Advance in biosynthesis of terpenoid indole alkaloids and its regulation in Catharanthus roseus / 中国中药杂志

Catharanthus roseus can produce a variety of terpenoid indole alkaloids (TIA), most of which exhibit strong pharmacological activities. Hence, biosynthesis and regulation of TIA have received recent attention. 3α (S)-strictosidine is an important node in TIA biosynthesis, which is a condensation product of secologanin and tryptamine. The former is produced in iridoid pathway, and the latter is produced in indole pathway. Vindoline and catharanthine, which are produced respectively by 3α (S)-strictosidine via multi-step enzymatic reaction, can form α-3, 4-anhydrovinblastine by the condensation reaction. Then, vinblastine and vincristine are generated from α-3, 4-anhydrovinblastine. Many transcription factors are involved in the regulation of TIA synthesis, such as AP2/ERF and WRKY. Illumination of biosynthetic pathway has laid a foundation for the study of synthetic biology. Today, 3α (S)-strictosidine and vindoline have been synthesized in heterologous hosts Saccharomyces cerevisiae.Research about synthetic biology and the regulation mechanisms will provide a guidance for the production and development of TIA drugs in C. roseus.

Codon usage bias of Catharanthus roseus / 中国中药杂志

This study aimed to provide guidance for the heterogenous gene expression, gene prediction and species evolution by analyzing codon usage bias of Catharanthus roseus.The codon composition and usage bias of 30 437 high-confidence coding sequences from C.roseus were analyzed and the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 25 genes involved in the biosynthesis of terpenoid indole alkaloids (TIAs) in C.roseus were calculated.The results showed that the average GC content of the genes was 42.47%; the average GC content of the third bases in codon was 35.89%.The relative synonymous codon usage (RSCU) of 28 codons were greater than 1 and 26 of them ended with A or T.The above 25 genes involved in TIA biosynthesis contained much more rare condons of E.coli than that of S.cerevisiae.It was concluded that C.roseus mainly prefered the codons ending with A or T and the rule of codon usage was more different to E.coli than S.cerevisiae.Thus, S.cerevisiae may be more suitable host for heterologous expression of these genes.

Comparative studies on codon usage bias of Ganoderma lucidum based on analysis of genomic and transcriptomic data / 药学学报

Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain.

New technologies used for Panax genus research / 中国中药杂志

The authors reviewed the new technologies used for Panax genus research, including molecular identification technologies (especially for DNA barcoding), modern biotechnologies (e. g. the first generation and second generation sequencing technologies), and gene cloning and identification in this paper. These technologies have been successfully applied to species identification, transcriptome analysis, secondary metabolite biosynthetic pathway and the key enzyme function identification, indicating that the application of modern biotechnologies provide guarantee for the molecular identification of Panax genus. The application of modern biotechnologies also reveals the genetic information of transcriptome and functional genomics, and promotes the design of Panax plants genomic map. In summary, the application of the new technologies lay the foundation for clarifying the molecular mechanisms of ginsenoside biosynthesis and enforcing the in vitro synthesis of important natural products and new drugs in future.

Development of the devices for synthetic biology of triterpene saponins at an early stage: cloning and expression profiling of squalene epoxidase genes in panax notoginseng / 药学学报

Synthetic biology of traditional Chinese medicine (TCM) is a new and developing subject based on the research of secondary metabolite biosynthesis for nature products. The early development of synthetic biology focused on the screening and modification of parts or devices, and establishment of standardized device libraries. Panax notoginseng (Burk.) F.H.Chen is one of the most famous medicinal plants in Panax species. Triterpene saponins have important pharmacological activities in P. notoginseng. Squalene epoxidase (SE) has been considered as a key rate-limiting enzyme in biosynthetic pathways of triterpene saponins and phytosterols. SE acts as one of necessary devices for biosynthesis of triterpene saponins and phytosterols in vitro via synthetic biology approach. Here we cloned two genes encoding squalene epoxidase (PnSE1 and PnSE2) and analyzed the predict amino acid sequences by bioinformatic analysis. Further, we detected the gene expression profiling in different organs and the expression level of SEs in leaves elicited by methyl jasmonate (MeJA) treatment in 4-year-old P notoginseng using real-time quantitative PCR (real-time PCR). The study will provide a foundation for discovery and modification of devices in previous research by TCM synthetic biology. PnSE1 and PnSE2 encoded predicted proteins of 537 and 545 amino acids, respectively. Two amino acid sequences predicted from PnSEs shared strong similarity (79%), but were highly divergent in N-terminal regions (the first 70 amino acids). The genes expression profiling detected by real-time PCR, PnSE1 mRNA abundantly accumulated in all organs, especially in flower. PnSE2 was only weakly expressed and preferentially in flower. MeJA treatment enhanced the accumulation of PnSEI mRNA expression level in leaves, while there is no obvious enhancement of PnSE2 in same condition. Results indicated that the gene expressions of PnSE1 and PnSE2 were differently transcribed in four organs, and two PnSEs differently responded to MeJA stimuli. It was strongly suggested that PnSEs play different roles in secondary metabolite biosynthesis in P. notoginseng. PnSE1 might be involved in triterpenoid biosynthesis and PnSE2 might be involved in phytosterol biosynthesis.

Genomics and synthetic biology of traditional Chinese medicine / 药学学报

Traditional Chinese medicine (TCM) genomics and TCM synthetic biology are two hot fields in the TCM modernization. TCM genomics, including transcriptomics, structural genomics, genomic markers and functional genomics, aims to elucidate the biosynthetic pathways of TCM bioactive compounds and mine the related genes encoding enzymes involved in these pathways by analyzing genetic information on the original species of TCM, thus promoting the development of TCM synthetic biology, genome-assisted molecular identification and molecular breeding, and elucidation of the genetic mechanism underlying "Daodi". Genomics and related research provide us much deeper understanding of life process and improve our ability to create new life or modify the present organisms. Based on TCM genomics, TCM synthetic biology sets up a series of procedures to realize the production of TCM pharmacological active compounds in microorganism, including screening and modification of parts and devices, establishment of standardized part and device libraries, and reconstruction and modification of the biosynthetic pathway of TCM pharmacological active compounds in microorganism. TCM synthetic biology will provide a new resource of TCM pharmacological active compounds for the pharmacological study and research & development of new drugs, thus enhancing the core competitiveness of our pharmaceutical industry in the international markets.