Class I and Class II TCP Transcription Factors Modulate SOC1-Dependent Flowering at Multiple Levels

Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.

GmTCP40 Promotes Soybean Flowering under Long-Day Conditions by Binding to the GmAP1a Promoter and Upregulating Its Expression

Soybean [Glycine max (L.) Merr.] is a short-day (SD) plant that is sensitive to photoperiod, which influences flowering, maturity, and even adaptation. TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors have been shown to regulate photoperiodic flowering. However, the roles of TCPs in SD plants such as soybean, rice, and maize remain largely unknown. In this study, we cloned the GmTCP40 gene from soybean and investigated its expression pattern and function. Compared with wild-type (WT) plants, GmTCP40-overexpression plants flowered earlier under long-day (LD) conditions but not under SD conditions. Consistent with this, the overexpression lines showed upregulation of the flowering-related genes GmFT2a, GmFT2b, GmFT5a, GmFT6, GmAP1a, GmAP1b, GmAP1c, GmSOC1a, GmSOC1b, GmFULa, and GmAG under LD conditions. Further investigation revealed that GmTCP40 binds to the GmAP1a promoter and promotes its expression. Analysis of the GmTCP40 haplotypes and phenotypes of soybean accessions demonstrated that one GmTCP40 haplotype (Hap6) may contribute to delayed flowering at low latitudes. Taken together, our findings provide preliminary insights into the regulation of flowering time by GmTCP40 while laying a foundation for future research on other members of the GmTCP family and for efforts to enhance soybean adaptability.

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development

TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of TCP genes in Dendrobium nobile, a crucial parent in genetic breeding and an excellent model material to explore perianth development in Dendrobium, has not been conducted. We identified 23 DnTCP genes unevenly distributed across 19 chromosomes and classified them as Class I PCF (12 members), Class II: CIN (10 members), and CYC/TB1 (1 member) based on the conserved domain and phylogenetic analysis. Most DnTCPs in the same subclade had similar gene and motif structures. Segmental duplication was the predominant duplication event for TCP genes, and no tandem duplication was observed. Seven genes in the CIN subclade had potential miR319 and -159 target sites. Cis-acting element analysis showed that most DnTCP genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 DnTCP genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, DnTCP4 and DnTCP18 play a role in early perianth development, and DnTCP5 and DnTCP10 are significantly expressed during late perianth development. DnTCP17, 20, 21, and 22 are the most likely to be involved in perianth and leaf development. DnTCP11 was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most DnTCP genes putative promoters, and two Class I DnTCPs were in the nucleus and interacted with each other or with the MADS-box. The interactions between TCP and the MADS-box have been described for the first time in orchids, which broadens our understanding of the regulatory network of TCP involved in perianth development in orchids.

SlTCP24 and SlTCP29 synergistically regulate compound leaf development through interacting with SlAS2 and activating transcription of SlCKX2 in tomato

The complexity of compound leaves results primarily from the leaflet initiation and arrangement during leaf development. However, the molecular mechanism underlying compound leaf development remains a central research question. SlTCP24 and SlTCP29, two plant-specific transcription factors with the conserved TCP motif, are shown here to synergistically regulate compound leaf development in tomato. When both of them were knocked out simultaneously, the number of leaflets significantly increased, and the shape of the leaves became more complex. SlTCP24 and SlTCP29 could form both homodimers and heterodimers, and such dimerization was impeded by the leaf polarity regulator SlAS2, which interacted with SlTCP24 and SlTCP29. SlTCP24 and SlTCP29 could bind to the TCP-binding cis-element of the SlCKX2 promoter and activate its transcription. Transgenic plants with SlTCP24 and SlTCP29 double-gene knockout had a lowered transcript level of SlCKX2 and an elevated level of cytokinin. This work led to the identification of two key regulators of tomato compound leaf development and their targeted genes involved in cytokinin metabolic pathway. A model of regulation of compound leaf development was proposed based on observations of this study.

Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean

Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.

Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species

TCP proteins, part of the transcription factors specific to plants, are recognized for their involvement in various aspects of plant growth and development. Nevertheless, a thorough investigation of TCPs in Chrysanthemum lavandulifolium, a prominent ancestral species of cultivated chrysanthemum and an excellent model material for investigating ray floret (RF) and disc floret (DF) development in Chrysanthemum, remains unexplored yet. Herein, a comprehensive study was performed to analyze the genome-wide distribution of TCPs in C. lavandulifolium. In total, 39 TCPs in C. lavandulifolium were identified, showing uneven distribution on 8 chromosomes. Phylogenetic and gene structural analyses revealed that ClTCPs were grouped into classes I and II. The class II genes were subdivided into two subclades, the CIN and CYC/TB1 subclades, with members of each clade having similar conserved motifs and gene structures. Four CIN subclade genes (ClTCP24, ClTCP25, ClTCP26, and ClTCP27) contained the potential miR319 target sites. Promoter analysis revealed that ClTCPs had numerous cis-regulatory elements associated with phytohormone responses, stress responses, and plant growth/development. The expression patterns of ClTCPs during capitulum development and in two different florets were determined using RNA-seq and qRT-PCR. The expression levels of TCPs varied in six development stages of capitula; 25 out of the 36 TCPs genes were specifically expressed in flowers. Additionally, we identified six key ClCYC2 genes, which belong to the class II TCP subclade, with markedly upregulated expression in RFs compared with DFs, and these genes exhibited similar expression patterns in the two florets of Chrysanthemum species. It is speculated that they may be responsible for RFs and DFs development. Subcellular localization and transactivation activity analyses of six candidate genes demonstrated that all of them were localized in the nucleus, while three exhibited self-activation activities. This research provided a better understanding of TCPs in C. lavandulifolium and laid a foundation for unraveling the mechanism by which important TCPs involved in the capitulum development.

