Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence

Current insights into plant volatile organic compound biosynthesis

Plant-derived volatile organic compounds (VOCs) are essential for various ecological interactions, including plant communication, pollinator attraction, and defense against herbivores. Some VOCs are active ingredients with significant economic and medicinal value. For example, monoterpenoids such as linalool, geraniol, menthol, camphor, borneol, citral, and thymol are well-known for their flavor and aroma. Most monoterpenoids have a strong scent and physiological activity; some compounds, like thymoquinone, have excellent anti-cancer activities, making them important for pharmaceuticals and also beneficial in food and cosmetics. VOCs encompass a diverse range of chemical classes, such as terpenoids, benzenoids/phenylpropanoids, amino acid derivatives, and fatty acid-derived compounds. With the development of genomic, transcriptomic, and metabolomic techniques, significant progress has been made in the discovery of genes for the biosynthesis of VOCs. Herein, recent advances in the biosynthesis of plant-derived VOCs, focusing on two main classes: benzenoids/phenylpropanoids and monoterpenes, are discussed. It highlights the identification of a peroxisomal enzyme, benzaldehyde synthase, in petunia that elucidates the biosynthetic pathway of benzaldehyde, and a bifunctional enzyme, geranyl/farnesyl diphosphate synthase (RcG/FPPS1), in roses (Rosa chinensis "Old Blush") that contributes to the production of cytosolic geranyl diphosphate. Current understanding about canonical and non-canonical pathways for monoterpene formation and some approaches that are useful for gene discovery have been discussed. Open questions and future perspectives in this field have also been presented.

The chromosome-scale genomes of two Tinospora species reveal differential regulation of the MEP pathway in terpenoid biosynthesis

BACKGROUND

The relationship between gene family expansion and the resulting changes in plant phenotypes has shown remarkable complexity during the evolution. The gene family expansion has contributed to the diversity in plant phenotypes, specifically metabolites through neo-functionalization and sub-functionalization. However, the negative regulatory effects associated with the gene family expansion remain poorly understood.

RESULTS

Here, we present the chromosome-scale genomes of Tinospora crispa and Tinospora sinensis. Comparative genomic analyses demonstrated conserved chromosomal evolution within the Menispermaceae family. KEGG analysis revealed a significant enrichment of genes related to terpenoid biosynthesis in T. sinensis. However, T. crispa exhibited a higher abundance of terpenoids compared to T. sinensis. Detailed analysis revealed the expansion of genes encoding 1-hydroxy-2-methyl 2-(E)-butenyl 4-diphosphate synthase (HDS), a key enzyme in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway of terpenoid biosynthesis in T. sinensis. TsiHDS4 retained the ancestral function of converting methylerythritol cyclic diphosphate (MEcPP) to (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP). However, the noncanonical CDS-derived small peptide TsiHDS5 was shown to interact with TsiHDS4, inhibiting its catalytic activity. This interaction reduced the levels of HMBPP and isopentenyl pyrophosphate (IPP), which represent key substrates for downstream terpenoid biosynthesis.

CONCLUSIONS

These findings offer clues to decipher the variations in the MEP pathway of terpenoid biosynthesis between T. crispa and T. sinensis and form a basis for further detailed research on the negative regulation of expanded genes.

Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma

Evolutionary dynamics of inversion and its impact on biochemical traits are a puzzling question. Here, we show abundance of inversions in three Curcuma species (turmeric, hidden ginger and Siam tulip). Genes within inversions display higher long terminal repeat content and lower expression level compared with genomic background, suggesting inversions in Curcuma experience relaxed genetic constraints. It is corroborated by depletion of selected SNPs and enrichment of deleterious mutations in inversions detected among 56 Siam tulip cultivars. Functional verification of tandem duplicated terpene synthase (TPS) genes reveals that genes within inversions become pseudogenes, while genes outside retain catalytic function. Our findings suggest that inversions act as a counteracting force against tandem duplication in balancing birth and death of TPS genes and modulating terpenoid contents in Curcuma. This study provides an empirical example that inversions are likely not adaptive but affect biochemical traits.

Functional Characterization and Catalytic Activity Improvement of Borneol Acetyltransferase from Wurfbainia longiligularis

In plant secondary metabolite biosynthesis, acylation is a diverse physiological process, with BAHD acyltransferases playing an essential role. Borneol acetyltransferase (BAT) is an alcohol acetyltransferase, which catalyzes borneol and acetyl-CoA to synthesize bornyl acetate (BA). However, the enzymes involved in the biosynthesis of BA have so far only been characterized in Wurfbainia villosa, the studies on the WvBATs have only been conducted in vitro, and the catalytic activity was relatively low. In this research, three genes (WlBAT1, WlBAT2, and WlBAT3) have been identified to encode BATs that are capable of acetylating borneol to synthesize BA in vitro. We also determined that WlBAT1 has the highest catalytic efficiency for borneol-type substrates, including (+)-borneol, (-)-borneol, and isoborneol. Furthermore, we found that BATs could catalyze a wide range of substrate types in vitro, but in vivo, they exclusively catalyzed borneol-type substrates. Through molecular simulations and site-directed mutagenesis, it was revealed that residues D32, N36, H168, N297, N355, and H384 are crucial for the catalytic activity of WlBAT1, while the R382I-D385R double mutant of WlBAT1 exhibited an increasing acylation efficiency for borneol-type substrates in vitro and in vivo. These findings offer key genetic elements for the metabolic engineering of plants and synthetic biology to produce BA.

