Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Abstract

BackgroundKalmegh (Andrographis paniculata) has been widely exploited in traditional medicine for the treatment of infectious diseases and health disorders. Ent-labdane-related diterpene (ent-LRD) specialized (i.e., secondary) metabolites of kalmegh such as andrographolide, neoandrographolide and 14-deoxy-11,12-didehydroandrographolide, are known for variety of pharmacological activities. However, due to the lack of genomic and transcriptomic information, underlying molecular basis of ent-LRDs biosynthesis has remained largely unknown. To identify candidate genes of the ent-LRD biosynthetic pathway, we performed comparative transcriptome analysis using leaf and root tissues that differentially accumulate ent-LRDs.ResultsDe novo assembly of Illumina HiSeq2000 platform-generated paired-end sequencing reads resulted into 69,011 leaf and 64,244 root transcripts which were assembled into a total of 84,628 unique transcripts. Annotation of these transcripts to the Uniprot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active Enzymes (CAZy) databases identified candidate transcripts of the ent-LRD biosynthetic pathway. These included transcripts that encode enzymes of the plastidial 2C-methyl-D-erythritol-4-phosphate pathway which provides C5 isoprenoid precursors for the ent-LRDs biosynthesis, geranylgeranyl diphosphate synthase, class II diterpene synthase (diTPS), cytochrome P450 monooxygenase and glycosyltransferase. Three class II diTPSs (ApCPS1, ApCPS2 and ApCPS3) that showed distinct tissue-specific expression profiles and are phylogenetically related to the dicotyledon ent-copalyl diphosphate synthases, are identified. ApCPS1, ApCPS2 and ApCPS3 encode for 832-, 817- and 797- amino acids proteins of 55–63 % identity, respectively. Spatio-temporal patterns of transcripts and ent-LRDs accumulation are consistent with the involvement of ApCPS1 in general (i.e., primary) metabolism for the biosynthesis of phytohormone gibberellin, ApCPS2 in leaf specialized ent-LRDs biosynthesis and ApCPS3 in root diterpene biosynthesis. Moreover, simple sequence repeats (SSRs) that might assist in genotyping and developing specific chemotypes were identified in transcripts of the specialized metabolic pathways, including ent-LRDs.ConclusionsComparative analysis of root and leaf transcriptomes disclosed novel genes of the ent-LRD biosynthetic pathway, including three class II diTPSs that showed discrete spatio-temporal expression patterns; thus, suggesting their participation into distinct diterpene metabolic pathways of kalmegh. Overall, these results will be useful in understanding molecular basis of the medicinal ent-LRDs biosynthesis and developing breeding strategies for improving their yields.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1864-y) contains supplementary material, which is available to authorized users.

The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide

“…From common backbones, diterpene scaffolds are often further modified to diterpenoids, prototypically by cytochrome P450 monooxygenases (CYPs), although 2‐oxoglutarate‐dependent dioxygenases (2OGDs) appear to play a role in certain cases as well (Swaminathan et al ., ; Wang et al ., 2012a; Kakizaki et al ., ; Xu and Song, ). Thus, although the biosynthesis of andrographolide and neoandrographolide is believed to rely on CYPs (Garg et al ., ; Cherukupalli et al ., ), 2OGDs may also play a role. In the A. paniculata genome, 278 CYP genes were found by automated matching to the relevant Hidden Markov Model (HMM), PF00067, with subsequent manual assignment to the appropriate CYP families (i.e.…”

De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids

“…Root-specific co-expression of CDPS and KS, key enzymes for the committed step towards biosynthesis of diterpene alkaloids, is consistent with previous reports on the accumulation of aconitine-type metabolites in the roots of A. carmichaelii . Several studies have reported that CDPS is involved in the tissue-specific accumulation of diterpene alkaloids [ 48 , 49 ]. Two CDPSs have been reported in rice to be localized differentially owing to their distinct biological role, with high expression in the vascular bundle tissues for GA biosynthesis (OsCPS1) and epidermal cells for the biosynthesis of phytoalexins (OsCPS2), respectively [ 50 ].…”

Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus

“…Since the last decade, different research groups have exploited these high throughput sequencing technology for better understanding of the molecular level information of various non model plant species such as Chickpea 17 , Cynara cardunculus 18 , lentil 19 , Centella asiatica 20 , Thlaspi arvense 21 , tomato 22 , Bupleurum chinens 23 , Cistus creticus 24 , Sesamum indicum L . 25 , Cucurbita pepo 26 , Camellia sinensis 27 , Camillia azalea 28 , Andrographis paniculata 29 , Asparagus racemosus 30 and many more. These studies provided us with much higher molecular level of information as compared to the past.…”

“…It is well documented that the leaf and sheath tissues of C. witerianus contains high amount of essential oils but root tissue lacks 31 32 . Biosynthesis and accumulation of secondary metabolite are often tissue-specific, and related genes of enzymes and regulators also show organ- or tissue-specific expression patterns 29 30 . Therefore, we hypothesized that DEG analysis between these two tissues will give a better understanding about the genes involve in secondary metabolite pathway and their regulation.…”