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

Genome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo)

BACKGROUND

TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done.

OBJECTIVE

The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions.

METHODS

The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein-protein interactions were analyzed using various databases and webtools.

RESULTS

A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification.

CONCLUSION

This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.

TCP23-WRKY15 module negatively regulates lignin deposition and xylem development of wood formation in Populus

Secondary wall, a critical component of wood, is influenced by multiple factors during its formation. The TCP family encodes plant-specific transcription factors (TFs) that play key roles in multiple aspects of plant development. In this study, we identified all TCP TFs in five poplar species and analyzed their evolutionary relationships, gene structures, tissue-specific expression patterns, and potential interactions with microRNAs. Additionally, we screened for TCP proteins associated with secondary wall development that are independent of miRNA regulation. Three candidate TFs were identified, with TCP23 showing high conservation across poplar species and the highest expression levels in the xylem of Populus trichocarpa and Populus wilsonii. The overexpression of TCP23 in poplar inhibited the expression of MYB TFs and structural genes involved in xylem biosynthesis, thereby reducing the lignin content within the stems. By contrast, CRISPR/Cas9-mediated knockout of TCP23 resulted in the opposite effect. Furthermore, we successfully identified WRKY15 as an interaction partner of TCP23 via a yeast two-hybrid library and demonstrated that TCP23 negatively regulates lignin synthesis and xylem development by enhancing the inhibitory function of WRKY15. Our study provides new insights into the transcriptional regulatory mechanisms underlying secondary wall formation.

Genome-Wide Exploration and Characterization of the TCP Gene Family's Expression Patterns in Response to Abiotic Stresses in Siberian Wildrye (Elymus sibiricus L.)

Siberian wildrye (Elymus sibiricus L.), a model Elymus Gramineae plant, has high eco-economic value but limited seed and forage yield. TCP transcription factors are widely regarded as influencing yield and quality and being crucial for growth and development; still, this gene family in Siberian wildrye remains unexplored. Therefore, this study looked at the Siberian wildrye TCP gene family's reaction to several abiotic stresses, its expression pattern, and its potential evolutionary path. Fifty-four members of the EsTCP gene family were discovered. There are two major subfamilies based on the phylogenetic tree: 27 of Class I (PCF) and 27 of Class II (12 CIN-type and 15 TB1/CYC-type). Gene structure, conserved motif, and sequence alignment analyses further validated this classification. Cis-elements found in the promoter region of EsTCPs are associated with lots of plant hormones and stress-related reactions, covering drought induction and cold tolerance. EsCYC5, EsCYC6, and EsCYC7 may regulate tillering and lateral branch development. EsPCF10's relative expression was significant under five stresses. Additionally, eight EsTCP genes are potential miR319 targets. These findings highlight the critical significance of the TCP gene family in Siberian wildrye, laying the groundwork for understanding the function of the EsTCP protein in abiotic stress studies and high-yield breeding.

Genome-Wide Identification and Expression Analysis of TCP Transcription Factors Responding to Multiple Stresses in Arachis hypogaea L

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses.

Unraveling TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Safflower: A Blueprint for Stress Resilience and Metabolic Regulation

Safflower (Carthamus tinctorius L.), a versatile medicinal and economic crop, harbors untapped genetic resources essential for stress resilience and metabolic regulation. The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors, exclusive to plants, are pivotal in orchestrating growth, development, and stress responses, yet their roles in safflower remain unexplored. Here, we report the comprehensive identification and characterization of 26 safflower TCP genes (CtTCPs), categorized into Class I (PROLIFERATING CELL FACTOR, PCF) and Class II (CINCINNATA and TEOSINTE BRANCHED1/CYCLOIDEA, CIN and CYC/TB1) subfamilies. Comparative phylogenetics, conserved motif, and gene structure analyses revealed a high degree of evolutionary conservation and functional divergence within the gene family. Promoter analyses uncovered light-, hormone-, and stress-responsive cis-elements, underscoring their regulatory potential. Functional insights from qRT-PCR analyses demonstrated dynamic CtTCP expression under abiotic stresses, including abscisic acid (ABA), Methyl Jasmonate (MeJA), Cold, and ultraviolet radiation b (UV-B) treatments. Notably, ABA stress triggered a significant increase in flavonoid accumulation, correlated with the upregulation of key flavonoid biosynthesis genes and select CtTCPs. These findings illuminate the complex regulatory networks underlying safflower's abiotic stress responses and secondary metabolism, offering a molecular framework to enhance crop resilience and metabolic engineering for sustainable agriculture.

