A Dual Repeat Cis-Element Determines Expression of GERANYL DIPHOSPHATE SYNTHASE for Monoterpene Production in Phalaenopsis Orchids

Fine-tuned terpene synthase gene expression, functional promiscuity, and subcellular localization: implications for the evolution of complex floral volatile bouquet in Caladenia orchids

Chemically mediated floral volatile signals are crucial for pollinator attraction across angiosperms. However, beyond model plant systems, the molecular mechanisms underpinning their tissue-specific biosynthesis, regulation, and emission are still poorly understood. In this study of a food-deceptive insect-pollinated orchid (Caladenia denticulata), we elucidated the molecular basis of α-pinene biosynthesis-the major floral volatile emitted by this species and diverse lower abundance monoterpenes and sesquiterpenes. To achieve this, we combined comparative transcriptomics between active glandular trichome-rich sepal tips and labellum and non-active remaining flower tissues, floral volatile headspace profiling, phylogenetic analysis of a multigene family, and protein functional assays. We found (i) multiple branch points of the terpene synthase (TPS) biosynthetic pathway were highly expressed and coordinately upregulated in the active floral tissues compared to non-active ones, (ii) the monoterpene synthase CdTPS-b3 underpinning α-pinene biosynthesis and a bona fide promiscuous TPS CdTPS-b4 that may contribute to the diverse array of low-abundance mono- and sesquiterpenes found in its flowers, and (iii) dual localization (plastid and cytosol) of CdTPS-b3 and CdTPS-b4. Our findings highlight metabolic pathway specialization at multiple TPS pathway branch points supporting the biosynthesis and emission of α-pinene in C. denticulata flowers that are implicated in its generalist pollinator attraction. Furthermore, the complexity of diverse floral terpenes in Caladenia is likely mediated by finely tuned TPS gene expression, functional promiscuity, and subcellular localization. We predict that the combination of these three mechanisms underpin the evolution of multiple deceptive pollination strategies in Caladenia.

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.

PfERF106, a novel key transcription factor regulating the biosynthesis of floral terpenoids in Primula forbesii Franch

BACKGROUND

Flowers can be a source of essential oils used in the manufacture of substances with high economic value. The ethylene response factor (ERF) gene family plays a key role in regulating secondary metabolite biosynthesis in plants. However, until now, little has been known about the involvement of ERF transcription factors (TFs) in floral terpenoid biosynthesis.

RESULTS

In this study, an aromatic plant, Primula forbesii Franch., was used as research material to explore the key regulatory effects of PfERF106 on the biosynthesis of terpenoids. PfERF106, which encodes an IXb group ERF transcription factor, exhibited a consistent expression trend in the flowers of P. forbesii and was transcriptionally induced by exogenous ethylene. Transient silencing of PfERF106 in P. forbesii significantly decreased the relative contents of key floral terpenes, including (z)-β-ocimene, sabinene, β-pinene, γ-terpinene, linalool, eremophilene, α-ionone, and α-terpineol. In contrast, constitutive overexpression of PfERF106 in transgenic tobacco significantly increased the relative contents of key floral terpenes, including cis-3-hexen-1-ol, linalool, caryophyllene, cembrene, and sclareol. RNA sequencing of petals of PfERF106-silenced plants and empty-vector control plants revealed 52,711 expressed unigenes and 9,060 differentially expressed genes (DEGs). KEGG annotation analysis revealed that the DEGs were enriched for involvement in secondary metabolic biosynthetic pathways, including monoterpene and diterpene synthesis. Notably, 10 downregulated DEGs were determined to be the downstream target genes of PfERF106 affecting the biosynthesis of terpenoids in P. forbesii.

CONCLUSION

This study characterized the key positive regulatory effects of PfERF106 on the biosynthesis of terpenoids, indicating high-quality genetic resources for aroma improvement in P. forbesii. Thus, this study advances the artificial and precise directional regulation of metabolic engineering of aromatic substances.

Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids

Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis-acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co-expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2-domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.

Hormonal control of promoter activities of Cannabis sativa prenyltransferase 1 and 4 and salicylic acid mediated regulation of cannabinoid biosynthesis

Cannabis sativa aromatic prenyltransferase 4 (CsPT4) and 1 (CsPT1) have been shown to catalyze cannabigerolic acid (CBGA) biosynthesis, a step that rate-limits the cannabinoid biosynthetic pathway; both genes are highly expressed in flowers. CsPT4 and CsPT1 promoter driven β-glucuronidase (GUS) activities were detected in leaves of cannabis seedlings, and strong CsPT4 promoter activities were associated with glandular trichomes. Hormonal regulation of cannabinoid biosynthetic genes is poorly understood. An in silico analysis of the promoters identified putative hormone responsive elements. Our work examines hormone-responsive elements in the promoters of CsPT4 and CsPT1 in the context of physiological responses of the pathway to the hormone in planta. Dual luciferase assays confirmed the regulation of promoter activities by the hormones. Further studies with salicylic acid (SA) demonstrated that SA pretreatment increased the expression of genes located downstream of the cannabinoid biosynthetic pathway. The results from all aspects of this study demonstrated an interaction between certain hormones and cannabinoid synthesis. The work provides information relevant to plant biology, as we present evidence demonstrating correlations between molecular mechanisms that regulate gene expression and influence plant chemotypes.