Comprehensive Analysis Reveals the Difference in Volatile Oil between Bupleurum marginatum var. stenophyllum (Wolff) Shan et Y. Li and the Other Four Medicinal Bupleurum Species

Volatile oil serves as a traditional antipyretic component of Bupleuri Radix. Bupleurum marginatum var. stenophyllum (Wolff) Shan et Y. Li belongs to the genus Bupleurum and is distinguished for its high level of saikosaponins and volatile oils; nonetheless, prevailing evidence remains inconclusive regarding its viability as an alternative resource of other official species. This study aims to systematically compare the volatile oil components of both dried and fresh roots of B. marginatum var. stenophyllum and the four legally available Bupleurum species across their chemical, molecular, bionics, and anatomical structures. A total of 962 compounds were determined via GC-MS from the dried roots; B. marginatum var. stenophyllum showed the greatest differences from other species in terms of hydrocarbons, esters, and ketones, which was consistent with the results of fresh roots and the e-nose analysis. A large number of DEGs were identified from the key enzyme family of the monoterpene synthesis pathway in B. marginatum var. stenophyllum via transcriptome analysis. The microscopic observation results, using different staining methods, further showed the distinctive high proportion of phloem in B. marginatum var. stenophyllum, the structure which produces volatile oils. Together, these pieces of evidence hold substantial significance in guiding the judicious development and utilization of Bupleurum genus resources.

Nudix hydrolase WvNUDX24 is involved in borneol biosynthesis in Wurfbainia villosa

Borneol, camphor, and bornyl acetate are highly promising monoterpenoids widely used in medicine, flavor, food, and chemical applications. Bornyl diphosphate (BPP) serves as a common precursor for the biosynthesis of these monoterpenoids. Although bornyl diphosphate synthase (BPPS) that catalyzes the cyclization of geranyl diphosphate (GPP) to BPP has been identified in multiple plants, the enzyme responsible for the hydrolysis of BPP to produce borneol has not been reported. Here, we conducted in vitro and in vivo functional characterization to identify the Nudix hydrolase WvNUDX24 from W. villosa, which specifically catalyzes the hydrolysis of BPP to generate bornyl phosphate (BP), and then BP forms borneol under the action of phosphatase. Subcellular localization experiments indicated that the hydrolysis of BPP likely occurs in the cytoplasm. Furthermore, site-directed mutagenesis experiments revealed that four critical residues (R84, S96, P98, and G99) for the hydrolysis activity of WvNUDX24. Additionally, the functional identification of phosphatidic acid phosphatase (PAP) demonstrated that WvPAP5 and WvPAP10 were able to hydrolyze geranylgeranyl diphosphate (GGPP) and farnesyl diphosphate (FPP) to generate geranylgeranyl phosphate (GGP) and farnesyl phosphate (FP), respectively, but could not hydrolyze BPP, GPP, and neryl diphosphate (NPP) to produce corresponding monophosphate products. These findings highlight the essential role of WvNUDX24 in the first step of BPP hydrolysis to produce borneol and provide genetic elements for the production of BPP-related terpenoids through plant metabolic engineering and synthetic biology.

Integrated transcriptomics and metabolomics analysis provides insights into aromatic volatiles formation in Cinnamomum cassia bark at different harvesting times

BACKGROUND

Cinnamomum cassia Presl, classified in the Lauraceae family, is widely used as a spice, but also in medicine, cosmetics, and food. Aroma is an important factor affecting the medicinal and flavoring properties of C. cassia, and is mainly determined by volatile organic compounds (VOCs); however, little is known about the composition of aromatic VOCs in C. cassia and their potential molecular regulatory mechanisms. Here, integrated transcriptomic and volatile metabolomic analyses were employed to provide insights into the formation regularity of aromatic VOCs in C. cassia bark at five different harvesting times.

RESULTS

The bark thickness and volatile oil content were significantly increased along with the development of the bark. A total of 724 differentially accumulated volatiles (DAVs) were identified in the bark samples, most of which were terpenoids. Venn analysis of the top 100 VOCs in each period showed that twenty-eight aromatic VOCs were significantly accumulated in different harvesting times. The most abundant VOC, cinnamaldehyde, peaked at 120 months after planting (MAP) and dominated the aroma qualities. Five terpenoids, α-copaene, β-bourbonene, α-cubebene, α-funebrene, and δ-cadinene, that peaked at 240 MAP could also be important in creating C. cassia's characteristic aroma. A list of 43,412 differentially expressed genes (DEGs) involved in the biosynthetic pathways of aromatic VOCs were identified, including phenylpropanoids, mevalonic acid (MVA) and methylerythritol phosphate (MEP). A gene-metabolite regulatory network for terpenoid and phenylpropanoid metabolism was constructed to show the key candidate structural genes and transcription factors involved in the biosynthesis of terpenoids and phenylpropanoids.

CONCLUSIONS

The results of our research revealed the composition and changes of aromatic VOCs in C. cassia bark at different harvesting stages, differentiated the characteristic aroma components of cinnamon, and illuminated the molecular mechanism of aroma formation. These foundational results will provide technical guidance for the quality breeding of C. cassia.