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Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.

Nag A, Karpinets TV, Chang CH, Bar-Peled M - Database (Oxford) (2012)

Bottom Line: In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa.The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB.The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s).

View Article: PubMed Central - PubMed

Affiliation: Computational Sciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA.

ABSTRACT
Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES.

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UDP-d-xylose biosynthesis pathway representation in PoplarCyc 1.0. Note that the pathway does not distinguish cytosolic reaction with EC # 4.1.1.35 from the corresponding reaction catalyzed by membrane-bound and Golgi-localized enzymes.
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bas013-F2: UDP-d-xylose biosynthesis pathway representation in PoplarCyc 1.0. Note that the pathway does not distinguish cytosolic reaction with EC # 4.1.1.35 from the corresponding reaction catalyzed by membrane-bound and Golgi-localized enzymes.

Mentions: Current experimental knowledge (6,8,27) indicates that UDP-d-xylose is synthesized from UDP-d-glucuronate in at least two separate compartments in A. thaliana, the cytosol and the Golgi lumen, as represented schematically in Figure 1. UDP-d-glucuronate is synthesized in the cytosol from UDP-d-glucose and NADH by the catalytic action of UDP-glucose 6-dehydrogenase. Any of the three cytosolic UDP-xylose synthase isozymes, AtUXS3, AtUXS5, AtUXS6, can catalyze the conversion of UDP-d-glucuronate to UDP-d-xylose in the cytosol (8). The UDP-d-glucuronate can also be transported to Golgi by a transporter (28) that is yet to be identified. In the Golgi apparatus, type II membrane-bound UDP-d-xylose synthase enzymes with catalytic portions facing the Golgi lumen (27) can convert UDP-d-glucuronate to UDP-d-xylose as represented schematically in Figure 1. However, as shown in Figure 2, the pathway representation of the same UDP-d-xylose biosynthesis pathway in the existing PoplarCyc 1.0 PGDB does not provide any information on (i) the sub-cellular localization of the metabolites that participate in the reactions constituting the pathway, (ii) the sub-cellular localization of the enzymes in the pathway and (iii) the orientation of the catalytic domains of the enzymes. For example, an enzyme bound to the Golgi membrane can have its catalytic domain in the cytosol or in the Golgi lumen. The graphical pathway representation in Figure 2 is incapable of showing the difference between these two orientations. The inability to display sub-cellular localization of metabolites in pathway diagrams by the existing Pathway Tools framework stems from the fact that in the current framework, sub-cellular localization information is displayed in the graphical representation of a complete pathway for only transport reactions in the pathway, even though such localization information can be associated with metabolites participating in any reaction. Also, the Pathway Tools framework can incorporate sub-cellular localization information about any enzyme or transporter by allowing the association of one or multiple Cellular Component Gene Ontology terms with the corresponding protein frame. However, this information is not directly evident in the representation of any pathway involving the protein as an enzyme or transporter.Figure 2.


Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.

Nag A, Karpinets TV, Chang CH, Bar-Peled M - Database (Oxford) (2012)

UDP-d-xylose biosynthesis pathway representation in PoplarCyc 1.0. Note that the pathway does not distinguish cytosolic reaction with EC # 4.1.1.35 from the corresponding reaction catalyzed by membrane-bound and Golgi-localized enzymes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3316911&req=5

bas013-F2: UDP-d-xylose biosynthesis pathway representation in PoplarCyc 1.0. Note that the pathway does not distinguish cytosolic reaction with EC # 4.1.1.35 from the corresponding reaction catalyzed by membrane-bound and Golgi-localized enzymes.
Mentions: Current experimental knowledge (6,8,27) indicates that UDP-d-xylose is synthesized from UDP-d-glucuronate in at least two separate compartments in A. thaliana, the cytosol and the Golgi lumen, as represented schematically in Figure 1. UDP-d-glucuronate is synthesized in the cytosol from UDP-d-glucose and NADH by the catalytic action of UDP-glucose 6-dehydrogenase. Any of the three cytosolic UDP-xylose synthase isozymes, AtUXS3, AtUXS5, AtUXS6, can catalyze the conversion of UDP-d-glucuronate to UDP-d-xylose in the cytosol (8). The UDP-d-glucuronate can also be transported to Golgi by a transporter (28) that is yet to be identified. In the Golgi apparatus, type II membrane-bound UDP-d-xylose synthase enzymes with catalytic portions facing the Golgi lumen (27) can convert UDP-d-glucuronate to UDP-d-xylose as represented schematically in Figure 1. However, as shown in Figure 2, the pathway representation of the same UDP-d-xylose biosynthesis pathway in the existing PoplarCyc 1.0 PGDB does not provide any information on (i) the sub-cellular localization of the metabolites that participate in the reactions constituting the pathway, (ii) the sub-cellular localization of the enzymes in the pathway and (iii) the orientation of the catalytic domains of the enzymes. For example, an enzyme bound to the Golgi membrane can have its catalytic domain in the cytosol or in the Golgi lumen. The graphical pathway representation in Figure 2 is incapable of showing the difference between these two orientations. The inability to display sub-cellular localization of metabolites in pathway diagrams by the existing Pathway Tools framework stems from the fact that in the current framework, sub-cellular localization information is displayed in the graphical representation of a complete pathway for only transport reactions in the pathway, even though such localization information can be associated with metabolites participating in any reaction. Also, the Pathway Tools framework can incorporate sub-cellular localization information about any enzyme or transporter by allowing the association of one or multiple Cellular Component Gene Ontology terms with the corresponding protein frame. However, this information is not directly evident in the representation of any pathway involving the protein as an enzyme or transporter.Figure 2.

Bottom Line: In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa.The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB.The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s).

View Article: PubMed Central - PubMed

Affiliation: Computational Sciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA.

ABSTRACT
Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES.

Show MeSH