Antioxidant activity and comparative RNA-seq analysis support mitigating effects of an algae-based biostimulant on drought stress in tomato plants

Drought is a significant global environmental stress. Biostimulants offer a sustainable solution to enhance crop tolerance and mitigate productivity losses. This study assessed the impact of foliar application of ERANTHIS®, a biostimulant derived from the algae Ascophyllum nodosum and Laminaria digitata and yeast extracts, on tomato plants under mild water stress. Evaluations were conducted at 5 and 24 hours after the third treatment. Under optimal water conditions, the biostimulant showed a priming effect, with an early increase of stress markers and a timing-specific modulation of ROS non enzymatic and enzymatic ROS scavenging activities. Under drought stress, the biostimulant later decreased stress markers, by aligning the majority of analyzed ROS scavengers closer to levels in well-irrigated plants. Transcriptome analysis using RNA-seq data revealed differentially expressed genes (DEGs) and multivariate data highlighted groups of co-regulated genes (k-means clustering). Genes involved in water channel activity, transcription regulator activity, and oxidoreductase activity were significantly modulated. Cluster analysis identified distinct gene clusters influenced by the biostimulant under optimal conditions, including early responses (cell wall modification, hormone signaling) and late responses (RNA modification, nutrient uptake process). Under water stress, early responses involved actin filament organization and MAPK signaling, while late responses were related to plasma membrane components and cell wall organization. This study, integrating biochemical and transcriptomic data, provides a comprehensive understanding of how a biostimulant primes plants under optimal conditions and mitigates water stress effects, offering valuable insights for sustainable agriculture.

Flowering time genes branching out

Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.

Exogenous Sodium Nitroprusside Affects the Redox System of Wheat Roots Differentially Regulating the Activity of Antioxidant Enzymes under Short-Time Osmotic Stress

Nitric oxide (NO) is a multifunctional signalling molecule involved in the regulation of plant ontogenesis and adaptation to different adverse environmental factors, in particular to osmotic stress. Understanding NO-induced plant protection is important for the improvement of plant stress tolerance and crop productivity under global climate changes. The root system is crucial for plant survival in a changeable environment. Damages that it experiences under water deficit conditions during the initial developmental periods seriously affect the viability of the plants. This work was devoted to the comparative analysis of the pretreatment of wheat seedlings through the root system with NO donor sodium nitroprusside (SNP) for 24 h on various parameters of redox homeostasis under exposure to osmotic stress (PEG 6000, 12%) over 0.5-24 h. The active and exhausted solutions of SNP, termed as (SNP/+NO) and (SNP/-NO), respectively, were used in this work at a concentration of 2 × 10-4 M. Using biochemistry and light microscopy methods, it has been revealed that osmotic stress caused oxidative damages and the disruption of membrane cell structures in wheat roots. PEG exposure increased the production of superoxide (O2•-), hydrogen peroxide (H2O2), malondialdehyde (MDA), and the levels of electrolyte leakage (EL) and lipid peroxidation (LPO). Stress treatment enhanced the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), the excretion of proline, and the rate of cell death and inhibited their division. Pretreatment with (SNP/+NO) decreased PEG-induced root damages by differently regulating the antioxidant enzymes under stress conditions. Thus, (SNP/+NO) pretreatment led to SOD, APX, and CAT inhibition during the first 4 h of stress and stimulated their activity after 24 h of PEG exposure when compared to SNP-untreated or (SNP/-NO)-pretreated and stress-subjected plants. Osmotic stress triggered the intense excretion of proline by roots into the external medium. Pretreatment with (SNP/+NO) in contrast with (SNP/-NO) additionally increased stress-induced proline excretion. Our results indicate that NO is able to mitigate the destructive effects of osmotic stress on the roots of wheat seedlings. However, the mechanisms of NO protective action may be different at certain periods of stress exposure.