A novel MORN-motif type gene GmMRF2 controls flowering time and plant height of soybean

The flowering time of soybean is a highly important agronomic characteristic, which affects the adaptability and yield. AtMRF1, a MORN-repeat motif gene, acts as a floral promoter in Arabidopsis, its functions in soybean are not yet understood. Here, we employed qRT-PCR to analyze the tissue expression patten of MRF1 homologs in soybean and determined that the GmMRF2 gene, containing a MORN-motif, highly expressed in the shoot and responded to photoperiod. GmMRF2 overexpression soybean lines exhibited earlier flowering time under long-day (LD) conditions, and increased plant height under both LD and short-day (SD) conditions compared to wild-type (WT) plants. The expression levels of gibberellic acid (GA) pathway genes that positively regulate plant height genes and flowering-promoting genes were up-regulated in the GmMRF2 overexpression lines, were up-regulated in the GmMRF2 overexpression lines. Further study revealed that GmMRF2 interacted with GmTCP15 to co-induce the expression of GmSOC1b. Together, our results preliminarily reveal the functions and mechanisms of GmMRF2 in regulating flowering time and plant height, provide a new promising gene for soybean crop improvement.

Overexpression of TCP9-like gene enhances salt tolerance in transgenic soybean

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors are a plant-specific family and play roles in plant growth, development, and responses to biotic and abiotic stresses. However, little is known about the functions of the TCP transcription factors in the soybean cultivars with tolerance to salt stress. In this study, TCP9-like, a TCP transcription factor, was identified in the soybean cultivars exposed to salt stress. The expression of TCP9-like gene in the roots of salt-tolerant soybean cultivars was higher than that in salt-sensitive cultivars treated with NaCl. The overexpression of TCP9-like enhanced the salt tolerance of the salt-sensitive soybean cultivar 'DN50'. In T2 generation, the plants with TCP9-like overexpression had significantly lower Na+ accumulation and higher K+ accumulation than the WT plants exposed to 200 or 250 mmol/L NaCl. The K+/Na+ ratio in the plants overexpressing TCP9-like was significantly higher than that in WT plants treated with 200 mmol/L NaCl. Meanwhile, the overexpression of TCP9-like up-regulated the expression levels of GmNHX1, GmNHX3, GmSOS1, GmSOS2-like, and GmHKT1, which were involved in the K+/Na+ homeostasis pathway. The findings indicated that TCP9-like mediated the regulation of both Na+ and K+ accumulation to improve the tolerance of soybean to salt stress.

TCP Transcription Factors in Plant Reproductive Development: Juggling Multiple Roles

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors (TFs) are plant-specific transcriptional regulators exerting multiple functions in plant growth and development. Ever since one of the founding members of the family was described, encoded by the CYCLOIDEA (CYC) gene from Antirrhinum majus and involved in the regulation of floral symmetry, the role of these TFs in reproductive development was established. Subsequent studies indicated that members of the CYC clade of TCP TFs were important for the evolutionary diversification of flower form in a multitude of species. In addition, more detailed studies of the function of TCPs from other clades revealed roles in different processes related to plant reproductive development, such as the regulation of flowering time, the growth of the inflorescence stem, and the correct growth and development of flower organs. In this review, we summarize the different roles of members of the TCP family during plant reproductive development as well as the molecular networks involved in their action.

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.

Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms

As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.

The N-terminal region located upstream of the TCP domain is responsible for the antagonistic action of the Arabidopsis thaliana TCP8 and TCP23 transcription factors on flowering time

TCP proteins (TCPs) are plant-exclusive transcription factors that exert effects on multiple aspects of plant development, from germination to flower and fruit formation. TCPs are divided into two main classes, I and II. In this study, we found that the Arabidopsis thaliana class I TCP transcription factor TCP8 is a positive regulator of flowering time. TCP8 mutation and constitutive expression delayed and accelerated flowering, respectively. Accordingly, TCP8 mutant plants showed a delay in the maximum expression of FT and reduced SOC1 transcript levels, while plants overexpressing TCP8 presented increased transcript levels of both genes. Notably, the related class I protein TCP23 showed the opposite behavior, since TCP23 mutation and overexpression accelerated and retarded flowering, respectively. To elucidate the molecular basis of these differences, we analyzed TCP8 and TCP23 comparatively. We found that both proteins are able to physically interact and bind class I TCP motifs, but only TCP8 shows transcriptional activation activity when expressed in plants, which is negatively affected by TCP23. From the analysis of plants expressing different chimeras between the TCPs, we found that the N-terminal region located upstream of the TCP domain is responsible for the opposite effect that TCP8 and TCP23 exert over flowering time and regulation of FT and SOC1 expression. These results suggest that structural features outside the TCP domain modulate the specificity of action of class I TCPs.

BREVIPEDICELLUS/KNAT1 targets TCP15 to modulate filament elongation during Arabidopsis late stamen development

The Arabidopsis homeodomain protein BREVIPEDICELLUS/KNAT1 represses the expression of the gene encoding the transcription factor TCP15 to limit filament growth at late stages of stamen development.

