Class I TCP transcription factor AtTCP8 modulates key brassinosteroid-responsive genes

RTN family and its response to abiotic stress in Oryza sativa

Abiotic stresses induced by climate change and soil pollution cause significant crop yield loss. Identifying stress-resistant genes for genetic improvement is urgent and necessary. Reticulon (RTN, also called RTNLB in plants) is a widely distributed endoplasmic reticulum-associated protein in eukaryotic cells, playing a crucial role in stress response activities, including autophagy, endoplasmic reticulum stress, and osmotic regulation. However, the diversity of RTNLBs in plants has hindered comprehensive analysis. This study identified 20 OsRTNLBs from Oryza sativa through a comprehensive whole-genome analysis. Detailed information on their chromosomal localization, protein motifs, phylogenetic relationships, and gene collinearity has been provided. The effects of five major abiotic stresses-cold, heat, heavy metals, salt, and drought-on rice seedling development have been assessed. The expression levels of RTNLBs under these abiotic stresses show significant changes, with an overall increase in transcription levels under simulated drought stress and a decrease under the other four stresses. Three OsRTNLBs (OsRTNLB4, OsRTNLB8 and OsRTNLB9) have been identified as key proteins contributing to abiotic stress.

CsTCP14-CsIAA4 module-mediated repression of auxin signaling regulates citrus somatic embryogenesis

Somatic embryogenesis (SE) is an important in vitro regeneration approach for plants, especially in biotechnological manipulations. However, SE capability is difficult to modulate and deteriorates over time. Glycerol medium is effective in SE induction of citrus, while the mechanisms remain unclear. We found that auxin signaling reduced soon after the citrus embryogenic callus (EC) was transferred to glycerol medium, and the expression of CsTCP14 and AUX/IAA gene CsIAA4 was induced by glycerol. Overexpression of CsIAAm that encodes a stable indole-3-acetic acid (IAA) protein suppressed auxin signaling in EC and enhanced SE. CsTCP14 bound to the promoter of CsIAA4 and activate CsIAA4 expression in EC with strong SE competence. Overexpression of CsTCP14 activated CsIAA4 expression and reduced auxin signaling in citrus EC, and thus enhanced SE. Application of exogenous IAA inhibits SE, while the auxin signaling inhibitor p-chlorophenoxyisobutyric acid (PCIB) enhances SE in citrus. The SE enhancement effect of CsIAA4 and CsTCP14 overexpression on EC was alleviated by exogenous IAA, but reinforced by PCIB. We uncover the regulatory pathway of CsTCP14-CsIAA4 module-mediated repression of auxin signaling in glycerol-induced citrus SE, which deepens our understanding of SE mechanisms in plants and supports modulation of SE in citrus breeding via biotechnological approaches.

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.

Mining the Candidate Transcription Factors Modulating Tanshinones' and Phenolic Acids' Biosynthesis Under Low Nitrogen Stress in Salvia miltiorrhiza

Mining valuable genes is helpful to breed high-quality Salvia miltiorrhiza exhibiting efficient nitrogen fertilizer utilization efficiency. In the present study, transcriptome sequencing was introduced to select the candidate transcription factors (TFs) involved in tanshinones' (TAs) and phenolic acids' (PHAs) biosynthesis as well as low nitrogen (LN) stress. In totally, 97.71 Gb clean data was obtained from fifteen sequencing samples and 30,975 unigenes were assembled. Among of them, 27,843 unigenes were successfully annotated. Overall, 8663 differential expression genes (DEGs) were identified, among of which 5034 unigenes were up-regulated, and 3629 unigenes were down-regulated. By enrichment of DEGs together with gene co-expression network construction, 10 candidate TFs including HSFB2b, LBD12, ERF1A, ERF98, LBD25, HSF24, RAM1, HSFA4B, TCP8, and WRKY24 were finally retrieved, which are predicted to participate in modulating TA and PHA biosynthesis under LN stress. Quantitative real-time polymerase chain reaction (qRT-PCR) detection was introduced to further detect the expression profile of candidate TFs under LN stress. These findings offer a valuable resource for in-depth study of TAs 'and PHAs' biosynthesis under LN stress in S. miltiorrhiza.

Integrative transcriptome and metabolome analysis reveals candidate genes related to terpene synthesis in Chrysanthemum × morifolium

BACKGROUND

Chrysanthemum (Chrysanthemum × morifolium) is one of the four major cut flowers worldwide and is valued for ornamental, culinary, and medicinal purposes. Terpenoids are key components of the fragrance of chrysanthemum; they not only serve to repel insect herbivores and promote pollination but also impact the value of the plant. However, the terpene production of chrysanthemum and the regulatory mechanisms involved remain unclear.

