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Characterization of the GGPP synthase gene family in Arabidopsis thaliana

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Abstract

Geranylgeranyl diphosphate (GGPP) is a key precursor of various isoprenoids that have diverse functions in plant metabolism and development. The annotation of the Arabidopsis thaliana genome predicts 12 genes to encode geranylgeranyl diphosphate synthases (GGPPS). In this study we analyzed GGPPS activity as well as the subcellular localization and tissue-specific expression of the entire protein family in A. thaliana. GGPPS2 (At2g18620), GGPPS3 (At2g18640), GGPPS6 (At3g14530), GGPPS7 (At3g14550), GGPPS8 (At3g20160), GGPPS9 (At3g29430), GGPPS10 (At3g32040) and GGPPS11 (At4g36810) showed GGPPS activity in Escherichia coli, similar to activities reported earlier for GGPPS1 (At1g49530) and GGPPS4 (At2g23800) (Zhu et al. in Plant Cell Physiol 38(3):357–361, 1997a; Plant Mol Biol 35(3):331–341, b). GGPPS12 (At4g38460) did not produce GGPP in E. coli. Based on DNA sequence analysis we propose that GGPPS5 (At3g14510) is a pseudogene. GGPPS–GFP (green fluorescent protein) fusion proteins of the ten functional GGPP synthases localized to plastids, mitochondria and the endoplasmic reticulum, with the majority of the enzymes located in plastids. Gene expression analysis using quantitative real time-PCR, GGPPS promoter-GUS (β-glucuronidase) assays and publicly available microarray data revealed a differential spatio-temporal expression of GGPPS genes. The results suggest that plastids and mitochondria are key subcellular compartments for the synthesis of ubiquitous GGPP-derived isoprenoid species. GGPPS11 and GGPPS1 are the major isozymes responsible for their biosynthesis. All remaining paralogs, encoding six plastidial isozymes and two cytosolic isozymes, were expressed in specific tissues and/or at specific developmental stages, suggesting their role in developmentally regulated isoprenoid biosynthesis. Our results show that of the 12 predicted GGPPS encoded in the A. thaliana genome 10 are functional proteins that can synthesize GGPP. Their specific subcellular location and differential expression pattern suggest subfunctionalization in providing GGPP to specific tissues, developmental stages, or metabolic pathways.

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Abbreviations

ABA:

Abscisic acid

DMAPP:

Dimethylallyl diphosphate

ER:

Endoplasmic reticulum

FPP:

Farnesyl diphosphate

GA:

Gibberellic acid

GFP:

Green fluorescent protein

GGPP:

Geranylgeranyl diphosphate

GGPPS:

Geranylgeranyl diphosphate synthase

GPP:

Geranyl diphosphate

GUS:

β-Glucuronidase

IPP:

Isopentenyl diphosphate

MEP:

Methylerythritol

MVA:

Mevalonate

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Acknowledgments

This work was supported by a grant from ETH Zurich (TH-51 06-1) and the EU FP7 contract 245143 (TiMet). The Spanish Ministerio de Ciencia e Innovacion (www.micinn.es) provided grants BIO2008-00432 and BIO2011-23680 to MRC and a doctoral FPI fellowship to ARS. We thank Biswapriya Biswavas Misra and Christian Barucker for their contribution to the work on subcellular localization. We thank Dr. Axel Schmidt for useful discussions on enzymatic activity assays.

Conflict of interest

The authors declare that they have no competing interests.

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  1. Eva Vranová

    Present address: Faculty of Science, Institute of Biology and Ecology, P. J. Šafárik University Košice, Mánesova 23, 041 54, Košice, Slovakia

Authors and Affiliations

  1. Department of Biology, Plant Biotechnology, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland

    Gilles Beck, Diana Coman, Edgar Herren, Wilhelm Gruissem & Eva Vranová

  2. Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193, Barcelona, Spain

    M. Águila Ruiz-Sola & Manuel Rodríguez-Concepción

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Correspondence to Eva Vranová.

Additional information

The gene ID numbers of the GGPPS characterized in this study are: GGPPS1 (GGPPS6 in Zhu et al. 1997b; Okada et al. 2000) is At1g49530; GGPPS2 is At2g18620; GGPPS3 (GGPPS4 in Okada et al. 2000) is At2g18640; GGPPS4 (GGPPS5 in Zhu et al. 1997a; GGPPS2 in Okada et al. 2000) is At2g23800; GGPPS5 is At3g14510; GGPPS6 is At3g14530; GGPPS7 (GGPPS3 in Okada et al. 2000) is At3g14550; GGPPS8 is At3g20160; GGPPS9 is At3g29430; GGPPS10 is At3g32040; GGPPS11 (GGPPS1 in Okada et al. 2000) is At4g36810; GGPPS12 (GGR in Okada et al. 2000) is At4g38640.

Gilles Beck, Diana Coman contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Table S1 as PDF Oligonucleotides used for GGPPSs amplification to construct pGEX-GGPPS (PDF 231 kb)

11103_2013_70_MOESM2_ESM.pdf

Supplemental Table S2 as PDF Oligonucleotides used for GGPPSs amplification to construct pENTR/D-TOPO-GGPPS-3` (PDF 235 kb)

Supplemental Table S3 as PDF Oligonucleotides used for RT-qPCR (PDF 248 kb)

11103_2013_70_MOESM4_ESM.pdf

Supplemental Table S4 as PDF Oligonucleotides used for GGPPSs promoter amplification to construct pENTR-D-TOPO-GGPPSpro (PDF 34 kb)

Supplemental Table S5 as PDF RT-qPCR and microarray expression of GGPPSs in seven Arabidopsis organs (PDF 2710 kb)

Supplemental Table S6 as PDF Microarray tissue-specific expression of the GGPPS genes (PDF 1986 kb)

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Beck, G., Coman, D., Herren, E. et al. Characterization of the GGPP synthase gene family in Arabidopsis thaliana . Plant Mol Biol 82, 393–416 (2013). https://doi.org/10.1007/s11103-013-0070-z

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