Genome-Wide Identification and Functional Characterization of the Trans-Isopentenyl Diphosphate Synthases Gene Family in Cinnamomum camphora

Abstract

Trans-isopentenyl diphosphate synthases (TIDSs) genes are known to be important determinants for terpene diversity and the accumulation of terpenoids. The essential oil of Cinnamomum camphora, which is rich in monoterpenes, sesquiterpenes, and other aromatic compounds, has a wide range of pharmacological activities and has therefore attracted considerable interest. However, the TIDS gene family, and its relationship to the camphor tree (C. camphora L. Presl.), has not yet been characterized. In this study, we identified 10 TIDS genes in the genome of the C. camphora borneol chemotype that were unevenly distributed on chromosomes. Synteny analysis revealed that the TIDS gene family in this species likely expanded through segmental duplication events. Furthermore, cis-element analyses demonstrated that C. camphora TIDS (CcTIDS) genes can respond to multiple abiotic stresses. Finally, functional characterization of eight putative short-chain TIDS proteins revealed that CcTIDS3 and CcTIDS9 exhibit farnesyl diphosphate synthase (FPPS) activity, while CcTIDS1 and CcTIDS2 encode geranylgeranyl diphosphate synthases (GGPPS). Although, CcTIDS8 and CcTIDS10 were found to be catalytically inactive alone, they were able to bind to each other to form a heterodimeric functional geranyl diphosphate synthase (GPPS) in vitro, and this interaction was confirmed using a yeast two-hybrid assay. Furthermore, transcriptome analysis revealed that the CcTIDS3, CcTIDS8, CcTIDS9, and CcTIDS10 genes were found to be more active in C. camphora roots as compared to stems and leaves, which were verified by quantitative real-time PCR (qRT-PCR). These novel results provide a foundation for further exploration of the role of the TIDS gene family in camphor trees, and also provide a potential mechanism by which the production of camphor tree essential oil could be increased for pharmacological purposes through metabolic engineering.

Effect of Developmental Stages on Genes Involved in Middle and Downstream Pathway of Volatile Terpene Biosynthesis in Rose Petals

“…chinensis is less than those reported in Arabidopsis thaliana (16), tomato (10), Cinnamomum camphora (10), and Oryza sativa (12), and more than or equal to that in Chlamydomonas reinhardtii (4) and Physcomitrella patens (7) ( Table S5 ) [ 25 , 28 , 58 ]. Unlike the TPT gene family in Cinnamomum camphora (Lauraceae) that has segmentally duplicated TPT genes [ 28 ], no such TPT genes were observed in the genome of R . chinensis , which may be due to that R. chinensis exhibited only the core eudicot-specific gamma whole-genome triplication with no recent polyploidization [ 59 ].…”

“…In total, 26 TPT protein sequences of Arabidopsis thaliana and tomato ( Solanum lycopersicum ) ( Table S1 ) were used as a query for BLASTP search with default parameters. A Hidden Markov Model (HMM) search were also conducted by using polyprenyl synthase domain (PF00348) [ 28 ], with an E-value < 0.001. The BLASTP and HMM search results were integrated to identify candidate TPT genes.…”

Full-length transcriptome sequencing reveals the molecular mechanism of monoterpene and sesquiterpene biosynthesis in Cinnamomum burmannii

“…The sequence alignment comprises the sequences of seven TPS genes reported earlier (CbTPS1-S7 in Ma et al, 2021) and those mentioned by Yang et al, 2020 (see Supplementary_data18, DOI: 10.7717/peerj.9311/supp-18). Besides, the sequences of the IDS genes were also aligned, as mentioned by Yang et al, 2021 (See Supplementary Table S3). We performed multiple alignments for the IDS and TPS genes of C. burmannii using MUSCLE (version 3.8.31) (Edgar 2004).…”

“…Typically, isopentenyl-diphosphate isomerases (IDI) isomerize IPP to DMAPP, which together produce geranyl diphosphate (GPP) and farnesyl diphosphate (FPP), the precursors of monoterpenoids. So far, six trans-IDI genes of C. camphora have been characterized (Yang et al, 2021), while those of C. burmannii remain ignored. Subsequent steps in the biosynthesis of monoterpenes and sesquiterpenes involve the action of terpene synthases (TPS), which have been reported in C. burmannii (Yang et al, 2020;Li et al, 2022;Ma et al, 2022), C. camphora (Zuo et al, 2017;Chen et al, 2018;Hou et al, 2020;Tian et al, 2021), C. kanehirae (Chaw et al, 2019), C. osmophloeum (Lin et al, 2014), C. porrectum (Qiu et al, 2019), and C. ternuipilum (Yang et al, 2005).…”

Advances in Biosynthesis and Pharmacological Effects of Cinnamomum camphora (L.) Presl Essential Oil

“…Moreover, with the rapid development of genomics, transcriptomics, proteomics and metabolomics, omics technologies have been applied to the study of the biosynthesis of CCEO. Moreover, the genes encoding the key enzymes in the biosynthesis of CCEO have been successfully isolated and cloned, and the protein structures, functions and mechanisms of more and more key enzymes have been studied [8][9][10][11][12]. These works lay a theoretical foundation for further research on the biosynthesis of CCEO.…”