RESULTS

We used gas chromatography‒mass spectrometry (GC‒MS) to identify 177 compounds, including 106 terpenes, in ten chrysanthemum cultivars. Monoterpene derivatives and sesquiterpenes were the most common. Next, we identified 27 candidate hub genes for terpene production in chrysanthemum via combined transcriptome and metabolome analysis, as well as weighted gene coexpression network analysis. The three terpenes synthesis-related genes were significantly expressed in the disc florets of the different chrysanthemum cultivars. We concluded that the transcription factors TCP8, TCP5, ATHB8, ATHB7, HAT22, TGA1, TGA4, and WHY1 may regulate terpene synthesis.

CONCLUSIONS

In this study, we profiled terpenes in chrysanthemum florets and constructed a key terpene-transcription factor network related to terpene synthesis. These findings lay the groundwork for future research into the mechanism of terpene synthesis in chrysanthemum as well as in other plants.

TaTCP21-A negatively regulates wheat cold tolerance via repressing expression of TaDREB1C

Cold stress is one of the important harmful factors that seriously affect wheat (Triticum aestivum) yield and quality. TCP transcription factor plays important roles in the process of plant cell proliferation and growth. In this study, we identified 60 TaTCP genes expressed in strong cold resistant winter wheat variety Dongnongdongmai1 (Dn1) under cold stress by previous transcriptome data, of which 13 TaTCPs showed significant differences in expression. The evolution of TaTCPs was analyzed, and the results showed that there were 2 homologous pairs in TaTCPs with AtTCPs and 90 homologous pairs in TaTCPs with OsTCPs. Expression patterns of 20 TaTCPs under cold stress were analyzed by qRT-PCR, and TCP21-A with significant expression differences was screened. We obtained tcp21-A mutant from the EMS mutant library of winter wheat Kenong9204. We observed that the mutation of TaTCP21-A significantly improved its cold resistance. Subsequently, transcriptome analysis revealed that TCP21-A inhibited expression of cold responsive gene TaDREB1C. Finally, subcellular localization and yeast one hybrid were used to verify that TCP21-A can act as a transcription factor to bind to the GGTCCC promoter element. Luciferase reporter gene experiment showed that TCP21-A inhibits the transcriptional activity of the TaDREB1C promoter. In summary, we systematically analyzed the expression patterns of TaTCP family members in Dn1 under cold stress and demonstrated that TaTCP21-A negatively regulated wheat cold tolerance by inhibiting expression of TaDREB1C. These results provide new insights into the functional mechanism of TaTCP transcription factors in response to cold stress.

The CaABCG14 transporter gene regulates the capsaicin accumulation in Pepper septum

Capsaicin (CAP), a crucial compound found in chili peppers, not only contributes to their spicy flavor but also possesses several industrial applications. CAP biosynthetic pathway is well known, while its transport mechanism remains elusive. Herein, we performed a comparative transcriptome analysis conducted on pepper fruit tissues at three different stages of development. Four important CAP transporter genes, including one MATE and three ABCs, were identified by differential expression and WGCNA analysis. Specifically, the expression patterns of three ABC genes were assessed in the septum of fruits from nine distinct genotypes of peppers with high capsaicin levels. Interestingly, CaABCG14 was associated with variations in CAP concentration and co-expressed with genes involved in CAP biosynthesis. Transient expression assay revealed that CaABCG14 is localized to the membrane and nucleus. Silencing of CaABCG14 resulted in a notable reduction in the levels of CAP contents and the expression of its biosynthetic genes in the septum of pepper. The overexpression of CaABCG14 greatly intensified the cytotoxic effects of CAP on the yeast cells. Taken together, we for the first time identified a new transporter gene CaABCG14, regulating the CAP accumulation in pepper septum. These findings offer a fresh molecular theoretical framework for CAP transport and accumulation.

Amaranth's Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene

Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50-200 mmol·L-1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L-1, while it was promoted at 50 mmol·L-1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L-1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.

Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors

SAG21/LEA5 is an unusual late embryogenesis abundant protein in Arabidopsis thaliana, that is primarily mitochondrially located and may be important in regulating translation in both chloroplasts and mitochondria. SAG21 expression is regulated by a plethora of abiotic and biotic stresses and plant growth regulators indicating a complex regulatory network. To identify key transcription factors regulating SAG21 expression, yeast-1-hybrid screens were used to identify transcription factors that bind the 1685 bp upstream of the SAG21 translational start site. Thirty-three transcription factors from nine different families bound to the SAG21 promoter, including members of the ERF, WRKY and NAC families. Key binding sites for both NAC and WRKY transcription factors were tested through site directed mutagenesis indicating the presence of cryptic binding sites for both these transcription factor families. Co-expression in protoplasts confirmed the activation of SAG21 by WRKY63/ABO3, and SAG21 upregulation elicited by oligogalacturonide elicitors was partially dependent on WRKY63, indicating its role in SAG21 pathogen responses. SAG21 upregulation by ethylene was abolished in the erf1 mutant, while wound-induced SAG21 expression was abolished in anac71 mutants, indicating SAG21 expression can be regulated by several distinct transcription factors depending on the stress condition.

