Comprehensive identification of bHLH transcription factors in Litsea cubeba reveals candidate gene involved in the monoterpene biosynthesis pathway

CitUNE1 inhibits (+)-valencene synthesis by regulating CsTPS1 in 'Newhall' sweet orange

(+)-Valencene is the characteristic volatile compound in 'Newhall' sweet orange, and CsTPS1 is the gene that codes for the (+)-valencene synthase. Here, four transcription factors, including CitUNE1, CitUNE3, CitSCL1, and CitSCL13, were screened as candidate proteins by yeast one-hybrid (Y1H) library screening with CsTPS1 promoter as the bait. Among them, CitUNE1 bound to the G-box on the promoter of CsTPS1 and suppressed CsTPS1 expression, confirmed by Y1H, dual-luciferase assay, point-mutation experiment and EMSA. The expression pattern of CitUNE1 showed a negative correlation with both the content of (+)-valencene and CsTPS1 transcripts level, both during fruit development and after ethylene treatment. Furthermore, the role of CitUNE1 in (+)-valencene synthesis was confirmed using the transient over-expression and silencing in 'Newhall' sweet orange. Transient over-expression of CitUNE1 inhibited CsTPS1 expression and reduced the accumulation of (+)-valencene, while silencing of CitUNE1 induced CsTPS1 expression and triggered (+)-valencene synthesis in 'Newhall' sweet orange.

Genome-wide identification of five fern bHLH families and functional analysis of bHLHs in lignin biosynthesis in Alsophila spinulosa

BACKGROUND

The basic helix-loop-helix (bHLH) transcription factors are involved in the biosynthesis of various secondary metabolites. However, genome-wide studies on the bHLH gene family in ferns and their role in lignin biosynthesis remain limited. As the second largest group of vascular plants, ferns are of significant interest for understanding plant evolution and secondary metabolism. Among ferns, Alsophila spinulosa stands out as one of the few tree ferns with a distinctive trunk structure. Investigating the genes potentially regulating lignin biosynthesis in A. spinulosa offers valuable insights into the growth and development mechanisms of its trunk, which is pivotal for the overall architecture and function of the plant.

RESULTS

In this study, we conducted a systematic study of bHLH gene families in five ferns, including 186 in A. spinulosa, 130 in A. capillus, 107 in A. filiculoides, 71 in S. cucullata, and 67 in C. richardii. Based on phylogenetic analysis, all bHLH genes were classified into 28 subgroups. The number of bHLH members in different ferns was closely related to their growth patterns and life habits, with the number in tree ferns being much larger than in other ferns. In addition, we identified tandem duplication in C. richardii and A. capillus as a key driver of their bHLH gene diversity, whereas in A. spinulosa, segmental duplication contributed more to gene expansion and evolution. Most of the bHLH genes in ferns are in a state of purifying selection. Additionally, tissue-specific expression patterns of AspbHLH genes suggest diverse functional roles in plant growth, development, and metabolite synthesis. We further focused on three genes, AspbHLH80, AspbHLH120, and AspbHLH185, which are specifically highly expressed in xylem. Results from weighted gene co-expression network analysis (WGCNA) and downstream target gene prediction indicate their potential regulatory roles in lignin biosynthesis.

CONCLUSION

This study presents a comprehensive genomic analysis of the bHLH gene family in five fern species. We found a strong correlation between bHLH gene number and fern growth morphology, with tree ferns exhibiting a significantly higher number of bHLH genes. Tandem duplications were key to bHLH gene diversity in C. richardii, A. capillus, and A. spinulosa, while segmental duplications contributed more to bHLH gene expansion in A. spinulosa. Evolutionary analysis indicated most fern bHLH genes are under purifying selection. Tissue-specific expression patterns of AspbHLH genes suggest roles in growth, development, and secondary metabolism. Furthermore, WGCNA and target gene predictions highlight three genes (AspbHLH80, AspbHLH120, and AspbHLH185) potentially involved in lignin biosynthesis. Overall, this work provides key insights into the mechanisms of wood formation in ferns and advances our understanding of plant secondary metabolism.

LcMYB43 enhances monoterpene biosynthesis by activating 1-deoxy-D-xylulose-5-phosphate synthase gene expression in Litsea cubeba

MYB transcription factors are crucial regulators involved in various metabolic processes in plants, including terpene biosynthesis. Litsea cubeba, a member of the Lauraceae family, is rich in monoterpenes and regulates their biosynthesis via the key enzyme DXS in the MEP pathway. Seven DXS genes have been identified in this species, but the role of the MYB family in terpene biosynthesis remains unclear. This study conducted a genome-wide characterization of the R2R3-MYB gene family in L. cubeba, analyzing its phylogenetics, expression, and regulatory functions. A total of 129 R2R3-MYB members were identified, with expansion mechanisms involving tandem and segmental duplications. Expression analysis revealed that LcMYB43 activates LcDXS5, a key enzyme in monoterpene biosynthesis. Overexpression of LcMYB43 significantly increased monoterpene accumulation. Y1H, EMSA, and dual-luciferase assays showed that LcMYB43 directly binds to the CAACAG motif in the LcDXS5 promoter, activating its expression. These findings suggest that LcMYB43 enhances monoterpene biosynthesis by promoting LcDXS5 expression, providing new insights into the regulatory mechanisms of monoterpene biosynthesis.

Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica

The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.

Transcriptome-wide investigation and functional characterization reveal a terpene synthase involved in γ-terpinene biosynthesis in Monarda citriodora

Monarda citriodora Cerv. ex Lag. is a rich source of industrially important compounds like γ-terpinene, carvacrol, thymol and thymoquinone. Understanding the regulation of γ-terpinene biosynthesis, a precursor for other monoterpenes, could facilitate upscaling of these metabolites in M. citriodora. Therefore, the present study aimed to unravel and characterize the terpene synthase (TPS) involved in γ-terpinene biosynthesis. Homology searches revealed 33 TPS members in the transcriptome assembly of M. citriodora. Based on the correlation of expression patterns and phytochemical profile, McTPS22 emerged as the putative TPS for γ-terpinene biosynthesis. Molecular docking suggested geranyl diphosphate (GPP) as a potential substrate for McTPS22. Heterologous expression in Escherichia coli and Nicotiana benthamiana confirmed the role of McTPS22 in γ-terpinene biosynthesis. Both in-silico prediction and confocal microscopy indicated plastidial localization of the McTPS22. Gene co-expression network analysis revealed 507 genes interacting with McTPS22, including 80 transcription factors (TFs). Of these, 46 TFs had binding sites in the McTPS22 promoter, and 36 showed significant correlations with γ-terpinene accumulation, suggesting they may be potential regulators. Promoter analysis indicated regulation by phytohormones and abiotic factors, confirmed by phytohormone elicitation and QRT-PCR. The histochemical GUS staining suggested that McTPS22 is primarily active in the glandular trichomes of M. citriodora. The present work provides insights into the molecular regulation of biosynthesis of γ-terpinene in M. citriodora.

Alternative splicing of CsbHLH133 regulates geraniol biosynthesis in tea plants

Geraniol is one of the most abundant aromatic compounds in fresh tea leaves and contributes to the pleasant odor of tea products. Additionally, it functions as an airborne signal that interacts with other members of the ecosystem. To date, the regulation of the geraniol biosynthesis in tea plants remains to be investigated. In this study, a correlation test of the content of geraniol and its glycosides with gene expression data revealed that nudix hydrolase, CsNudix26, and its transcription factor, CsbHLH133 are involved in geraniol biosynthesis. In vitro enzyme assays and metabolic analyses of genetically modified tea plants confirmed that CsNudix26 is responsible for the formation of geraniol. Yeast one-hybrid, dual-luciferase reporter, and EMSA assays were used to verify the binding of CsbHLH133 to the CsNudix26 promoter. Overexpression of CsbHLH133 in tea leaves enhanced CsNudix26 expression and geraniol accumulation, whereas CsbHLH133 silencing reduced CsNudix26 transcript levels and geraniol content. Interestingly, CsbHLH133-AS, produced by alternative splicing, was discovered and proved to be the primary transcript expressed in response to various environmental stresses. Furthermore, geraniol release was found to be affected by various factors that alter the expression patterns of CsbHLH133 and CsbHLH133-AS. Our findings indicate that distinct transcript splicing patterns of CsbHLH133 regulate geraniol biosynthesis in tea plants in response to different regulatory factors.

Genome-wide identification of bHLH transcription factors in Kenaf (Hibiscus cannabinus L.) and gene function analysis of HcbHLH88

Among plants' transcription factor families, the bHLHs family has a significant influence on plant development processes and stress tolerance. However, there have been no relevant studies performed on the bHLHs family in kenaf (Hibiscus cannabinus L). Here, the bHLH transcription factors in kenaf were found using bioinformatics, and a total of 141 kenaf HcbHLH transcription factors were identified. Phylogenetic analysis revealed that these transcription factors were irregularly distributed on 18 chromosomes and separated into 20 subfamilies. Additionally, utilizing the transcriptome data under diverse abiotic pressures, the expression of HcbHLH members was analyzed under different stress conditions. A typical HcbHLH abiotic stress transcription factor, HcbHLH88, was exposed to salt, drought, heavy metals, and ABA. The findings revealed that HcbHLH88 might be activated under salt, drought, cadmium stress, and ABA conditions. Furthermore, HcbHLH88's function under salt stress conditions was studied after it was silenced using the virus-induced gene silencing (VIGS) technique. Reduced antioxidant enzyme activity and stunted plant development were seen in VIGS-silenced seedlings. Stress-related genes were shown to be considerably downregulated in the HcbHLH88-silenced kenaf plants, according to the qRT-PCR study. In conclusion, this study provides the first systematic gene family analysis of the kenaf bHLH gene family and provides a preliminary validation of the salt tolerance function of the HcbHLH88 gene. This study lays the foundation for future research on the regulatory mechanisms of bHLH genes in response to abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01504-y.

