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• Most plastid isoprenoids, including photosynthesis-related metabolites such as carotenoids and the side chain of chlorophylls, tocopherols (vitamin E), phylloquinones (vitamin K), and plastoquinones, derive from geranylgeranyl diphosphate (GGPP) synthesized by GGPP synthase (GGPPS) enzymes. Seven out of 10 functional GGPPS isozymes in Arabidopsis thaliana reside in plastids. We aimed to address the function of different GGPPS paralogues for plastid isoprenoid biosynthesis. • We constructed a gene co-expression network (GCN) using GGPPS paralogues as guide genes and genes from the upstream and downstream pathways as query genes. Furthermore, knock-out and/or knock-down ggpps mutants were generated and their growth and metabolic phenotypes were analyzed. Also, interacting protein partners of GGPPS11 were searched for. • Our data showed that GGPPS11, encoding the only plastid isozyme essential for plant development, functions as a hub gene among GGPPS paralogues and is required for the production of all major groups of plastid isoprenoids. Furthermore, we showed that the GGPPS11 protein physically interacts with enzymes that use GGPP for the production of carotenoids, chlorophylls, tocopherols, phylloquinone, and plastoquinone. • GGPPS11 is a hub isozyme required for the production of most photosynthesis-related isoprenoids. Both gene co-expression and protein-protein interaction likely contribute to the channeling of GGPP by GGPPS11. [ABSTRACT FROM AUTHOR]

Isoprenyl diphosphate synthases (IDSs) catalyze some of the most basic steps in terpene biosynthesis by producing the prenyl diphosphate precursors of each of the various terpenoid classes. Most plants investigated have distinct enzymes that produce the short-chain all-trans (E) prenyl diphosphates geranyl diphosphate (GDP, C10), farnesyl diphosphate (FDP, C15) or geranylgeranyl diphosphate (GGDP, C20). In the genome of Arabidopsis thaliana, 15 trans-product-forming IDSs are present. Ten of these have recently been shown to produce GGDP by genetic complementation of a carotenoid pathway engineered into Escherichia coli. When verifying the product pattern of IDSs producing GGDP by a new LC-MS/MS procedure, we found that five of these IDSs produce geranylfarnesyl diphosphate (GFDP, C25) instead of GGDP as their major product in enzyme assays performed in vitro. Over-expression of one of the GFDP synthases in A. thaliana confirmed the production of GFDP in vivo. Enzyme assays with A. thaliana protein extracts from roots but not other organs showed formation of GFDP. Furthermore, GFDP itself was detected in root extracts. Subcellular localization studies in leaves indicated that four of the GFDP synthases were targeted to the plastoglobules of the chloroplast and one was targeted to the mitochondria. Sequence comparison and mutational studies showed that the size of the R group of the 5th amino acid residue N-terminal to the first aspartate-rich motif is responsible for C25 versus C20 product formation, with smaller R groups (Ala and Ser) resulting in GGDP (C20) as a product and a larger R group (Met) resulting in GFDP (C25). [ABSTRACT FROM AUTHOR]

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. A 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 (http://www.arabidopsis.org/biocyc) and Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg) often is not sufficiently comprehensive and current. Therefore, we built a database of manually curated isoprenoid pathway models and genes, the Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; http://www.atipd.ethz.ch). The database was compiled using information on pathways and pathway genes from BioPathAt (Lange and Ghassemian, 2003, 2005), KEGG, AraCyc, SUBA (http://suba.plantenergy.uwa.edu.au), and from the literature. AtlPD 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 (http://mapman.gabipd.org/web/guest/mapman). Additionally, we built SBML XML files of the isoprenoid pathway images using the Cell Designer tool (http://www.celldesigner.org). Users can download all image and annotation files for customization, such as adding pathway structural and regulatory network elements or modifying pathway images to visualize other quantitative protein or metabolite data. AtlPD therefore represents a valuable resource for isoprenoid network analysis. [ABSTRACT FROM AUTHOR]

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. A 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 (http://www.arabidopsis.org/biocyc) and Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg) often is not sufficiently comprehensive and current. Therefore, we built a database of manually curated isoprenoid pathway models and genes, the Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; http://www.atipd.ethz.ch). The database was compiled using information on pathways and pathway genes from BioPathAt (Lange and Ghassemian, 2003, 2005), KEGG, AraCyc, SUBA (http://suba.plantenergy.uwa.edu.au), and from the literature. AtlPD 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 (http://mapman.gabipd.org/web/guest/mapman). Additionally, we built SBML XML files of the isoprenoid pathway images using the Cell Designer tool (http://www.celldesigner.org). Users can download all image and annotation files for customization, such as adding pathway structural and regulatory network elements or modifying pathway images to visualize other quantitative protein or metabolite data. AtlPD therefore represents a valuable resource for isoprenoid network analysis. [ABSTRACT FROM AUTHOR]

The AKT3 potassium channel protein was identified as a strongly interacting partner of the Arabidopsis thaliana protein phosphatase 2C (AtPP2CA) in a yeast two-hybrid screen. A deletion analysis indicated that the catalytic domain of AtPP2CA was essential for the interaction with AKT3. Furthermore, the related PP2C phosphatase ABI1 did not interact with AKT3 in yeast. [ABSTRACT FROM AUTHOR]

Examines the effects of biological oxidative stress, heat shock and drought on the expression of Nicotiana tabacum protein phosphatase 2C. Down-regulation of expression; Percentage of amino acid identity in tobacco.

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.