin pigments [42]. These genes are required for aleurone cell fate and cell differentiation. Genetic mutations of the IDD genes Zmiddveg9 and Zmidd9 lead to naked endosperm phenotypes, decreases in germination rates, starch accumulation, delayed anthesis, less seed weight, and a propensity for vivipary [42,43]. NKD1 and NKD2 can directly regulate transcription and activate viviparous1 and opaque2 genes. Further, NKD2 functions as a negative regulator of NKD1 [42,43].
In Arabidopsis, AtIDD1 acts as either an activator or a repressor of germination, depending on the absence or presence of gibberellic acid, respectively. GID1b encoding a GA receptor is the target of GAF1/AtIDD1. Ectopic expression of IDD1/ENY under CaMV35S leads to disrupted seed development, delayed endosperm depletion, testa senescence, and an impaired maturation program. Subsequently, mature 2x35S:ENY seeds have high endosperm-specific fatty acids, starch retention, and defective mucilage extrusion with low expression of GID1b [4,5]. Studying the molecular mechanisms of IDD function, including transcriptional regulation of downstream gene networks, will provide a better understanding of regulated seed development, and the knowledge attained can be expanded to important work on cereal grain quality.

Modulation of Plant Architecture, Shoot Gravitropism, and Secondary Cell Wall Formation
Plant architecture influences plant fitness and productivity. IDDs play a role in organ development, and thereby plant architecture. In rice, secondary cell wall formation is negatively regulated by OsIDD2 [44]. Transgenic plants overexpressing OsIDD2 display dwarfism, fragile leaves, and decreased lignin content [45], whereas an osidd2 knockdown mutant produced by the CRISPR/Cas9 technique showed high lignin content. In particular, OsIDD2 downregulates genes involved in lignin biosynthesis and sucrose metabolism [44]. The Loose Plant Architecture1 (LPA1) gene, a functional ortholog of AtIDD15/SGR5 in rice, also affects the plant architecture, especially shoot gravitropism [46,47]. The lpa1 mutant coleoptile exhibits slower sedimentation rate of amyloplasts compared to wild-type [47]. The coleoptile of the lpa1 mutant exhibits negative gravitropism, indicating that signal transduction or gravity sensing is disturbed in the mutant. LPA1 also blocks auxin signaling through its interaction with C-22-hydroxylated and 6-deoxo brassinosteroids (BRs), which in turn regulate lamina inclination [46,47]. lpa1 mutants display indole-3-acetic acid (IAA) hypersensitivity during the lamina inclination response, which can be suppressed by brassinazole (Brz) (an inhibitor of C-22 hydroxylase involved in BR synthesis). Roles of LPA1 in OsPIN gene expression (OsPIN1a, OsPIN1c, and OsPIN3a) further indicate that the LPA1-mediated lamina inclination in rice might be due to auxin flux [46,47].
In barley, IDD protein BLF1 acts as a regulator of the leaf-width growth [48]. The blf1-1 mutation leads to wider but slightly shorter leaves than wild-type, because of a perturbation in the longitudinal cell numbers in leaves. A BLF1-vYFP fusion protein indicates BLF1 expression in the shoot apical meristem, epidermis, and prospective veins of leaf primordia. Given the economic and agronomical value of leaf traits in crop plants [49,50], BLF1 might be an ideal candidate for optimizing crop architecture.
In Arabidopsis, some IDD genes are associated with cellular patterning. Among them, AtIDD14-A (a spliced variant of AtIDD14), AtIDD15, and AtIDD16 regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport [6]. Since IDDs are also involved in starch metabolism, coordination between auxin accumulation and starch metabolism may underlie plant development. For example, the zinc finger transcription factor, SHOOT GRAVITROPISM5 (SGR5)/AtIDD15, has a crucial role in the early events of gravitropic responses in the inflorescence. The SGR5 gene has two splice variants: the truncated SGR5β form that lacks the functional ZF motifs and the full-size SGR5α transcription factor [51]. A truncated form of SGR5β inhibits SGR5α function, possibly by forming non-functional complex heterodimers. High temperatures might accelerate the alternative splicing of SGR5, resulting in a high level of accumulation of SGR5β proteins. SGR5β over-expression plants exhibit reduced gravitropic response of the inflorescence stem, similar to that of the atsgr5-1 phenotype [52].
JACKDAW (JKD/AtIDD10) and MAGPIE (MGP/AtIDD3) modulate the expression of SHORT-ROOT (SHR) and SCARECROW (SCR) in the root apex [53][54][55] (Figure 6). SCR and SHR are two GRAS family transcription factors, which are required for quiescent center and ground tissue formation in roots. JKD directly regulates SCR and MGP expression in cooperation with SHR [54]. SHR is a crucial regulator that directly activates the expression of SCL23 and SCR. In the SHR-SCR-SCL23 complex, SHR level is modulated by SCL23. The SHR-SCR-SCL23 complex plays a crucial role in endodermis formation in the hypocotyl [56]. JKD also modulates the repression of SCM that leads to the activity of the GLABRA3 (GL3)/ENHANCER OF GLABRA3 (EGL3)/TRANSPARENT TESTA GLABRA1 (TTG1) complex. This complex depends on the relative abundance of an MYB transcription factor, WEREWOLF (WER). WER triggers the trichoblasts (T cell) to inhibit GL2 and atrichoblasts (A cell) to lead cell division [53,57]. OsPIN gene expression (OsPIN1a, OsPIN1c, and OsPIN3a) further indicate that the LPA1-mediated 190 lamina inclination in rice might be due to auxin flux [46,47].

