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Structural and biochemical perspectives in plant isoprenoid biosynthesis

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Abstract

The isoprenoid family represents one of the most ancient and widespread classes of structurally and functionally rich biomolecules known to man. Although these natural products are synthesized in all organisms, the plant kingdom exhibits tremendous variation in their chemistry and roles, ranging from primary metabolism to secondary metabolism and specialized ecological interactions with the environment. Despite enormous diversity in structure and function, all isoprenoids are derived from the universal C5 precursor isoprene. The isoprenoid biosynthetic pathway has three major stages, viz., (1) synthesis of the isoprene building blocks, followed by their (2) assembly into flexible linear and branched hydrocarbon substrates, which then undergo (3) multistep reaction cascades to generate the vast assortment of isoprenoid end products. One of the most interesting aspects of isoprenoid biosynthesis is its being finely tuned by a multilayered and complex regulatory network, which excellently controls the machinery producing one of the most heterogeneous groups of molecules in plants. Terpene synthases, enzymes of the final stage, are key players in the generation of isoprenoid diversity, catalyzing one of the most complex reactions known to chemistry and biology. Unraveling the mechanism by which a minimal pool of substrates is thus converted into tens of thousands of regiospecific and stereospecific products, is a promising research avenue: This knowledge may be practically used for rational design of novel compounds by metabolic engineering, in order to yield plants with improved nutritional efficacy, stress resistance, bio-pharmaceutical properties etc. This review is an attempt to summarize the biochemical, molecular, physiological, structural, genomic and evolutionary aspects of isoprenoid biosynthesis, providing new insights into how these enzymes utilize various innovative strategies for creation of the so-called final terpenome.

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Abbreviations

3-D:

Three-dimensional

AACT:

Acetoacetyl-coenzyme A thiolase

Ac-CoA:

Acetyl-coenzyme A

AcAc-CoA:

Acetoacetyl-coenzyme A

ABA:

Abscisic acid

ADP:

Adenosine diphosphate

ATP:

Adenosine triphosphate

CCN:

Cloud condensation nuclei

CDP-ME:

4-Diphosphocytidyl-2C-methyl-d-erythritol

CDP-MEP:

4-Diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate

CMK:

4-Diphosphocytidyl-2C-methyl-d-erythritol kinase

CDP:

Cytidine diphosphate

CLR:

Cavity lining residues

CMC:

Cambial meristematic cells

CMP:

Cytidine monophosphate

CPS:

ent-copalyl diphosphate synthase

CTP:

Cytidine triphosphate

DDC:

Dedifferentiated cells

DMAPP:

Dimethylallyl diphosphate

DOXP:

Deoxyxylulose phosphate

DX:

1-Deoxy-d-xylulose

DXP:

1-Deoxy-d-xylulose 5-phosphate

DXR:

1-Deoxy-d-xylulose 5-phosphate reducto-isomerase

DXS:

1-Deoxy-d-xylulose 5-phosphate synthase

EAS:

epi-aristolochene synthase

ER:

Endoplasmic reticulum

FPPS:

Farnesyl pyrophosphate synthase

FPP:

Farnesyl diphosphate

G6P:

Glucose 6-phosphate

GA:

Gibberellic acids

GAP:

D-glyceraldehyde 3-phosphate

GGPPS:

Geranylgeranyl pyrophosphate synthase

GHMP:

Galacto-homoserine-mevalonate-phosphomevalonate

GPP:

Geranyl diphosphate

GGPP:

Geranylgeranyl diphosphate

GUS:

β-Glucuronidase

HDR:

1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase

HDS:

1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase

HGT:

Horizontal gene transfer

HMBPP:

1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate

HMG-CoA:

3-Hydroxy-3-methylglutaryl coenzyme A

HMGR:

3-Hydroxy-3-methylglutaryl coenzyme A reductase

HMGS:

3-Hydroxy-3-methylglutaryl coenzyme A synthase

HR:

Hypersensitive response

IDI:

Isopentenyl-diphosphate isomerase

IPP:

Isopentenyl diphosphate

KO:

Knock-out

LDL:

Low density lipoproteins

LGT:

Lateral gene transfer

MDS:

2C-Methyl-d-erythritol 2,4-cyclodiphosphate synthase

LSU:

Large subunit

MCT:

2C-Methyl-d-erythritol 4-phosphate cytidyltransferase

ME:

2C-Methyl-d-erythritol

ME-cPP:

2C-Methyl-d-erythritol 2,4-cyclodiphosphate

MEP:

2C-Methyl-d-erythritol 4-phosphate

MVA:

Mevalonic acid/mevalonate

MK:

Mevalonate kinase

MVADP:

Mevalonate 5-diphosphate

NADPH:

Reduced nicotinamide adenine dinucleotide phosphate

NGF:

Nerve growth factor

NMP:

Nucleoside monophosphate

PDB:

Protein data bank

PDP:

Prenyl diphosphates

PPMD:

Diphospho-mevalonate decarboxylase

PMK:

Phospho-mevalonate kinase

PPi:

Pyrophosphate leaving group

PT:

Prenyl transferases

RCSB:

Research collaboratory for structural bioinformatics

RMSD:

Root mean square deviation

SSU:

Small subunit

THC:

Tetra hydro cannabinol

TPS:

Terpene synthase

UDS:

Undecaprenyl pyrophosphate synthase

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Acknowledgments

Authors’ thanks are due to Director NIPGR for encouragement, the Innovative Young Biotechnologist Award (IYBA) grant to GY for financial support, the Biotechnology Information System Network (BTISNET) program of Department of Biotechnology (DBT), Govt of India, for computational resources, the Council of Scientific and Industrial Research (CSIR) for Senior Research Fellowship (SRF) to SK and PP, the DBT for SRF to GM, and finally, to the anonymous reviewer for his thorough review, which significantly contributed to improving this work.

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  1. Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India

    Sangita Kumari, Piyush Priya, Gopal Misra & Gitanjali Yadav

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  1. Sangita Kumari
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  2. Piyush Priya
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Correspondence to Gitanjali Yadav.

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Sangita Kumari and Piyush Priya contributed equally to this work.

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Kumari, S., Priya, P., Misra, G. et al. Structural and biochemical perspectives in plant isoprenoid biosynthesis. Phytochem Rev 12, 255–291 (2013). https://doi.org/10.1007/s11101-013-9284-6

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