Functions and Regulatory Mechanisms of bHLH Transcription Factors during the Responses to Biotic and Abiotic Stresses in Woody Plants

Environmental stresses, including abiotic and biotic stresses, have complex and diverse effects on the growth and development of woody plants, which have become a matter of contention due to concerns about the outcomes of climate change on plant resources, genetic diversity, and world food safety. Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes and play an important role in biotic and abiotic stress responses of woody plants. In recent years, an increasing body of studies have been conducted on the bHLH TFs in woody plants, and the roles of bHLH TFs in response to various stresses are increasingly clear and precise. Therefore, it is necessary to conduct a systematic and comprehensive review of the progress of the research of woody plants. In this review, the structural characteristics, research history and roles in the plant growth process of bHLH TFs are summarized, the gene families of bHLH TFs in woody plants are summarized, and the roles of bHLH TFs in biotic and abiotic stresses in woody plants are highlighted. Numerous studies mentioned in this review have shown that bHLH transcription factors play a crucial role in the response of woody plants to biotic and abiotic stresses. This review serves as a reference for further studies about enhancing the stress resistance and breeding of woody plants. Also, the future possible research directions of bHLH TFs in response to various stresses in woody plants will be discussed.

Gas Chromatography-Mass Spectrometry Metabolites and Transcriptome Profiling Reveal Molecular Mechanisms and Differences in Terpene Biosynthesis in Two Torrya grandis Cultivars during Postharvest Ripening

Terpene aroma compounds are key quality attributes of postharvest Torreya grandis nuts, contributing to their commercial value. However, terpene biosynthesis and regulatory networks in different T. grandis cvs. are still poorly understood. Here, chief cvs. 'Xi Fei' and 'Xiangya Fei' were investigated for their differences in terpene biosynthesis and gene expression levels during postharvest ripening using headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) and transcriptomic datasets. A total of 28 and 22 aroma compounds were identified in 'Xi Fei' and 'Xiangya Fei', respectively. Interestingly, differences in aroma composition between the two cvs. were mostly attributed to D-limonene and α-pinene levels as key determinants in Torreya nuts' flavor. Further, transcriptome profiling, correlation analysis, and RT-qPCR annotated two novel genes, TgTPS1 in 'Xi Fei' and TgTPS2 in 'Xiangya Fei', involved in terpene biosynthesis. In addition, six transcription factors (TFs) with comparable expression patterns to TgTPS1 and four TFs to TgTPS2 were identified via correlation analysis of a volatile and transcriptome dataset to be involved in terpene biosynthesis. Our study provides novel insight into terpene biosynthesis and its regulation at the molecular level in T. grandis nut and presents a valuable reference for metabolic engineering and aroma improvement in this less explored nut.

LcWRKY17, a WRKY Transcription Factor from Litsea cubeba, Effectively Promotes Monoterpene Synthesis

The WRKY gene family is one of the most significant transcription factor (TF) families in higher plants and participates in many secondary metabolic processes in plants. Litsea cubeba (Lour.) Person is an important woody oil plant that is high in terpenoids. However, no studies have been conducted to investigate the WRKY TFs that regulate the synthesis of terpene in L. cubeba. This paper provides a comprehensive genomic analysis of the LcWRKYs. In the L. cubeba genome, 64 LcWRKY genes were discovered. According to a comparative phylogenetic study with Arabidopsis thaliana, these L. cubeba WRKYs were divided into three groups. Some LcWRKY genes may have arisen from gene duplication, but the majority of LcWRKY evolution has been driven by segmental duplication events. Based on transcriptome data, a consistent expression pattern of LcWRKY17 and terpene synthase LcTPS42 was found at different stages of L. cubeba fruit development. Furthermore, the function of LcWRKY17 was verified by subcellular localization and transient overexpression, and overexpression of LcWRKY17 promotes monoterpene synthesis. Meanwhile, dual-Luciferase and yeast one-hybrid (Y1H) experiments showed that the LcWRKY17 transcription factor binds to W-box motifs of LcTPS42 and enhances its transcription. In conclusion, this research provided a fundamental framework for future functional analysis of the WRKY gene families, as well as breeding improvement and the regulation of secondary metabolism in L. cubeba.