Acetylation of transcription factor BpTCP20 by acetyltransferase BpPDCE23 modulates salt tolerance in birch

Teosinte branched 1/Cycloidea/Proliferating cell factor (TCP) transcription factors function in abiotic stress responses. However, how TCPs confer salt tolerance is unclear. Here, we characterized a TCP transcription factor, BpTCP20, that responds to salt stress in birch (Betula platyphylla Suk). Plants overexpressing BpTCP20 displayed increased salt tolerance, and Bptcp20 knockout mutants displayed reduced salt tolerance relative to the wild-type (WT) birch. BpTCP20 conferred salt tolerance by mediating stomatal closure and reducing reactive oxygen species (ROS) accumulation. Chromatin immunoprecipitation sequencing showed that BpTCP20 binds to NeuroD1, T-box, and two unknown elements (termed TBS1 and TBS2) to regulate target genes. In birch, salt stress led to acetylation of BpTCP20 acetylation at lysine 259. A mutated BpTCP20 variant (abolished for acetylation, termed BpTCP20259) was overexpressed in birch, which led to decreased salt tolerance compared with plants overexpressing BpTCP20. However, BpTCP20259-overexpressing plants still displayed increased salt tolerance relative to untransformed WT plants. BpTCP20259 showed reduced binding to the promoters of target genes and decreased target gene activation, leading to decreased salt tolerance. In addition, we identified dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (BpPDCE23), an acetyltransferase that interacts with and acetylates BpTCP20 to enhance its binding to DNA motifs. Together, these results suggest that BpTCP20 is a transcriptional regulator of salt tolerance, whose activity is modulated by BpPDCE23-mediated acetylation.

Class I TCP in fruit development: much more than growth

Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.

Genome-wide characterization of TCP family and their potential roles in abiotic stress resistance of oat (Avena sativa L.)

The TCP gene family members play multiple functions in plant growth and development and were named after the first three family members found in this family, TB1 (TEOSINTE BRANCHED 1), CYCLOIDEA (CYC), and Proliferating Cell Factor 1/2 (PCF1/2). Nitrogen (N) is a crucial element for forage yield; however, over-application of N fertilizer can increase agricultural production costs and environmental stress. Therefore, the discovery of low N tolerance genes is essential for the genetic improvement of superior oat germplasm and ecological protection. Oat (Avena sativa L.), is one of the world's staple grass forages, but no genome-wide analysis of TCP genes and their roles in low-nitrogen stress has been performed. This study identified the oat TCP gene family members using bioinformatics techniques. It analyzed their phylogeny, gene structure analysis, and expression patterns. The results showed that the AsTCP gene family includes 49 members, and most of the AsTCP-encoded proteins are neutral or acidic proteins; the phylogenetic tree classified the AsTCP gene family members into three subfamilies, and each subfamily has different conserved structural domains and functions. In addition, multiple cis-acting elements were detected in the promoter of the AsTCP genes, which were associated with abiotic stress, light response, and hormone response. The 49 AsTCP genes identified from oat were unevenly distributed on 18 oat chromosomes. The results of real-time quantitative polymerase chain reaction (qRT-PCR) showed that the AsTCP genes had different expression levels in various tissues under low nitrogen stress, which indicated that these genes (such as AsTCP01, AsTCP03, AsTCP22, and AsTCP38) played multiple roles in the growth and development of oat. In conclusion, this study analyzed the AsTCP gene family and their potential functions in low nitrogen stress at the genome-wide level, which lays a foundation for further analysis of the functions of AsTCP genes in oat and provides a theoretical basis for the exploration of excellent stress tolerance genes in oat. This study provides an essential basis for future in-depth studies of the TCP gene family in other oat genera and reveals new research ideas to improve gene utilization.