The Arabidopsis transcription factor TCP9 modulates root architectural plasticity, reactive oxygen species-mediated processes, and tolerance to cyst nematode infections

Infections by root-feeding nematodes have profound effects on root system architecture and consequently shoot growth of host plants. Plants harbor intraspecific variation in their growth responses to belowground biotic stresses by nematodes, but the underlying mechanisms are not well understood. Here, we show that the transcription factor TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR-9 (TCP9) modulates root system architectural plasticity in Arabidopsis thaliana in response to infections by the endoparasitic cyst nematode Heterodera schachtii. Young seedlings of tcp9 knock-out mutants display a significantly weaker primary root growth inhibition response to cyst nematodes than wild-type Arabidopsis. In older plants, tcp9 reduces the impact of nematode infections on the emergence and growth of secondary roots. Importantly, the altered growth responses by tcp9 are most likely not caused by less biotic stress on the root system, because TCP9 does not affect the number of infections, nematode development, and size of the nematode-induced feeding structures. RNA-sequencing of nematode-infected roots of the tcp9 mutants revealed differential regulation of enzymes involved in reactive oxygen species (ROS) homeostasis and responses to oxidative stress. We also found that root and shoot growth of tcp9 mutants is less sensitive to exogenous hydrogen peroxide and that ROS accumulation in nematode infection sites in these mutants is reduced. Altogether, these observations demonstrate that TCP9 modulates the root system architectural plasticity to nematode infections via ROS-mediated processes. Our study further points at a novel regulatory mechanism contributing to the tolerance of plants to root-feeding nematodes by mitigating the impact of belowground biotic stresses.

AtHB40 modulates primary root length and gravitropism involving CYCLINB and auxin transporters

Gravitropism is a finely regulated tropistic response based on the plant perception of directional cues. Such perception allows them to direct shoot growth upwards, above ground, and root growth downwards, into the soil, anchoring the plant to acquire water and nutrients. Gravity sensing occurs in specialized cells and depends on auxin distribution, regulated by influx/efflux carriers. Here we report that AtHB40, encoding a transcription factor of the homeodomain-leucine zipper I family, was expressed in the columella and the root tip. Athb40 mutants exhibited longer primary roots. Enhanced primary root elongation was in agreement with a higher number of cells in the transition zone and the induction of CYCLINB transcript levels. Moreover, athb40 mutants and AtHB40 overexpressors displayed enhanced and delayed gravitropistic responses, respectively. These phenotypes were associated with altered auxin distribution and deregulated expression of the auxin transporters LAX2, LAX3, and PIN2. Accordingly, lax2 and lax3 mutants also showed an altered gravitropistic response, and LAX3 was identified as a direct target of AtHB40. Furthermore, AtHB40 is induced by AtHB53 when the latter is upregulated by auxin. Altogether, these results indicate that AtHB40 modulates cell division and auxin distribution in the root tip thus altering primary root length and gravitropism.

The novel ZmTCP7 transcription factor targets AGPase-encoding gene ZmBt2 to regulate storage starch accumulation in maize

The process of starch biosynthesis is a major developmental event that affects the final grain yield and quality in maize (Zea mays L.), and transcriptional regulation plays a key role in modulating the expression of the main players in the pathway. ZmBt2, which encodes the small subunits of AGPase, is a rate-controlling gene of the pathway; however, much remains unknown about its transcriptional regulation. Our earlier study identifies a short functional fragment of ZmBt2 promoter (394-bp), and further shows it contains multiple putative cis-acting regulatory elements, demonstrating that several transcription factors may govern ZmBt2 expression. Here, we identified a novel TCP transcription factor (TF), ZmTCP7, that interacted with the functional fragment of the ZmBt2 promoter in a yeast one hybrid screening system. We further showed that ZmTCP7 is a non-autonomous TF targeted to the nucleus and predominantly expressed in maize endosperm. Using promoter deletion analyzes by transient expression in maize endosperm protoplasts combined with electrophoretic mobility shift assays, we found that ZmTCP7 bound to GAACCCCAC elements on the ZmBt2 promoter to suppress its expression. Transgenic overexpression of ZmTCP7 in maize caused a significant repression of ZmBt2 transcription by ~77.58%, resulting in a 21.51% decrease in AGPase activity and a 9.58% reduction in the endosperm starch content of transgenic maize. Moreover, the expressions of ZmBt1, ZmSSI, ZmSSIIa, and ZmSSIIIa were increased, while those of ZmSh2 and ZmSSIV reduced significantly in the endosperm of the transgenic maize. Overall, this study shows that ZmTCP7 functions as a transcriptional repressor of ZmBt2 and a negative regulator of endosperm starch accumulation, providing new insights into the regulatory networks that govern ZmBt2 expression and starch biosynthesis pathway in maize.

Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense

Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.

TCP15 interacts with GOLDEN2-LIKE 1 to control cotyledon opening in Arabidopsis

After germination, exposure to light promotes the opening and expansion of the cotyledons and the development of the photosynthetic apparatus in a process called de-etiolation. This process is crucial for seedling establishment and photoautotrophic growth. TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are important developmental regulators of plant responses to internal and external signals that are grouped into two main classes. In this study, we identified GOLDEN2-LIKE 1 (GLK1), a key transcriptional regulator of photomorphogenesis, as a protein partner of class I TCPs during light-induced cotyledon opening and expansion in Arabidopsis. The class I TCP TCP15 and GLK1 are mutually required for cotyledon opening and the induction of SAUR and EXPANSIN genes, involved in cell expansion. TCP15 also participates in the expression of photosynthesis-associated genes regulated by GLK1, like LHCB1.4 and LHCB2.2. Furthermore, GLK1 and TCP15 bind to the same promoter regions of different target genes containing either GLK or TCP binding motifs and binding of TCP15 is affected in a GLK1-deficient background, suggesting that a complex between TCP15 and GLK1 participates in the induction of these genes. We postulate that GLK1 helps to recruit TCP15 for the modulation of cell expansion genes in cotyledons and that the functional interaction between these transcription factors may serve to coordinate the expression of cell expansion genes with that of genes involved in the development of the photosynthetic apparatus.

