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: 6.84). 05/2011; 156(4):1655-60. DOI: 10.1104/pp.111.177758
Source: PubMed


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.

Download full-text


Available from: Eva Vranová
  • Source
    • "Then, prenyl diphosphate synthases catalyze chain elongation reactions by coupling IPP to DMAPP producing allylic prenyl diphosphates of different length (Vranová et al., 2013). Most of the essential plant isoprenoids are derived from the C15 and C20 allylic prenyl diphosphates farnesyl-PP (FPP) and geranylgeranyl-PP (GGPP), whose pools represent nodes of the major metabolic branch points in the isoprenoid synthesis (Vranová et al., 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate (GGPP) exist in plants. GGPP is produced in the isoprenoid pathway and is a central precursor for various primary and specialized plant metabolites. Therefore, its biosynthesis is an essential regulatory point in the isoprenoid pathway. We selected 119 GGPPSs from 48 species representing all major plant lineages, based on stringent homology criteria. After the diversification of land plants, the number of GGPPS paralogs per species increases. Already in the moss Physcomitrella patens, GGPPS appears to be encoded by multiple paralogous genes. In gymnosperms, neofunctionalization of GGPPS may have enabled optimized biosynthesis of primary and specialized metabolites. Notably, lineage-specific expansion of GGPPS occurred in land plants. As a representative species we focused here on Arabidopsis thaliana, which retained the highest number of GGPPS paralogs (twelve) among the 48 species we considered in this study. Our results show that the A. thaliana GGPPS gene family is an example of evolution involving neo- and subfunctionalization as well as pseudogenization. We propose subfunctionalization as one of the main mechanisms allowing the maintenance of multiple GGPPS paralogs in A. thaliana genome. Accordingly, the changes in the expression patterns of the GGPPS paralogs occurring after gene duplication led to developmental and/or condition specific functional evolution.
    Full-text · Article · May 2014 · Frontiers in Plant Science
  • Source
    • "Expression of the remaining paralogs, which encode six plastid and two cytosolic isozymes, was Fig. 1 Subcellular compartmentalization of isoprenoid biosynthesis in A. thaliana. Based on the pathway network constructed by Vranová et al. (2011). Enzymes are shown in grey and isoprenoids in black. "
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Jun 2013 · Plant Molecular Biology
  • Source
    • "Forty two V. vinifera putative carotenoid metabolic gene orthologues were identified by in silico screening of the PLAZA [4,5] grapevine database using the Arabidopsis sequences obtained from AtIPD [16]. A multiple alignment was created using the 42 Vitis sequences and the corresponding Arabidopsis orthologues and a maximum likelihood method [17] used to generate a bootstrapped molecular phylogenetic tree (Figure 1). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Carotenoids are a heterogeneous group of plant isoprenoids primarily involved in photosynthesis. In plants the cleavage of carotenoids leads to the formation of the phytohormones abscisic acid and strigolactone, and C13-norisoprenoids involved in the characteristic flavour and aroma compounds in flowers and fruits and are of specific importance in the varietal character of grapes and wine. This work extends the previous reports of carotenoid gene expression and photosynthetic pigment analysis by providing an up-to-date pathway analysis and an important framework for the analysis of carotenoid metabolic pathways in grapevine. Results Comparative genomics was used to identify 42 genes putatively involved in carotenoid biosynthesis/catabolism in grapevine. The genes are distributed on 16 of the 19 chromosomes and have been localised to the physical map of the heterozygous ENTAV115 grapevine sequence. Nine of the genes occur as single copies whereas the rest of the carotenoid metabolic genes have more than one paralogue. The cDNA copies of eleven corresponding genes from Vitis vinifera L. cv. Pinotage were characterised, and four where shown to be functional. Microarrays provided expression profiles of 39 accessions in the metabolic pathway during three berry developmental stages in Sauvignon blanc, whereas an optimised HPLC analysis provided the concentrations of individual carotenoids. This provides evidence of the functioning of the lutein epoxide cycle and the respective genes in grapevine. Similarly, orthologues of genes leading to the formation of strigolactone involved in shoot branching inhibition were identified: CCD7, CCD8 and MAX1. Moreover, the isoforms typically have different expression patterns, confirming the complex regulation of the pathway. Of particular interest is the expression pattern of the three VvNCEDs: Our results support previous findings that VvNCED3 is likely the isoform linked to ABA content in berries. Conclusions The carotenoid metabolic pathway is well characterised, and the genes and enzymes have been studied in a number of plants. The study of the 42 carotenoid pathway genes of grapevine showed that they share a high degree of similarity with other eudicots. Expression and pigment profiling of developing berries provided insights into the most complete grapevine carotenoid pathway representation. This study represents an important reference study for further characterisation of carotenoid biosynthesis and catabolism in grapevine.
    Full-text · Article · Jun 2012 · BMC Genomics
Show more