title: De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer's properties.
abstract: BACKGROUND
  The major medicinal alkaloids isolated from Uncaria rhynchophylla (gouteng in chinese) capsules are rhynchophylline (RIN) and isorhynchophylline (IRN). Extracts containing these terpene indole alkaloids (TIAs) can inhibit the formation and destabilize preformed fibrils of amyloid β protein (a pathological marker of Alzheimer's disease), and have been shown to improve the cognitive function of mice with Alzheimer-like symptoms. The biosynthetic pathways of RIN and IRN are largely unknown.
  
  
  RESULTS
  In this study, RNA-sequencing of pooled Uncaria capsules RNA samples taken at three developmental stages that accumulate different amount of RIN and IRN was performed. More than 50 million high-quality reads from a cDNA library were generated and de novo assembled. Sequences for all of the known enzymes involved in TIAs synthesis were identified. Additionally, 193 cytochrome P450 (CYP450), 280 methyltransferase and 144 isomerase genes were identified, that are potential candidates for enzymes involved in RIN and IRN synthesis. Digital gene expression profile (DGE) analysis was performed on the three capsule developmental stages, and based on genes possessing expression profiles consistent with RIN and IRN levels; four CYP450s, three methyltransferases and three isomerases were identified as the candidates most likely to be involved in the later steps of RIN and IRN biosynthesis.
  
  
  CONCLUSIONS
  A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the capsule extract from Uncaria, and provides information that may aid in metabolic engineering to increase yields of these important alkaloids.
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Guo
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin 150030, China. xjma@public.bta.net.cn.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Ma
authors.forename: Shugen
authors.initials: S
authors.lastname: Wei
authors.forename: Deyou
authors.initials: D
authors.lastname: Qiu
authors.forename: Iain W
authors.initials: IW
authors.lastname: Wilson
authors.forename: Peng
authors.initials: P
authors.lastname: Wu
authors.forename: Qi
authors.initials: Q
authors.lastname: Tang
authors.forename: Lijun
authors.initials: L
authors.lastname: Liu
authors.forename: Shoukun
authors.initials: S
authors.lastname: Dong
authors.forename: Wei
authors.initials: W
authors.lastname: Zu
mesh_terms: D000544:Alzheimer Disease / Q000188:drug therapy*; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D026121:Indole Alkaloids / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D000078183:Oxindoles; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D032070:Uncaria / Q000235:genetics* / Q000378:metabolism*
chemical_list: D026121:Indole Alkaloids; D000078183:Oxindoles; C052714:rhyncophylline
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