Characterization of the TCP Gene Family in Chrysanthemum nankingense and the Role of CnTCP4 in Cold Tolerance

Plant-specific TCP transcription factors play a key role in plant development and stress responses. Chrysanthemum nankingense shows higher cold tolerance than its ornamental polyploid counterpart. However, whether the TCP gene family plays a role in conferring cold tolerance upon C. nankingense remains unknown. Here, we identified 23 CnTCP genes in C. nankingense, systematically analyzed their phylogenetic relationships and synteny with TCPs from other species, and evaluated their expression profiles at low temperature. Phylogenetic analysis of the protein sequences suggested that CnTCP proteins fall into two classes and three clades, with a typical bHLH domain. However, differences between C. nankingense and Arabidopsis in predicted protein structure and binding sites suggested a unique function of CnTCPs in C. nankingense. Furthermore, expression profiles showed that expression of most CnTCPs were downregulated under cold conditions, suggesting their importance in plant responses to cold stress. Notably, expression of miR319 and of its predicted target genes, CnTCP2/4/14, led to fast responses to cold. Overexpression of Arabidopsis CnTCP4 led to hypersensitivity to cold, suggesting that CnTCP4 might play a negative role in C. nankingense responses to cold stress. Our results provide a foundation for future functional genomic studies on this gene family in chrysanthemum.

Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum

Erythronium japonicum Decne (Liliaceae) flowers in early spring after overwintering. Its sexual reproduction process includes an underground development process of floral organs, but the underlying molecular mechanisms are obscure. The present study is aimed at exploring the transcriptional changes and key genes involved at underground floral developmental stages, including flower primordium differentiation, perianth differentiation, stamen differentiation, and pistil differentiation in E. japonicum. Multistage high-quality transcriptomic data resulted in identifying putative candidate genes for underground floral differentiation in E. japonicum. A total of 174,408 unigenes were identified, 28,508 of which were differentially expressed genes (DEGs) at different floral developmental stages, while only 44 genes were identified with conserved regulation between different stages. Further annotation of DEGs resulted in the identification of 270 DEGs specific to floral differentiation. In addition, ELF3, PHD, cullin 1, SE14, ZSWIM3, GIGNATEA, and SERPIN B were identified as potential candidate genes involved in the regulation of floral differentiation. Besides, we explored transcription factors with differential regulation at different developmental stages and identified bHLH, FAR1, mTERF, MYB-related, NAC, Tify, and WRKY TFs for their potential involvement in the underground floral differentiation process. Together, these results laid the foundation for future molecular works to improve our understanding of the underground floral differentiation process and its genetic regulation in E. japonicum.

Comprehensive evolutionary analysis of the TCP gene family: Further insights for its origin, expansion, and diversification

TCP proteins are plant-specific transcription factors, which are involved in a broad range of physiological processes of plant growth and development. However, the origin and evolutionary history of this gene family is not fully resolved. Here, we present a genome-wide survey of TCP genes in 59 species (including 42 genomes and 17 transcriptomes) covering all main lineages of green plants, and reconstruct the evolutionary history of this gene family. Our results suggested that the origin of TCP genes predated the emergence of land plants, possibly in the common ancestor of Phragmoplastophyta. The TCP gene family gradually experienced a continuous expansion and grew from a few members in algae, moss and lycophytes to dozens, and sometimes over 50 members in angiosperms. Phylogenetic analysis indicated that at least four subclades (Class I and three subclades of Class II) have been occurred in the ancestor of spermatophyte (seed plant). Both dispersed duplication and segmental duplication or whole-genome duplication (WGD) contributed significantly to the expansion of the TCP gene family over the course of evolution. Our findings provide a comprehensive evolutionary analysis of the TCP gene family and highlight the importance of gene duplications in the evolution of this plant-specific transcription factors.

TCP7 interacts with Nuclear Factor-Ys to promote flowering by directly regulating SOC1 in Arabidopsis

The success of plant reproduction depends on the timely transition from the vegetative phase to reproductive growth, a process often referred to as flowering. Although several plant-specific transcription factors belonging to the Teosinte Branched 1/Cycloidea/Proliferating Cell Factor (TCP) family are reportedly involved in the regulation of flowering in Arabidopsis, the molecular mechanisms, especially for Class I TCP members, are poorly understood. Here, we genetically identified Class I TCP7 as a positive regulator of flowering time. Protein interaction analysis indicated that TCP7 interacted with several Nuclear Factor-Ys (NF-Ys), known as the 'pioneer' transcription factors; CONSTANS (CO), a main photoperiod regulator of flowering. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was differentially expressed in the dominant-negative mutant of TCP7 (lcu) and the loss-of-function mutant of Class I TCP members (septuple). Additionally, we obtained genetic and molecular evidence showing that TCP7 directly activates the flowering integrator gene, SOC1. Moreover, TCP7 synergistically activated SOC1 expression upon interacting with CO and NF-Ys in vivo. Collectively, our results provide compelling evidence that TCP7 synergistically interacts with NF-Ys to activate the transcriptional expression of the flowering integrator gene SOC1.