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In barley, IDD protein BLF1 acts as a regulator of the leaf-width growth [48].

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In Arabidopsis, some IDD genes are associated with cellular patterning. Among them, AtIDD14-

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A (a spliced variant of AtIDD14), AtIDD15, and AtIDD16 regulate lateral organ morphogenesis and 199 gravitropism by promoting auxin biosynthesis and transport [6]. Since IDDs are also involved in

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The SGR5 gene has two splice variants: the truncated SGR5β form that lacks the functional ZF motifs 204 and the full-size SGR5α transcription factor [51].

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SHR is a crucial regulator that directly activates the expression of SCL23 and SCR. In the SHR-SCR-

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SCL23 complex, SHR level is modulated by SCL23. The SHR-SCR-SCL23 complex plays a crucial role 215 in endodermis formation in the hypocotyl [56]. JKD also modulates the repression of SCM that leads 220 221 Figure 6. Role of the MGP/AtIDD3 and JKD/AtIDD10 in cell division. JKD regulates the formation cells through two pathways: (1) Complex SHR-MGP-SCR-JKD with putative target (X) genes. SHR enhances expression of SCL23 and SCR and MGP. SHR negatively regulated via protein-protein interaction to SCL23 and SCR. Both SCR, MGP, and SCL23 can self-control their transcription. JKD directly regulates SCR and MGP expression in cooperation with MGP, SCR, and SHR. (2) JKD modulates the repression of SCM that leads to the activity of the GL3/EGL3/TTG1 complex, which depends on the relative abundance of an MYB transcription factor, WEREWOLF (WER). WER triggers the trichoblasts (T cell) to inhibit GL2 and atrichoblasts (A cell) to lead cell division. Arrows and bars represent positive regulation and negative regulation, respectively. Transcriptional controls are depicted with black arrows, protein-protein interactions are described with red arrows. The distinction of box color and shape describes different genes in this network.