MtTCP18 Regulates Plant Structure in Medicago truncatula

Plant structure has a large influence on crop yield formation, with branching and plant height being the important factors that make it up. We identified a gene, MtTCP18, encoding a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor highly conserved with Arabidopsis gene BRC1 (BRANCHED1) in Medicago truncatula. Sequence analysis revealed that MtTCP18 included a conserved basic helix-loop-helix (BHLH) motif and R domain. Expression analysis showed that MtTCP18 was expressed in all organs examined, with relatively higher expression in pods and axillary buds. Subcellular localization analysis showed that MtTCP18 was localized in the nucleus and exhibited transcriptional activation activity. These results supported its role as a transcription factor. Meanwhile, we identified a homozygous mutant line (NF14875) with a mutation caused by Tnt1 insertion into MtTCP18. Mutant analysis showed that the mutation of MtTCP18 altered plant structure, with increased plant height and branch number. Moreover, we found that the expression of auxin early response genes was modulated in the mutant. Therefore, MtTCP18 may be a promising candidate gene for breeders to optimize plant structure for crop improvement.

Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding

Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.

The brassinosteroid-responsive protein OCTOPUS is a novel regulator of Arabidopsis thaliana immune signaling

Phloem is a critical tissue for transport of photosynthates and extracellular signals in vascular plants. However, it also represents an ideal environment for pathogens seeking access to valuable host nutrients. Although many vascular pathogens induce economically relevant crop damage, there is still little known about the mechanisms by which immune signaling operates through the phloem. An existing phosphoproteomic dataset was mined to identify proteins that were both phosphorylated in response to the defense-elicitor flagellin (flg22) and expressed in vascular cells. A single candidate, OCTOPUS (OPS), is polarly associated with the plasma membrane of sieve element cells and has been characterized as an inhibitor of brassinosteroid insensitive-2 in promotion of brassinosteroid-related phytohormone signaling. The observation that OPS is differentially phosphorylated in response to flg22 led us to the examine whether OPS may also regulate flg22-induced immune signaling. Two independent alleles of ops exhibited enhanced immunity outputs across multiple signaling branches of PAMP-triggered immunity (PTI), constitutively and in response to flg22 treatment. Together with our observation that interactions between OPS and brassinosteroid insensitive-2 were disrupted by induction of salicylic acid and depletion of brassinosteriod, these data support a model whereby OPS modulates brassinolide and immune signaling to control downstream responses. We present OPS as a novel addition to the list of proteins with documented roles in PAMP-PTI signaling. These results further indicate that immune signaling in the phloem may be a significant and unique component of the host detection and response to pathogens in vascular plants.

Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)

Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.

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.

Advances in Research on the Regulation of Floral Development by CYC-like Genes

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.

Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus

Introduction

The anti-tumor vindoline and catharanthine alkaloids are naturally existed in Catharanthus roseus (C. roseus), an ornamental plant in many tropical countries. Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play important roles in various plant developmental processes. However, the roles of C. roseus TCPs (CrTCPs) in terpenoid indole alkaloid (TIA) biosynthesis are largely unknown.

Methods

Here, a total of 15 CrTCP genes were identified in the newly updated C. roseus genome and were grouped into three major classes (P-type, C-type and CYC/TB1).

Results

Gene structure and protein motif analyses showed that CrTCPs have diverse intron-exon patterns and protein motif distributions. A number of stress responsive cis-elements were identified in promoter regions of CrTCPs. Expression analysis showed that three CrTCP genes (CrTCP2, CrTCP4, and CrTCP7) were expressed specifically in leaves and four CrTCP genes (CrTCP13, CrTCP8, CrTCP6, and CrTCP10) were expressed specifically in flowers. HPLC analysis showed that the contents of three classic TIAs, vindoline, catharanthine and ajmalicine, were significantly increased by ultraviolet-B (UV-B) and methyl jasmonate (MeJA) in leaves. By analyzing the expression patterns under UV-B radiation and MeJA application with qRT-PCR, a number of CrTCP and TIA biosynthesis-related genes were identified to be responsive to UV-B and MeJA treatments. Interestingly, two TCP binding elements (GGNCCCAC and GTGGNCCC) were identified in several TIA biosynthesis-related genes, suggesting that they were potential target genes of CrTCPs.

Discussion

These results suggest that CrTCPs are involved in the regulation of the biosynthesis of TIAs, and provide a basis for further functional identification of CrTCPs.