Identification of apple TFL1-interacting proteins uncovers an expanded flowering network

MdTFL1, a floral repressor, forms protein complexes with several proteins and could compete with MdFT1 to regulate reproductive development in apple. Floral transition is a key developmental stage in the annual growth cycle of perennial fruit trees that directly determines the fruit development in the subsequent stage. FLOWERING LOCUS T (FT)/TERMINAL FLOWER1 (TFL1) family is known to play a vital regulatory role in plant growth and flowering. In apple, the two TFL1-like genes (MdTFL1-1 and MdTFL1-2) function as floral inhibitors; however, their mechanism of action is still largely unclear. This study aimed to functionally validate MdTFL1 and probe into its mechanism of action in apple. MdTFL1-1 and MdTFL1-2 were expressed mainly in stem and apical buds of vegetative shoots, with little expression in flower buds and young fruit. Expression of MdTFL1-1 and MdTFL1-2 rapidly decreased during floral induction. On the other hand, transgenic Arabidopsis, which ectopically expressed MdTFL1-1 or MdTFL1-2, flowered later than wild-type plants; demonstrating their in planta capability to function redundantly as flower repressors. Furthermore, we identified hundreds of novel interaction proteins of the two apple MdTFL1 proteins using yeast two-hybrid screens. Independent experiments for several proteins confirmed the yeast two-hybrid interactions. Among them, the transcription factor Nuclear Factor-Y subunit C (MdNF-YC2) functions as a promoter of flowering in Arabidopsis by activating LEAFY (LFY) and APETALA1 (AP1) expression. MdFT1 showed a similar interaction pattern as MdTFL1, implying a possible antagonistic action in the regulation of flowering. These newly identified TFL1-interacting proteins (TIPs) not only expand the floral regulatory network, but may also introduce new roles for TFL1 in plant development.

Arabidopsis thaliana TCP15 interacts with the MIXTA-like transcription factor MYB106/NOECK

MYB106 and MYB16 are MIXTA-like transcription factors that control trichome maturation and cuticle formation in Arabidopsis. In a recent study, we found that the TEOSINTE BRANCHED 1, CYCLOIDEA and PROLIFERATING CELL FACTORS (TCP) transcription factor TCP15 also acts as an important regulator of aerial epidermis specialization in Arabidopsis through the control of trichome development and cuticle formation. TCP15 and MYB106 regulate the expression of common groups of genes, including genes coding for transcription factors and enzymes of the cuticle biosynthesis pathway. In this study, we report that TCP15 physically interacts with MYB106 when both proteins are expressed in yeast cells or Nicotiana bentamiana leaves. Furthermore, we also observed interaction in leaves of Arabidopsis thaliana. Altogether, our findings raise the possibility that TCP15 and MYB106 bind together to the promoters of target genes to exert their action. Our data provide a base to investigate the role of TCP-MIXTA complexes in the context of cuticle development in Arabidopsis thaliana.

Pathogen Effectors: Exploiting the Promiscuity of Plant Signaling Hubs

Pathogens produce effectors to overcome plant immunity, thereby threatening crop yields and global food security. Large-scale interactomic studies have revealed that pathogens from different kingdoms of life target common plant proteins during infection, the so-called effector hubs. These hubs often play central roles in numerous plant processes through their ability to interact with multiple plant proteins. This ability arises partly from the presence of intrinsically disordered domains (IDDs) in their structure. Here, we highlight the role of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) and JASMONATE-ZIM DOMAIN (JAZ) transcription regulator families as plant signaling and effector hubs. We consider different evolutionary hypotheses to rationalize the existence of diverse effectors sharing common targets and the possible role of IDDs in this interaction.

Comparative Genomic Analysis of TCP Genes in Six Rosaceae Species and Expression Pattern Analysis in Pyrus bretschneideri

TCP is a plant-specific transcription factor that plays an important role in flowering, leaf development and other physiological processes. In this study, we identified a total of 155 TCP genes: 34 in Pyrus bretschneideri, 19 in Fragaria vesca, 52 in Malus domestica, 19 in Prunus mume, 17 in Rubus occidentalis and 14 in Prunus avium. The evolutionary relationship of the TCP gene family was examined by constructing a phylogenetic tree, tracking gene duplication events, performing a sliding window analysis. The expression profile analysis and qRT-PCR results of different tissues showed that PbTCP10 were highly expressed in the flowers. These results indicated that PbTCP10 might participated in flowering induction in pear. Expression pattern analysis of different developmental stages showed that PbTCP14 and PbTCP15 were similar to the accumulation pattern of fruit lignin and the stone cell content. These two genes might participate in the thickening of the secondary wall during the formation of stone cells in pear. Subcellular localization showed that PbTCPs worked in the nucleus. This study explored the evolution of TCP genes in six Rosaceae species, and the expression pattern of TCP genes in different tissues of “Dangshan Su” pear. Candidate genes related to flower induction and stone cell formation were identified. In summary, our research provided an important theoretical basis for improving pear fruit quality and increasing fruit yield by molecular breeding.

