TCP Transcription Factors Involved in Shoot Development of Ma Bamboo (Dendrocalamus latiflorus Munro)

Continuous light induces adventitious root formation in Robinia pseudoacacia L. through the auxin response factor RpARF12 lacking the CTD domain

We report a novel mechanism in adventitious root formation, where a non-canonical auxin response factor, RpARF12, uniquely integrates continuous light (CL) signals with auxin pathways to regulate adventitious root formation in Robinia pseudoacacia L. (black locust). Unlike typical ARFs, the RpARF12 lacks the C-terminal dimerization (CTD) domain, suggesting its function through auxin-independent regulatory pathways. Our comprehensive analysis revealed that RpARF12 expression is significantly induced by CL and plays a crucial role in adventitious root formation under these conditions. Heterologous transformation of RpARF12 into model plants, including Arabidopsis thaliana, Nicotiana tabacum, and Populus alba × P. glandulosa (poplar 84K), significantly promoted adventitious root formation, particularly under CL. Additionally, the application of exogenous auxin further increased the number and length of roots in RpARF12-overexpressed A. thaliana plants under CL by 1.60 and 1.37 times, respectively, compared to wild-type plants. The auxin polar transport inhibitor NPA decreased root formation in the RpARF12-overexpressed A. thaliana plants under CL conditions. This study provides valuable insights into the regulatory role of photoperiod, specifically CL, on adventitious root formation and highlights the important role of RpARF12 in this process.

Advances in bamboo genomics: Growth and development, stress tolerance, and genetic engineering

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

TEOSINTE BRANCHED1/CYCLOIDEA/PCF protein PeTCP4s positively regulate lateral bud development by activating PePIN2a expression in Phyllostachys edulis

The development of lateral buds on the underground rhizome in bamboo is a major determinant of the yield of bamboo shoots. However, the regulating factors influencing this developmental process and the molecular mechanisms remain largely unknown. Here, we found that treatment with the Cytokinin significantly increased the lateral bud outgrowth of Moso bamboo (Phyllostachys edulis). A pair of plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) genes, PeTCP4a and PeTCP4b, were identified in Moso bamboo. The expression of both PeTCP4 genes was promoted by Cytokinin and synchronized with the development of lateral buds. Overexpression of PeTCP4 genes exhibited increased rosette-leaf branches. PeTCP4s upregulated the expression of auxin efflux carrier PIN-FORMED (PIN2) gene and those genes involved in lateral organ such as KNAT2, KNAT6, STM and IAA3 in transgenic plants. Similar to PeTCP4 genes, the expression of PePIN2a in Moso bamboo was also promoted by Cytokinin. Subsequently, we found both PeTCP4 proteins directly bound to the PePIN2a gene and activated its expression. Our data suggested that PeTCP4s, induced by Cytokinin, promote lateral bud outgrowth by activating PePIN2a expression and upregulating the expression of those genes involved in lateral organ. This study may provide new insights into the mechanism of lateral bud development of bamboo.

Interplay Between Phytohormones and Sugar Metabolism in Dendrocalamus latiflorus

Dendrocalamus latiflorus, a species of giant bamboo, holds significant ecological and economic value. This review delves into the intricate interplay between phytohormones and sugar metabolism in Dendrocalamus latiflorus, emphasizing species-specific mechanisms that enhance its ecological adaptability and rapid growth. By synthesizing recent research, this work highlights how phytohormones, including auxins, cytokinins, and abscisic acid, regulate sugar metabolism pathways such as glycolysis and starch degradation in response to environmental stimuli. These hormones influence crucial plant processes, including cell division, elongation, stress responses, and sugar metabolism pathways such as glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation. Geographic variations in these processes are examined, demonstrating their role in environmental adaptation and ecological resilience. For instance, populations in nutrient-rich soils exhibit enhanced cytokinin activity and sugar transport efficiency, while those in water-limited areas display elevated abscisic acid levels, aiding drought tolerance. This targeted focus on D. latiflorus provides novel insights into its potential applications in sustainable forestry and agroforestry systems. By integrating recent advances, this review highlights the critical role of phytohormone-sugar interplay in improving the productivity and stress resilience of D. latiflorus, with implications for agroforestry systems and climate change adaptation.

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.

Genome-Wide Identification and Role of the bHLH Gene Family in Dendrocalamus latiflorus Flowering Regulation

The basic helix-loop-helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, we identified 309 bHLH genes and divided them into 23 subfamilies. Structural analysis revealed that proteins in specific DlbHLH subfamilies are highly conserved. Collinearity analysis indicates that the amplification of the DlbHLH gene family primarily occurs through segmental duplications. The structural diversity of these duplicated genes may account for their functional variability. Many DlbHLHs are expressed during flower development, indicating the bHLH gene's significant role in this process. In the promoter region of DlbHLHs, different homeopathic elements involved in light response and hormone response co-exist, indicating that DlbHLHs are related to the regulation of the flower development of D. latiflorus.