PbABCG1 and PbABCG2 transporters are required for the emission of floral monoterpenes in Phalaenopsis bellina

Terrestrial plants emit volatiles into the atmosphere to attract both pollinators and the enemies of herbivores, for defense. Phalaenopsis bellina is a scented orchid species in which the main scent components are monoterpenes, including linalool and geraniol, and their derivatives. Here, we investigated whether ABC transporters are involved in floral scent emission. We carried out whole-genome identification of ABC transporter-related genes using four floral transcriptomics libraries of P. bellina. We identified 86 ABC subfamily G genes related to terpenoid transport. After comparing the gene expression patterns of P. bellina with that of Phalaenopsis aphrodite subsp. formosana, a scentless species, followed by gene-to-gene correlation analysis, PbABCG1 and PbABCG2 were selected. The temporal expression of both PbABCG1 and PbABCG2 was highly correlated with that of the key enzyme PbGDPS and the major transcription factor PbbHLH4 in monoterpene biosynthesis, with optimal expression on day 5 post-anthesis. Spatial gene expression analysis showed that PbABCG1 was highly expressed in sepals, whereas PbABCG2 was expressed in the lip. Subcellular localization with a GFP fusion protein revealed that both PbABCG1 and PbABCG2 are cytoplasmic membrane proteins. Co-downregulation of PbABCG1 and PbABCG2 using both double-strand RNA interference and tobacco rattle virus-based gene silencing led to a significant decrease in monoterpene emission, accompanied by an increase in the internal monoterpene pools. Furthermore, ectopic expression of PbABCG1 and PbABCG2 in an ABC16^- mutant yeast strain rescued its tolerance to geraniol. Altogether, our results indicate that PbABCG1 and PbABCG2 play substantial roles in monoterpene transport/emission in P. bellina floral scent.

Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum

Background

Multiprotein bridging factor 1 (MBF1) is a crucial transcriptional coactivator in animals, plants, and some microorganisms, that plays a necessary role in growth development and stress tolerance. Zanthoxylum armatum is an important perennial plant for the condiments and pharmaceutical industries, whereas the potential information in the genes related to stress resistance remains poorly understood in Z. armatum. 

Results

Herein, six representative species were selected for use in a genome-wide investigation of the MBF1 family, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Citrus sinensis, Ginkgo biloba, and Z. armatum. The results showed that the MBF1 genes could be divided into two groups: Group I contained the MBF1a and MBF1b subfamilies, and group II was independent of the MBF1c subfamily.. Most species have at least two different MBF1 genes, and MBF1c is usually an essential member. The three ZaMBF1 genes were respectively located on ZaChr26, ZaChr32, and ZaChr4 of Zanthoxylum chromosomes. The collinearity were occurred between three ZaMBF1 genes, and ZaMBF1c showed the collinearity between Z. armatum and both P. trichocarpa and C. sinensis. Moreover, many cis-elements associated with abiotic stress and phytohormone pathways were detected in the promoter regions of MBF1 of six representative species. The ERF binding sites were the most abundant targets in the sequences of the ZaMBF1 family, and some transcription factor sites related to floral differentiation were also identified in ZaMBF1c, such as MADS, LFY, Dof, and AP2. ZaMBF1a was observed to be very highly expressed in 25 different samples except in the seeds, and ZaMBF1c may be associated with the male and female floral initiation processes. In addition, expression in all the ZaMBF1 genes could be significantly induced by water-logging, cold stress, ethephon, methyl jasmonate, and salicylic acid treatments, especially in ZaMBF1c.

Conclusion

The present study carried out a comprehensive bioinformatic investigation related to the MBF1 family in six representative species, and the responsiveness of ZaMBF1 genes to various abiotic stresses and phytohormone inductions was also revealed. This work not only lays a solid foundation to uncover the biological roles of the ZaMBF1 family in Z. armatum, but also provides some broad references for conducting the MBF1 research in other plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08863-4.