Identification of a consensus DNA-binding site for the TCP domain transcription factor TCP2 and its important roles in the growth and development of Arabidopsis

TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1 (TCP) transcription factors control multiple aspects of growth and development in various plant species. However, few genes were reported to be directly targeted and regulated by them through their specific binding sites, and then uncover their functions in plants. A consensus DNA-binding site motif of TCP2 was identified by random binding site selection (RBSS). DNA recognized by TCP2 contained the motif G(G/T)GGNCC(A/C), which showed high consistency with motifs bound by other TCP domain proteins. Consequently, this motif was regarded as the specific DNA-binding sites of TCP2. Circadian clock associated 1 (CCA1) and EARLY FLOWERING 3 (ELF3) were subsequently considered as potential target genes owing to the containing of the similar TCP2 binding sites or core binding sites GGNCC and found to be positively regulated by TCP2 via DNA binding. Phenotype analysis results showed that mutation and over-expression of TCP2 resulted in variations in leaf morphogenesis, especially the double or triple mutations of TCP2, 4 and 10. Mutations in TCPs caused late flowering. Finally, TCP2 was shown to influence hypocotyl elongation by mediating the jasmonate signaling pathway. Overall, these results provide a basis for future studies aimed at distinguishing the target genes of TCP2 and elucidating the important roles of TCP2 in plant growth and development.

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.

Beyond flowering time: diverse roles of an APETALA2-like transcription factor in shoot architecture and perennial traits

Polycarpic perennials maintain vegetative growth after flowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) in Arabis alpina regulates flowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to flower and have reduced return to vegetative growth as all of their axillary branches become reproductive. To identify additional genes that regulate flowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele. eop055 flowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a floral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to flower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing flowering of axillary buds before and during cold exposure. We conclude that AaTOE2 is instrumental in fine tuning different developmental traits in the perennial life cycle of A. alpina.

EjRAV1/2 Delay Flowering Through Transcriptional Repression of EjFTs and EjSOC1s in Loquat

Most species in Rosaceae usually need to undergo several years of juvenile phase before the initiation of flowering. After 4-6 years' juvenile phase, cultivated loquat (Eriobotrya japonica), a species in Rosaceae, enters the reproductive phase, blooms in the autumn and sets fruits during the winter. However, the mechanisms of the transition from a seedling to an adult tree remain obscure in loquat. The regulation networks controlling seasonal flowering are also largely unknown. Here, we report two RELATED TO ABI3 AND VP1 (RAV) homologs controlling juvenility and seasonal flowering in loquat. The expressions of EjRAV1/2 were relatively high during the juvenile or vegetative phase and low at the adult or reproductive phase. Overexpression of the two EjRAVs in Arabidopsis prolonged (about threefold) the juvenile period by repressing the expressions of flowering activator genes. Additionally, the transformed plants produced more lateral branches than the wild type plants. Molecular assays revealed that the nucleus localized EjRAVs could bind to the CAACA motif of the promoters of flower signal integrators, EjFT1/2, to repress their expression levels. These findings suggest that EjRAVs play critical roles in maintaining juvenility and repressing flower initiation in the early life cycle of loquat as well as in regulating seasonal flowering. Results from this study not only shed light on the control and maintenance of the juvenile phase, but also provided potential targets for manipulation of flowering time and accelerated breeding in loquat.

Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition

Water ferns of the genus Azolla and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled the colonization of the water surface with traits highly desirable for the development of more sustainable crops: their floating mats capture CO₂ and fix N₂ at high rates using light energy. Their mode of sexual reproduction is heterosporous. The regulation of the transition from the vegetative phase to the spore forming phase in ferns is largely unknown, yet a prerequisite for Azolla domestication, and of particular interest as ferns represent the sister lineage of seed plants. Sporocarps induced with far red light could be crossed so as to verify species attribution of strains from the Netherlands but not of the strain from the Anzali lagoon in Iran; the latter strain was assigned to a novel species cluster from South America. Red-dominated light suppresses the formation of dissemination stages in both gametophyte- and sporophyte-dominated lineages of plants, the response likely is a convergent ecological strategy to open fields. FR-responsive transcripts included those from MIKC^C homologues of CMADS1 and miR319-controlled GAMYB transcription factors in the fern, transporters in N. azollae, and ycf2 in chloroplasts. Loci of conserved microRNA (miRNA) in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Phylogenomic analyses of MIKC^C TFs suggested that the control of flowering and flower organ specification may have originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.

Class I TCP transcription factors regulate trichome branching and cuticle development in Arabidopsis

Trichomes and the cuticle are two specialized structures of the aerial epidermis that are important for plant organ development and interaction with the environment. In this study, we report that Arabidopsis thaliana plants affected in the function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 show overbranched trichomes in leaves and stems and increased cuticle permeability. We found that TCP15 regulates the expression of MYB106, a MIXTA-like transcription factor involved in epidermal cell and cuticle development, and overexpression of MYB106 in a tcp14 tcp15 mutant reduces trichome branch number. TCP14 and TCP15 are also required for the expression of the cuticle biosynthesis genes CYP86A4, GPAT6, and CUS2, and of SHN1 and SHN2, two AP2/EREBP transcription factors required for cutin and wax biosynthesis. SHN1 and CUS2 are also targets of TCP15, indicating that class I TCPs influence cuticle formation acting at different levels, through the regulation of MIXTA-like and SHN transcription factors and of cuticle biosynthesis genes. Our study indicates that class I TCPs are coordinators of the regulatory network involved in trichome and cuticle development.

Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R² between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

Genetic and molecular basis of floral induction in Arabidopsis thaliana

Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.