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.

Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants

Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.

DNA barcoding and comparative RNA-Seq analysis provide new insights into leaf formation using a novel resource of high-yielding Epimedium koreanum

Epimedium koreanum Nakai, a well-known traditional Chinese medicinal herb, has been widely used to treat osteoporosis and sexual dysfunction for thousands of years. However, due to the decreasing population of East Asian natural resources, yearly output of Epimedium crude herb has been in low supply year by year. In this study, an unusual variety of E. koreanum was discovered in Dunhua, Jilin Province, the northernmost area where this variety was found containing 6 individuals, with three branches that had 27 leaflets, which is much more than the typical leaflet number of 9. Firstly, the novel E. koreanum varety was identified using DNA barcodes. Then, 1171 differentially expressed genes (DEGs) were discovered through parallel RNA-seq analysis between the newly discovered variety and wild type (WT) E. koreanum plant. Furthermore, the results of bioinformatics investigation revealed that 914 positively and 619 negatively correlated genes associated with the number of leaflets. Additionally, based on RNA-Seq and qRT-PCR analysis, two homologous hub TCP genes, which were commonly implicated in plant leaf development, and shown to be up regulated and down regulated in the discovered newly variety, respectively. Thus, our study discovered a novel wild resource for leaf yield rewarding medicinal Epimedium plant breeding, provided insights into the relationship between plant compound leaf formation and gene expression of TCPs transcription factors and other gene candidates, providing bases for creating high yield cultivated Epimedium variety by using further molecular selection and breeding techniques in the future.

Antifungal Action of Arabidopsis thaliana TCP21 via Induction of Oxidative Stress and Apoptosis

The realm of antimicrobial proteins in plants is extensive but remains relatively uncharted. Understanding the mechanisms underlying the action of plant antifungal proteins (AFPs) holds promise for antifungal strategies. This study aimed to bridge this knowledge gap by comprehensively screening Arabidopsis thaliana species to identify novel AFPs. Using MALDI-TOF analysis, we identified a member of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) family of transcription factors as a novel AFP, A. thaliana TCP21 (AtTCP21; accession number NP_196450). Bacterially purified recombinant AtTCP21 inhibited the growth of various pathogenic fungal cells. AtTCP21 was more potent than melittin, a well-known AFP, in combating Colletotrichum gloeosporioides. Growth inhibition assays against various fungal pathogens and yeasts confirmed the pH-dependent antimicrobial activity of AtTCP21. Without inducing any membrane alterations, AtTCP21 penetrates the fungal cell wall and membrane, where it instigates a repressive milieu for fungal cell growth by generating intracellular reactive oxygen species and mitochondrial superoxides; resulting in morphological changes and apoptosis. Our findings demonstrate the redox-regulating effects of AtTCP21 and point to its potential as an antimicrobial agent.

scPlant: A versatile framework for single-cell transcriptomic data analysis in plants

Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth, development, and responses to external stimuli. However, single-cell transcriptomic data analysis in plants is not trivial, given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies. Here, we present scPlant, a versatile framework for exploring plant single-cell atlases with minimum input data provided by users. The scPlant pipeline is implemented with numerous functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution, trajectory inference, cross-species data integration, and cell-type-specific gene regulatory network construction. In addition, a variety of visualization tools are bundled in a built-in Shiny application, enabling exploration of single-cell transcriptomic data on the fly.

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.

Regulatory Mechanisms of Transcription Factors in Plant Morphology and Function

Plants develop organs such as flowers and leaves with different morphologies [...].