AtIPD: a curated database of Arabidopsis isoprenoid pathway models and genes for isoprenoid network analysis.

Department of Biology, Eidgenössisch Technische Hochschule Zurich, 8129 Zurich, Switzerland.
Plant physiology (Impact Factor: 6.56). 05/2011; 156(4):1655-60. DOI:10.1104/pp.111.177758
Source: PubMed

ABSTRACT Isoprenoid biosynthesis is one of the essential metabolic pathways in plants and other organisms. Despite the importance of isoprenoids for plant functions, not much is known about the regulation of isoprenoid synthesis. Quantitative technologies and systems approaches are now increasingly used to investigate the regulation of metabolic pathways and networks. Prerequisite for systems approaches is the knowledge of network elements and topologies. Information that can be extracted from the public metabolic pathway databases such as AraCyc and KEGG is often not sufficiently comprehensive and current. Therefore we have built a database of manually curated isoprenoid pathway models and genes, the Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; The database was compiled using information on pathways and pathway genes from BioPathAt (Lange and Ghassemian, 2003, 2005), KEGG (, AraCyc (, SUBA (, and from the literature. AtIPD can be searched or browsed to extract data and external links related to isoprenoid pathway models, enzyme activities or subcellular enzyme localizations. To display quantitative gene-related data on curated pathway models, we created image annotation and mapping files for integrated use with the MapMan tool ( Additionally, we built SBML XML files of the isoprenoid pathway images using the Cell DesignerTM tool ( Users can download all image and annotation files for customization, e.g., adding pathway structural and regulatory network elements or modifying pathway images to visualize other quantitative protein or metabolite data. AtIPD therefore represents a valuable resource for isoprenoid network analysis.

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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.
    Plant Molecular Biology 06/2013; · 3.52 Impact Factor
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    ABSTRACT: BACKGROUND: Carotenoids are a heterogeneous group of plant isoprenoids primarily involved inphotosynthesis. In plants the cleavage of carotenoids leads to the formation of thephytohormones abscisic acid and strigolactone, and C13-norisoprenoids involved in thecharacteristic flavour and aroma compounds in flowers and fruits and are of specificimportance in the varietal character of grapes and wine. This work extends the previousreports of carotenoid gene expression and photosynthetic pigment analysis by providing anup-to-date pathway analysis and an important framework for the analysis of carotenoidmetabolic pathways in grapevine. RESULTS: Comparative genomics was used to identify 42 genes putatively involved in carotenoidbiosynthesis/catabolism in grapevine. The genes are distributed on 16 of the 19 chromosomesand have been localised to the physical map of the heterozygous ENTAV115 grapevinesequence. Nine of the genes occur as single copies whereas the rest of the carotenoidbiosynthetic genes have more than one paralogue. The cDNA copies of eleven correspondinggenes from Vitis vinifera L. cv. Pinotage were characterised, and four where shown to befunctional. Microarrays provided expression profiles of 39 accessions in the metabolicpathway during three berry developmental stages in Sauvignon blanc, whereas an optimisedHPLC analysis provided the concentrations of individual carotenoids. This provides evidenceof the functioning of the lutein epoxide cycle and their respective genes in grapevine.Similarly, orthologues of genes leading to the formation of strigolactone involved in shootbranching inhibition were identified: CCD7, CCD8 and MAX1. Moreover, the isoformstypically have different expression patterns, confirming the complex regulation of thepathway. Of particular interest is the expression pattern of the three VvNCEDs: Our resultssupport previous findings that VvNCED3 is likely the isoform linked to ABA content inberries. CONCLUSIONS: The carotenoid biosynthetic pathway is well characterised, and the genes and enzymes havebeen studied in a number of plants. The study of the 42 carotenoid pathway genes ofgrapevine showed that they share a high degree of similarity with other eudicots. Expressionand pigment profiling of developing berries provided insights into the most completegrapevine carotenoid pathway representation. This study represents an important referencestudy for further characterisation of carotenoid biosynthesis and catabolism in grapevine.
    BMC Genomics 06/2012; 13(1):243. · 4.40 Impact Factor
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    ABSTRACT: Isoprenoid biosynthesis is essential for all living organisms, and isoprenoids are also of industrial and agricultural interest. All isoprenoids are derived from prenyl diphosphate (prenyl-PP) precursors. Unlike isoprenoid biosynthesis in other living organisms, prenyl-PP, as the precursor of all isoprenoids in plants, is synthesized by two independent pathways: the mevalonate (MVA) pathway in the cytoplasm and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in plastids. This review focuses on progress in our understanding of how the precursors for isoprenoid biosynthesis are synthesized in the two subcellular compartments, how the underlying pathway gene networks are organized and regulated, and how network perturbations impact each pathway and plant development. Because of the wealth of data on isoprenoid biosynthesis, we emphasize research in Arabidopsis thaliana and compare the synthesis of isoprenoid precursor molecules in this model plant with their synthesis in other prokaryotic and eukaryotic organisms. Expected final online publication date for the Annual Review of Plant Biology Volume 64 is April 29, 2013. Please see for revised estimates.
    Annual Review of Plant Biology 03/2013; · 18.71 Impact Factor


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