Transcriptomic analysis of flower induction for long-day pitaya by supplementary lighting in short-day winter season

BACKGROUND

Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary to provide supplementary lighting at night to induce flowering. To further explore the molecular regulating mechanisms of flower induction in pitaya plants exposed to supplementary lighting, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya plants subjected to light induction.

RESULTS

We assembled 68,113 unigenes in total, comprising 29,782 unigenes with functional annotations in the NR database, 20,716 annotations in SwissProt, 18,088 annotations in KOG, and 11,059 annotations in KEGG. Comparisons between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormone signaling were detected. Moreover, we identified many CONSTANS-LIKE, FLOWERING LOCUS T, and other DEGs involved in the direct regulation of flowering including CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we verified 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis.

CONCLUSIONS

The identified DEGs may include some key genes controlling the pitaya floral-induction network, the flower induction and development is very complicated, and it involves photoperiod perception and different phytohormone signaling. These findings will increase our understanding to the molecular mechanism of floral regulation of long-day pitaya plants in short-day winter season induced by supplementary lighting.

CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants

CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.

Overexpression of TCP8 delays Arabidopsis flowering through a FLOWERING LOCUS C-dependent pathway

BACKGROUND

Flowering is a key process in the life cycle of plants. The transition from vegetative to reproductive growth is thus under sophisticated regulation by endogenous and environmental signals. The plant-specific Teosinte Branched 1/Cycloidea/Proliferating Cell Factors (TCP) family transcription factors are involved in many biological processes, but their roles in regulating flowering have not been totally elucidated.

RESULTS

We explored the role of Arabidopsis TCP8 in plant development and, especially, in flowering control. Overexpression of TCP8 significantly delayed flowering under both long-day and short-day conditions and dominant repression by TCP8 led to various growth defects. The upregulation of TCP8 led to more accumulated mRNA level of FLOWERING LOCUS C (FLC), a central floral repressor of Arabidopsis. TCP8 functions in an FLC-dependent manner, as TCP8 overexpression in the flc-6 loss-of-function mutant failed to delay flowering. The vernalization treatment could reverse the late flowering phenotype caused by TCP8 overexpression.

CONCLUSIONS

Our results provide evidence for a role of TCP8 in flowering control and add to our knowledge of the molecular basis of TCP8 function.

AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots

In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.

TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis

TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR) proteins, a family of plant-specific transcription factors, play important roles in many developmental processes. However, genetic and functional redundancy among class I TCP limits the analysis of their biological roles. Here, we identified a dominant-negative mutant of Arabidopsis thaliana TCP7 named leaf curling-upward (lcu), which exhibits smaller leaf cells and shorter hypocotyls than the wild type, due to defective endoreplication. A septuple loss-of-function mutant of TCP7, TCP8, TCP14, TCP15, TCP21, TCP22, and TCP23 displayed similar developmental defects to those of lcu. Genome-wide RNA-sequencing showed that lcu and the septuple mutant share many misexpressed genes. Intriguingly, TCP7 directly targets the CYCLIN D1;1 (CYCD1;1) locus and activates its transcription. We determined that the C-terminus of TCP7 accounts for its transcriptional activation activity. Furthermore, the mutant protein LCU exhibited reduced transcriptional activation activity due to the introduction of an EAR-like repressive domain at its C-terminus. Together, these observations indicate that TCP7 plays important roles during leaf and hypocotyl development, redundantly, with at least six class I TCPs, and regulates the expression of CYCD1;1 to affect endoreplication in Arabidopsis.

Class I TCP Transcription Factors Target the Gibberellin Biosynthesis Gene GA20ox1 and the Growth-Promoting Genes HBI1 and PRE6 during Thermomorphogenic Growth in Arabidopsis

Plants respond to a rise in ambient temperature by increasing the growth of petioles and hypocotyls. In this work, we show that Arabidopsis thaliana class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 are required for optimal petiole and hypocotyl elongation under high ambient temperature. These TCPs influence the levels of the DELLA protein RGA and the expression of growth-related genes, which are induced in response to an increase in temperature. However, the class I TCPs are not required for the induction of the auxin biosynthesis gene YUCCA8 or for auxin-dependent gene expression responses. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the growth regulatory genes HBI1 and PRE6. Several of the genes regulated by TCP15 are also targets of the growth regulator PIF4 and show an enrichment of PIF4- and TCP-binding motifs in their promoters. PIF4 binding to GA20ox1 and HBI1 is enhanced in the presence of the TCPs, indicating that TCP14 and TCP15 directly participate in the induction of genes involved in gibberellin biosynthesis and cell expansion by high temperature functionally interacting with PIF4. In addition, overexpression of HBI1 rescues the growth defects of tcp14 tcp15 double mutants, suggesting that this gene is a major outcome of regulation by both class I TCPs during thermomorphogenesis.

Direct Regulation of the EFR-Dependent Immune Response by Arabidopsis TCP Transcription Factors

One layer of the innate immune system allows plants to recognize pathogen-associated molecular patterns (PAMPS), activating a defense response known as PAMP-triggered immunity (PTI). Maintaining an active immune response, however, comes at the cost of plant growth and development; accordingly, optimization of the balance between defense and development is critical to plant fitness. The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor family consists of well-characterized transcriptional regulators of plant development and morphogenesis. The three closely related class I TCP transcription factors TCP8, TCP14, and TCP15 have also been implicated in the regulation of effector-triggered immunity, but there has been no previous characterization of PTI-related phenotypes. To identify TCP targets involved in PTI, we screened a PAMP-induced gene promoter library in a yeast one-hybrid assay and identified interactions of these three TCPs with the EF-Tu RECEPTOR (EFR) promoter. The direct interactions between TCP8 and EFR were confirmed to require an intact TCP binding site in planta. A tcp8 tcp14 tcp15 triple mutant was impaired in EFR-dependent PTI and exhibited reduced levels of PATHOGENESIS-RELATED PROTEIN 2 and induction of EFR expression after elicitation with elf18 but also increased production of reactive oxygen species relative to Col-0. Our data support an increasingly complex role for TCPs at the nexus of plant development and defense.

Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.

Alterations of plant architecture and phase transition by the phytoplasma virulence factor SAP11

As key mediators linking developmental processes with plant immunity, TCP (TEOSINTE-BRANCHED, CYCLOIDEA, PROLIFERATION FACTOR 1 and 2) transcription factors have been increasingly shown to be targets of pathogenic effectors. We report here that TB/CYC (TEOSINTE-BRANCHED/CYCLOIDEA)-TCPs are destabilized by phytoplasma SAP11 effectors, leading to the proliferation of axillary meristems. Although a high degree of sequence diversity was observed among putative SAP11 effectors identified from evolutionarily distinct clusters of phytoplasmas, these effectors acquired fundamental activity in destabilizing TB/CYC-TCPs. In addition, we demonstrate that miR156/SPLs and miR172/AP2 modules, which represent key regulatory hubs involved in plant phase transition, were modulated by Aster Yellows phytoplasma strain Witches' Broom (AY-WB) protein SAP11. A late-flowering phenotype with significant changes in the expression of flowering-related genes was observed in transgenic Arabidopsis plants expressing SAP11AYWB. These morphological and molecular alterations were correlated with the ability of SAP11 effectors to destabilize CIN (CINCINNATA)-TCPs. Although not all putative SAP11 effectors display broad-spectrum activities in modulating morphological and physiological changes in host plants, they serve as core virulence factors responsible for the witches' broom symptom caused by phytoplasmas.

Jasmonate promotes artemisinin biosynthesis by activating the TCP14-ORA complex in Artemisia annua

Artemisia annua produces the valuable medicinal component, artemisinin, which is a sesquiterpene lactone widely used in malaria treatment. AaORA, a homolog of CrORCA3, which is involved in activating terpenoid indole alkaloid biosynthesis in Catharanthus roseus, is a jasmonate (JA)-responsive and trichome-specific APETALA2/ETHYLENE-RESPONSE FACTOR that plays a pivotal role in artemisinin biosynthesis. However, the JA signaling mechanism underlying AaORA-mediated artemisinin biosynthesis remains enigmatic. Here, we report that AaORA forms a transcriptional activator complex with AaTCP14 (TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 14), which is also predominantly expressed in trichomes. AaORA and AaTCP14 synergistically bind to and activate the promoters of two genes, double bond reductase 2 (DBR2) and aldehyde dehydrogenase 1 (ALDH1), both of which encode enzymes vital for artemisinin biosynthesis. AaJAZ8, a repressor of the JA signaling pathway, interacts with both AaTCP14 and AaORA and represses the ability of the AaTCP14-AaORA complex to activate the DBR2 promoter. JA treatment induces AaJAZ8 degradation, allowing the AaTCP14-AaORA complex to subsequently activate the expression of DBR2, which is essential for artemisinin biosynthesis. These data suggest that JA activation of the AaTCP14-AaORA complex regulates artemisinin biosynthesis. Together, our findings reveal a novel artemisinin biosynthetic pathway regulatory network and provide new insight into how specialized metabolism is modulated by the JA signaling pathway in plants.

TCP Transcription Factors Interact With NPR1 and Contribute Redundantly to Systemic Acquired Resistance

In Arabidopsis, TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factors (TF) play critical functions in developmental processes. Recent studies suggest they also function in plant immunity, but whether they play an important role in systemic acquired resistance (SAR) is still unknown. NON-EXPRESSER OF PR GENES 1 (NPR1), as an essential transcriptional regulatory node in SAR, exerts its regulatory role in downstream genes expression through interaction with TFs. In this work, we provide biochemical and genetic evidence that TCP8, TCP14, and TCP15 are involved in the SAR signaling pathway. TCP8, TCP14, and TCP15 physically interacted with NPR1 in yeast two-hybrid assays, and these interactions were further confirmed in vivo. SAR against the infection of virulent strain Pseudomonas syringae pv. maculicola (Psm) ES4326 in the triple T-DNA insertion mutant tcp8-1 tcp14-5 tcp15-3 was partially compromised compared with Columbia 0 (Col-0) wild type plants. The induction of SAR marker genes PR1, PR2, and PR5 in local and systemic leaves was dramatically decreased in the tcp8-1 tcp14-5 tcp15-3 mutant compared with that in Col-0 after local treatment with Psm ES4326 carrying avrRpt2. Results from yeast one-hybrid and chromatin immunoprecipitation (ChIP) assays demonstrated that TCP15 can bind to a conserved TCP binding motif, GCGGGAC, within the promoter of PR5, and this binding was enhanced by NPR1. Results from RT-qPCR assays showed that TCP15 promotes the expression of PR5 in response to salicylic acid induction. Taken together, these data reveal that TCP8, TCP14, and TCP15 physically interact with NPR1 and function redundantly to establish SAR, that TCP15 promotes the expression of PR5 through directly binding a TCP binding site within the promoter of PR5, and that this binding is enhanced by NPR1.