ATG10S promotes IFNL1 expression and autophagic degradation of multiple viral proteins mediated by IFNL1

ATG10S is a newly discovered subtype of the autophagy protein ATG10. It promotes complete macroautophagy/autophagy, degrades multiple viral proteins, and increases the expression of type III interferons. Here, we aimed to investigate the mechanism of ATG10S cooperation with IFNL1 to degrade viral proteins from different viruses. Using western blot, immunoprecipitation (IP), tandem sensor RFP-GFP-LC3B and in situ proximity ligation assays, we showed that exogenous recombinant ATG10S protein (rHsATG10S) could enter into cells through clathrin, and ATG10S combined with ATG7 with IFNL1 assistance to facilitate ATG12-ATG5 conjugation, thereby contributing to the autophagosome formation in multiple cell lines containing different virions or viral proteins. The results of DNA IP and luciferase assays also showed that ATG10S was able to directly bind to a core motif (CAAGGG) within a binding site of transcription factor ZNF460 on the IFNL1 promoter, by which IFNL1 transcription was activated. These results clarified that ATG10S promoted autophagosome formation with the assistance of IFNL1 to ensure autophagy flux and autophagic degradation of multiple viral proteins and that ATG10S could also act as a novel transcription factor to promote IFNL1 gene expression. Importantly, this study further explored the antiviral mechanism of ATG10S interaction with type III interferon and provided a theoretical basis for the development of ATG10S into a new broad-spectrum antiviral protein drug.Abbreviation: ATG: autophagy related; ATG10S: the shorter isoform of autophagy-related 10; CC50: half cytotoxicity concentration; CCV: clathrin-coated transport vesicle; CLTC: clathrin heavy chain; CM: core motif; co-IP: co-immunoprecipitation; CPZ: chlorpromazine; ER: endoplasmic reticulum; HCV: hepatitis C virus; HBV: hepatitis B virus; HsCoV-OC43: Human coronavirus OC43; IFN: interferon; PLA: proximity ligation assay; rHsATG10S: recombinant human ATG10S protein; RLU: relative light unit; SQSTM1: sequestosome 1; ZNF: zinc finger protein.

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.

Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng

Panax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.

Histone deacetylase MdHDA6 is an antagonist in regulation of transcription factor MdTCP15 to promote cold tolerance in apple

Understanding the molecular regulation of plant cold response is the basis for cold resistance germplasm improvement. Here, we revealed that the apple histone deacetylase MdHDA6 can perform histone deacetylation on cold-negative regulator genes and repress their expression, leading to the positive regulation of cold tolerance in apples. Moreover, MdHDA6 directly interacts with the transcription factor MdTCP15. Phenotypic analysis of MdTCP15 transgenic apple lines and wild types reveals that MdTCP15 negatively regulates cold tolerance in apples. Furthermore, we found that MdHDA6 can facilitate histone deacetylation of MdTCP15 and repress the expression of MdTCP15, which positively contributes to cold tolerance in apples. Additionally, the transcription factor MdTCP15 can directly bind to the promoter of the cold-negative regulator gene MdABI1 and activate its expression, and it can also directly bind to the promoter of the cold-positive regulator gene MdCOR47 and repress its expression. However, the co-expression of MdHDA6 and MdTCP15 can inhibit MdTCP15-induced activation of MdABI1 and repression of MdCOR47, suggesting that MdHDA6 suppresses the transcriptional regulation of MdTCP15 on its downstream genes. Our results demonstrate that histone deacetylase MdHDA6 plays an antagonistic role in the regulation of MdTCP15-induced transcriptional activation or repression to positively regulate cold tolerance in apples, revealing a new regulatory mechanism of plant cold response.

Identification and characterization of the cupin_1 domain-containing proteins in ma bamboo (Dendrocalamus latiflorus) and their potential role in rhizome sprouting

Cupin_1 domain-containing protein (CDP) family, which is a member of the cupin superfamily with the most diverse functions in plants, has been found to be involved in hormone pathways that are closely related to rhizome sprouting (RS), a vital form of asexual reproduction in plants. Ma bamboo is a typical clumping bamboo, which mainly reproduces by RS. In this study, we identified and characterized 53 Dendrocalamus latiflorus CDP genes and divided them into seven subfamilies. Comparing the genetic structures among subfamilies showed a relatively conserved gene structure within each subfamily, and the number of cupin_1 domains affected the conservation among D. latiflorus CDP genes. Gene collinearity results showed that segmental duplication and tandem duplication both contributed to the expansion of D. latiflorus CDP genes, and lineage-specific gene duplication was an important factor influencing the evolution of CDP genes. Expression patterns showed that CDP genes generally had higher expression levels in germinating underground buds, indicating that they might play important roles in promoting shoot sprouting. Transcription factor binding site prediction and co-expression network analysis indicated that D. latiflorus CDPs were regulated by a large number of transcription factors, and collectively participated in rhizome buds and shoot development. This study significantly provided new insights into the evolutionary patterns and molecular functions of CDP genes, and laid a foundation for further studying the regulatory mechanisms of plant rhizome sprouting.

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.