Delineating genetic regulation of cannabinoid biosynthesis during female flower development in Cannabis sativa

Cannabinoids are predominantly produced in the glandular trichomes on cannabis female flowers. There is little known on how cannabinoid biosynthesis is regulated during female flower development. We aim to understand the rate-limiting step(s) in the cannabinoid biosynthetic pathway. We investigated the transcript levels of cannabinoid biosynthetic genes together with cannabinoid contents during 7 weeks of female flower development. We demonstrated that the enzymatic steps for producing cannabigerol (CBG), which involve genes GPPS, PT, TKS, and OAC, could rate limit cannabinoid biosynthesis. Our findings further suggest that upregulation of cannabinoid synthases, CBDAS and THCAS in a commercial hemp and medical marijuana variety, respectively, is not critical for cannabinoid biosynthesis. The cannabinoid biosynthetic genes are generally upregulated during flower maturation; increased expression occurs coincident with glandular trichome development and cannabinoid production in the maturing flower. The results also suggest that different cannabis varieties may experience discrete transcriptional regulation of cannabinoid biosynthetic genes. In addition, we showed that methyl jasmonate (MeJA) can potentially increase cannabinoid production. We propose that biweekly applications of 100 μM MeJA starting from flower initiation would be efficacious for promoting cannabinoid biosynthesis. Our findings provide important genetic information for cannabis breeding to generate new varieties with favorable traits.

Terpene Synthase-b and Terpene Synthase-e/f Genes Produce Monoterpenes for Phalaenopsis bellina Floral Scent

Orchids are the most species-rich plants and highly interactive with pollinators via visual or olfactory cues. Biosynthesis and emission of volatile organic compounds (VOCs) to the atmosphere facilitate the olfactory cues and ensure successful pollination. Phalaenopsis bellina is a scented orchid with monoterpenes as major VOCs, comprising linalool, geraniol, and their derivatives. Comparative transcriptomics analysis identified four terpene synthase-b (TPS-b) genes and two TPS-e/f genes with differential gene expression between scented and scentless Phalaenopsis species. Here, we confirmed their differential expression between scented and scentless Phalaenopsis orchids and excluded one TPS-b candidate. We analyzed the temporal and spatial expression and functionally characterized these TPSs. Both TPS-b and TPS-e/f genes showed an increased expression on blooming day or 3 days post-anthesis (D + 3) before the optimal emission of floral scent on D + 5, with especially high expression of PbTPS5 and PbTPS10. The TPS-b genes are expressed exclusively in reproductive organs, whereas the TPS-e/f genes are expressed in both reproductive and vegetative organs. In planta functional characterization of both PbTPS5 and PbTPS10 in tobacco and scentless Phalaenopsis plants did not produce terpenoids. Further ectopic expression in scented Phalaenopsis cultivar P. I-Hsin Venus showed that linalool was the main product, with PbTPS10 displaying 3-fold higher activity than PbTPS5. On in vitro enzyme assay with purified recombinant TPS-b proteins ectopically expressed in Escherichia coli, geraniol was the product catalyzed by PbTPS5 and PbTPS9. PbTPS3 was a linalool/(β)-cis-ocimene synthase and PbTPS4 a linalool synthase. In conclusion, both TPS-b and TPS-e/f enzymes orchestrated floral monoterpene biosynthesis in P. bellina.

Expression regulation of MALATE SYNTHASE involved in glyoxylate cycle during protocorm development in Phalaenopsis aphrodite (Orchidaceae)

Orchid (Orchidaceae) is one of the largest families in angiosperms and presents exceptional diversity in lifestyle. Their unique reproductive characteristics of orchid are attracted by scientist for centuries. One of the synapomorphies of orchid plants is that their seeds do not contain endosperm. Lipids are used as major energy storage in orchid seeds. However, regulation and mobilization of lipid usage during early seedling (protocorm) stage of orchid is not understood. In this study, we compared transcriptomes from developing Phalaenopsis aphrodite protocorms grown on 1/2-strength MS medium with sucrose. The expression of P. aphrodite MALATE SYNTHASE (PaMLS), involved in the glyoxylate cycle, was significantly decreased from 4 days after incubation (DAI) to 7 DAI. On real-time RT-PCR, both P. aphrodite ISOCITRATE LYASE (PaICL) and PaMLS were down-regulated during protocorm development and suppressed by sucrose treatment. In addition, several genes encoding transcription factors regulating PaMLS expression were identified. A gene encoding homeobox transcription factor (named PaHB5) was involved in positive regulation of PaMLS. This study showed that sucrose regulates the glyoxylate cycle during orchid protocorm development in asymbiotic germination and provides new insights into the transcription factors involved in the regulation of malate synthase expression.

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes

Background

Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol.

Results

Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis.

Conclusions

We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.

RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes

BACKGROUND

Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant.

RESULTS

In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage.

CONCLUSIONS

RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.