Biomolecules, Vol. 12, Pages 1790: Profiles of Metabolic Genes in Uncaria rhynchophylla and Characterization of the Critical Enzyme Involved in the Biosynthesis of Bioactive Compounds-(iso)Rhynchophylline

Conceptualisation, R.L. and B.Y.; methodology, M.Y. and R.L.; software, M.Y. and R.L.; validation, M.Y., B.Y. and R.L.; formal analysis M.Y. and R.L.; investigation, M.Y. and R.L.; resources, M.Y.; data curation, M.Y. and R.L.; writing—original draft preparation, M.Y.; writing—review and editing, M.Y.; visualisation, B.Y. and R.L.; supervision, R.L. and B.Y.; project administration, M.Y. and B.Y.; funding acquisition, B.Y. All authors have read and agreed to the published version of the manuscript.

Figure 1. Proposed biosynthetic pathway of rhynchophylline and isorhynchophylline. (A) Metabolites and enzymes involved in the indole alkaloids biosynthetic pathway in U. rhynchophylla. (B) The homologs (P450 and FMO) for spiro-indole alkaloids formation in microbial natural product biosynthesis.

Figure 1. Proposed biosynthetic pathway of rhynchophylline and isorhynchophylline. (A) Metabolites and enzymes involved in the indole alkaloids biosynthetic pathway in U. rhynchophylla. (B) The homologs (P450 and FMO) for spiro-indole alkaloids formation in microbial natural product biosynthesis.

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Figure 2. Specific indole alkaloids in U. rhynchophylla and LC-MS spectrum for indole alkaloids. Structures for rhynchophylline, corynoxeine and 3α-dihydrocadambine are shown in black, and their isomers (isorhynchophylline, isocorynoxeine, and 3β-dihydrocadambine) are shown in blue.

Figure 2. Specific indole alkaloids in U. rhynchophylla and LC-MS spectrum for indole alkaloids. Structures for rhynchophylline, corynoxeine and 3α-dihydrocadambine are shown in black, and their isomers (isorhynchophylline, isocorynoxeine, and 3β-dihydrocadambine) are shown in blue.

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Figure 3. (A) the distribution of unigene length. (B) unigenes annotation by public databases. (C) Veen diagram of unigene annotation. (D) distribution of annotated species.

Figure 3. (A) the distribution of unigene length. (B) unigenes annotation by public databases. (C) Veen diagram of unigene annotation. (D) distribution of annotated species.

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Figure 4. KEGG pathway annotation. (A) cellular processes; (B) environmental information processing; (C) genetic information processing; (D) metabolism; and (E) organismal systems.

Figure 4. KEGG pathway annotation. (A) cellular processes; (B) environmental information processing; (C) genetic information processing; (D) metabolism; and (E) organismal systems.

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Figure 5. Histogram of GO classifications. Upper: biological process; Lower: cellular component and molecular function.

Figure 5. Histogram of GO classifications. Upper: biological process; Lower: cellular component and molecular function.

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Figure 6. Transcription Factor (TF) were predicted into 80 subgroups, and the histogram showed the abundance of the top 15 subgroups.

Figure 6. Transcription Factor (TF) were predicted into 80 subgroups, and the histogram showed the abundance of the top 15 subgroups.

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Figure 7. (A) tryptamine and analogues were proposed to be accepted by UrSTR for strictosidine and analogue formation. (B) biochemical characterization of UrSTR in vitro. (i) with tryptamine, (ii) with N-methyltryptamine and (iii) with N-dimethyltryptamine. (C) phylogenetic tree of STRs from indole alkaloids producing plants.

Figure 7. (A) tryptamine and analogues were proposed to be accepted by UrSTR for strictosidine and analogue formation. (B) biochemical characterization of UrSTR in vitro. (i) with tryptamine, (ii) with N-methyltryptamine and (iii) with N-dimethyltryptamine. (C) phylogenetic tree of STRs from indole alkaloids producing plants.

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Figure 8. Docking results for tryptamine and analogues. (A) the structure of UrSTR in wheat and RsSTR in pale green and tryptamine in the active pocket. (B) the distance between the substrate (tryptamine, N-methyltryptamine and N,N-dimethyltryptamine) and the catalytic residue Glu309 (E309).

Figure 8. Docking results for tryptamine and analogues. (A) the structure of UrSTR in wheat and RsSTR in pale green and tryptamine in the active pocket. (B) the distance between the substrate (tryptamine, N-methyltryptamine and N,N-dimethyltryptamine) and the catalytic residue Glu309 (E309).

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Figure 9. Candidate CYP450s and FMOs involved in spiroindole alkaloids. Phylogenetic analysis of CYP450s (A) and FMOs (B). (C) the co-expression analysis of candidate CYP450s and FMOs.

Figure 9. Candidate CYP450s and FMOs involved in spiroindole alkaloids. Phylogenetic analysis of CYP450s (A) and FMOs (B). (C) the co-expression analysis of candidate CYP450s and FMOs.

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Table 1. Overview of the sequencing and assembly of transcriptome of U. rhynchophylla.

Table 1. Overview of the sequencing and assembly of transcriptome of U. rhynchophylla.

ItemsRAW READSClean ReadsClean BasesLeaf71,187,46269,670,55010.45 GStem Bark56,685,48055,496,1548.32 GRoot55,949,24054,721,6308.21 GBud57,681,41456,408,8608.46 GTotal data241,503,596236,297,19435.44 GUnigenes ≥ 500 bp311,204N50 (bp)2887

Table 2. Summary of unigenes’ annotations of U. rhynchophylla.

Table 2. Summary of unigenes’ annotations of U. rhynchophylla.

Number of UnigenesPercentage (%)Annotated in NR137,09383.18Annotated in NT102,05761.92Annotated in KO59,28935.97Annotated in SwissProt109,51966.45Annotated in PFAM102,23162.02Annotated in GO102,23162.02Annotated in KOG43,52126.4Annotated in Total141,74786

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