Regulation of Hormonal Signaling
Hormone signaling has diverse and crucial roles in plant development. Hormone interactions control the formation of all organs in the plant by regulating meristem function. Gibberellins (GA), auxin, cytokinin (CK), brassinosteroids (BRs), and strigolactones (SLs) play vital roles during plant development, from embryogenesis to senescence [58]. DELLAs, the GRAS transcriptional regulators containing a GRAS domain at the C terminus and a DELLA/TVHYNP motif at the N terminus [9], act as key players in the regulation of GA responses. They lack a DNA binding domain, and act as transcriptional coregulators with other DNA-binding factors. Notably, five IDD members, AtIDD3, AtIDD4, AtIDD5, AtIDD9, and AtIDD10, interact with DELLA and regulate the GA-positive regulator, SCARECROW-LIKE3 (SCL3) [8,9,59,60]. Further experiments have indicated that DELLA and SCL3 act as coregulators and require IDDs as transcriptional scaffolds for DNA binding to check GA feedback regulation. IDD binding to DNA represents the balance of the SCL3 and DELLA protein levels to regulate downstream gene expression.
Auxin is another essential plant hormone that has a crucial role in controlling plant development processes, including embryogenesis, gametogenesis, patterning, lateral organ formation, tropic responses, and branching [61,62]. Auxin-mediated developmental and growth events are shaped by auxin biosynthesis and intercellular polar transport [61,63]. Some IDDs regulate auxin biosynthesis and transport. The epinastic leaves in plants overexpressing IDDs (IDD14, IDD15, and IDD16) are similar to those in auxin overproduction plants [6,[64][65][66][67]. The IDD proteins directly bind to the promoter regions of TAA1, PIN1, and YUC5 and activate their expression. IDD-regulated auxin signaling might be further regulated by ZAT6 [68]. Further study of crosstalk between hormone metabolism and the surrounding environment will lead to a better understanding of the role of IDD proteins in the regulation of hormonal signaling.

Ammonium Metabolism
In the roots of higher plants, ammonium and nitrates are the primary sources of nitrogen (N). Asparagine and glutamine are the primary forms of organic N, and are transported to the shoots from the roots via the xylem [69]. Many reports have suggested a possible role of N in the various developmental and metabolic processes [70][71][72][73][74]. In rice, OsIDD10 directly activates the transcription of AMT1;2 (ammonium transporter) and GDH2 (glutamate dehydrogenase, which degrades glutamate to ammonia and alpha-ketoglutarate). Further, OsIDD10 also upregulates genes involved in N-linked metabolism, including nitrite reductases, glutamine synthetase 2, and trehalose 6-phosphate synthase [10,75]. Notably, OsIDD10 plays an essential role in the interaction between NH 4 + and auxin signaling in rice roots [76]. The gravity response was delayed in osidd10 roots and accelerated in OsIDD10 overexpression (IDD10-OX) roots in the absence and presence of NH 4 + , respectively [69,76]. However, treatment with 1-N-naphthylphthalamic acid (NPA), a polar auxin transport inhibitor, suppressed the NH 4 + -induced root specific phenotype of the osidd10. The expression of NH 4 + -mediated auxin-related genes is affected in osidd10 and OsIDD10 overexpression plants. Phenotypes and expression patterns triggered by NH 4 + are influenced by the actions of auxin during root development, suggesting a regulatory circuit in rice between NH 4 + and auxin signaling that functions in root development [76]. The fact that IDD10 induces the expression of genes for trehalose-6-phosphate synthase, aminotransferase, and cytokinin dehydrogenase further strengthens the possibility of functional involvement of the gene in N-linked metabolism [10]. Therefore, it will be essential to perform a metabolite analysis to determine the possible agricultural benefits of manipulating IDD10 to enhance the efficiency of N metabolism in crop plants.

Conclusions
The IDD protein family comprises plant-specific transcription factors that have primary functions in inflorescence, leaf architecture, root architecture, seed development, and sugar homeostasis [77].
Most IDD genes have been mainly characterized in Arabidopsis; however, a few have been functionally characterized in other plants (Table 1). They are involved in seed maturation and germination, GA signaling, root development, sugar metabolism, leaf polarity, starch metabolism, cold-stress signaling, auxin biosynthesis and transport, flowering, plant architecture, shoot gravitropism, ammonium uptake, and endosperm development (Figure 7) [4,5,[7][8][9]25,32,36,[42][43][44]47,48,[53][54][55]75,[77][78][79][80][81][82]. IDD activity regulates many traits that have a direct or indirect impact on crop yield. Specifically, traits such as leaf angle contribute to overall plant architecture. Sugar metabolism and flowering time contribute to the allocation of carbon and grain yield, and endosperm development to seed maturation. Based on the fact that IDDs govern nearly all aspects of plant growth and development, information about IDDs will provide invaluable insights into the genetic programs underlying signaling networks in the regulation of plant development and metabolism with connections to external environmental fluctuations.

Conflicts of Interest:
None of the authors has any conflict of interest to disclose.