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Deciphering the Biosynthetic Pathways of Bioactive Compounds In Planta Using Omics Approaches

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Medicinal Plants - Recent Advances in Research and Development

Abstract

“Plant bioactive compounds” are secondary metabolites mainly composed of terpenoids, alkaloids, and phenolics that are observed to have varied pharmacological effects in preventing or intervening in human disorders. Due to the great potential of plant secondary metabolites for use in the nutraceutical and pharmaceutical industries, genetic engineering techniques and bioreactor approaches may be efficient ways to mass produce bioactive compounds for industrial use. However, before mass production strategies can be implemented to fulfill industrial needs, a full understanding of the biosynthetic pathways and underlying regulation mechanisms must be gained. The conventional “one enzyme, one gene” study approach is insufficient for elucidating the biosynthetic pathways of most bioactive compounds, especially those of non-model medicinal plants due to lack of available whole genome information. It is foreseen that the emerging “omics” technologies will be useful platforms to provide more global genomics, transcriptomics, proteomics, and metabolomics information to help uncover the biosynthesis pathways of secondary metabolites, especially in medicinal plants. The aim of this review is to summarize the current research progress and knowledge in deciphering the biosynthesis pathways of plant bioactive secondary metabolites selected from the three major compound types using omics approaches.

*Author contributed equally with all other contributors.

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Abbreviations

3′OMT:

3′-O-Methyltransferase

4′OMT:

3′-Hydroxyl-N-methylcoclaurine 4′-O-methyltransferase

6OMT:

Norcoclaurine 6-O-methyltransferase

7DLGT:

7-Deoxyloganetic acid glucosyltransferase

8HGO:

8-Hydroxygeraniol oxidoreductase

16OMT:

O-Methyltransferase

β-AS:

β-Amyrin synthase

ANR:

Anthocyanidin reductase

ANS:

Anthocyanidin synthase

AVLBS:

Anhydrovinblastine synthase

BBE:

Berberine bridge enzyme

BIA:

Benzylisoquinoline alkaloid

BIS1:

bHLH iridoid synthase 1

CHI:

Chalcone isomerase

CHS:

Chalcone synthase

CNMT:

Coclaurine N-methyltransferase

CODM:

Codeine O-demethylase

COR:

Codeinone reductase

CPP:

Copalyl diphosphate

CPR:

Cytochrome P450 reductase

CPS:

Copalyl diphosphate synthase

CYP:

Cytochrome P450

CYP82:

N-Methylcanadine 1-hydroxylase

D4H:

Desacetoxyvindoline-4-hydroxylase

DAT:

Deacetylvindoline-4-O-acetyltransferase

DDS:

Dammarenediol synthase

DFR:

Dihydroflavonol reductase

DL7H:

7-Deoxyloganic acid 7-hydroxylase

DMAPP:

Dimethylallyl diphosphate

DXS:

1-Deoxy-D-xylulose-5-phosphate synthase

EST:

Expressed sequence tag

F3′5′H:

Flavonoid 3′,5′-hydroxylase

F3′H:

Flavonoid 3′-hydroxylase

FLS:

Flavone synthase

FPP:

Farnesyl diphosphate

FPKM:

Fragments per kilobase of transcript per million mapped reads

FPPS:

Farnesyl diphosphate synthase

G8O:

Geraniol-8-oxidase

G10H:

Geranyl 10-hydroxylase

GGPP:

Geranylgeranyl diphosphate

GGPPS:

GGPP synthase

GT:

Glycosyltransferase

IFS:

Isoflavone synthase

IO:

Iridoid oxidase

IPP:

Isopentenyl diphosphate

IPPI:

IPP isomerase

IS:

Iridoid synthase

JA:

Jasmonic acid

KSL:

Kaurene synthase-like diphosphate synthase

LAMT:

Loganic acid methyltransferase

LAR:

Leucocyanidin 4-reductase

LDOX:

Leucocyanidin dioxygenase

MEP:

2-C-Methyl-D-erythritol 4-phosphate

MeJA:

Methyl jasmonate

MVA:

Mevalonate

N7OMT:

Norreticuline 7-O-methyltransferase

NCS:

Norcoclaurine synthase

NGS:

Next generation sequencing

NMCH:

(S)-N-methylcoclaurine 3′-hydroxylase

NMT:

N-Methyltransferase

OAS:

Oleanolic acid synthase

ORCA3:

Octadecanoid-responsive Catharanthus APETALA2-domain 3

P5βR:

Progesterone-5β-reductase

PPD:

Protopanaxadiol

PPDS:

Protopanaxadiol synthase

PPT:

Protopanaxatriol

PPTS:

Protopanaxatriol synthase

RPKM:

Reads per kilobase per million mapped reads

SM:

Secondary metabolite

SalAT:

Salutaridinol 7-O-acetyltransferase

SalR:

Salutaridine reductase

SalSyn:

Salutaridine synthase

SE:

Squalene epoxidase

SGD:

Strictosidine β-D-glucosidase

SLS:

Secologanin synthase

SQ:

Squalene

SS:

Squalene synthase

STOX:

(S)-Tetrahydroprotoberberine oxidase

STR:

Strictosidine synthase

STS:

Stilbene synthase

T16H:

Tabersonine 16-hydroxylase

T6ODM:

Thebaine 6-O-demethylase

TDC:

Tryptophan decarboxylase

THAS:

Tetrahydroalstonine synthase

TF:

Transcription factors

TIA:

Terpenoid indole alkaloid

TNMT:

Tetrahydroprotoberberine N-methyltransferase

TPS:

Terpene synthases

UGT:

UDP-dependent glycosyltransferase

VIGS:

Virus-induced gene silencing

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    Authors and Affiliations

    1. Department of Horticulture, National Ilan University, Yilan, 26047, Taiwan

      Hsiao-Hang Chung

    2. Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan

      Yi-Chang Sung & Lie-Fen Shyur

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    1. Hsiao-Hang Chung
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    3. Lie-Fen Shyur
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    Correspondence to Lie-Fen Shyur .

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    1. Department of Applied Chemistry, Chaoyang University of Technology, Taichung, Taiwan

      Hsin-Sheng Tsay

    2. Agricultural Biotechnology Research Center, Taipei, Taiwan

      Lie-Fen Shyur

    3. Department of Applied Chemistry, Chaoyang University of Technology, Taichung, Taiwan

      Dinesh Chandra Agrawal

    4. School of Pharmacy and Chinese Herbal Medicine Research Center, China Medical University, Taichung, Taiwan

      Yang-Chang Wu

    5. College of Agriculture and Natural Resources, Department of Forestry, National Chung Hsing University, Taichung, Taiwan

      Sheng-Yang Wang

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    Chung, HH., Sung, YC., Shyur, LF. (2016). Deciphering the Biosynthetic Pathways of Bioactive Compounds In Planta Using Omics Approaches. In: Tsay, HS., Shyur, LF., Agrawal, D., Wu, YC., Wang, SY. (eds) Medicinal Plants - Recent Advances in Research and Development. Springer, Singapore. https://doi.org/10.1007/978-981-10-1085-9_5

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