Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpa

Nag, Ambarish; Karpinets, Tatiana V.; Chang, Christopher H.; Bar-Peled, Maor

doi:10.1093/database/bas013

Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpa

Journal Article · Sun Jan 01 04:00:00 EST 2012 · Database: The Journal of Biological Databases and Curation

DOI:https://doi.org/10.1093/database/bas013· OSTI ID:1044473

Nag, Ambarish; Karpinets, Tatiana V.; Chang, Christopher H.; Bar-Peled, Maor

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).

Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science, BioEnergy Science Center; National Science Foundation

DOE Contract Number:: AC36-08GO28308

OSTI ID:: 1044473

Report Number(s):: NREL/JA-2C00-55001

Journal Information:: Database: The Journal of Biological Databases and Curation, Journal Name: Database: The Journal of Biological Databases and Curation Journal Issue: 2012 Vol. 2012

Country of Publication:: United States

Language:: English

References (30)

From genomics to chemical genomics: new developments in KEGG Kanehisa, M. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj102	journal	January 2006
Predotar: A tool for rapidly screening proteomes forN-terminal targeting sequences Small, Ian; Peeters, Nemo; Legeai, Fabrice PROTEOMICS, Vol. 4, Issue 6 https://doi.org/10.1002/pmic.200300776	journal	June 2004
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins Guda, C.; Fahy, E.; Subramaniam, S. Bioinformatics, Vol. 20, Issue 11 https://doi.org/10.1093/bioinformatics/bth171	journal	March 2004
WoLF PSORT: protein localization predictor Horton, P.; Park, K. -J.; Obayashi, T. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm259	journal	May 2007
Functional UDP-xylose Transport across the Endoplasmic Reticulum/Golgi Membrane in a Chinese Hamster Ovary Cell Mutant Defective in UDP-xylose Synthase Bakker, Hans; Oka, Takuji; Ashikov, Angel Journal of Biological Chemistry, Vol. 284, Issue 4 https://doi.org/10.1074/jbc.M804394200	journal	November 2008
Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges: ANALYTICAL APPROACHES Helyar, S. J.; Hemmer-Hansen, J.; Bekkevold, D. Molecular Ecology Resources, Vol. 11 https://doi.org/10.1111/j.1755-0998.2010.02943.x	journal	January 2011
Identification of Galacturonic Acid-1-phosphate Kinase, a New Member of the GHMP Kinase Superfamily in Plants, and Comparison with Galactose-1-phosphate Kinase Yang, Ting; Bar-Peled, Liron; Gebhart, Lindsay Journal of Biological Chemistry, Vol. 284, Issue 32 https://doi.org/10.1074/jbc.M109.014761	journal	June 2009
AraCyc: A Biochemical Pathway Database for Arabidopsis Mueller, Lukas A.; Zhang, Peifen; Rhee, Seung Y. Plant Physiology, Vol. 132, Issue 2 https://doi.org/10.1104/pp.102.017236	journal	June 2003
Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants Zhang, Peifen; Dreher, Kate; Karthikeyan, A. Plant Physiology, Vol. 153, Issue 4 https://doi.org/10.1104/pp.110.157396	journal	June 2010
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction Blum, Torsten; Briesemeister, Sebastian; Kohlbacher, Oliver BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-274	journal	September 2009
Biosynthesis of UDP-xylose: characterization of membrane-bound AtUxs2 Pattathil, Sivakumar; Harper, April D.; Bar-Peled, Maor Planta, Vol. 221, Issue 4 https://doi.org/10.1007/s00425-004-1471-7	journal	January 2005
Support vector machine approach for protein subcellular localization prediction Hua, S.; Sun, Z. Bioinformatics, Vol. 17, Issue 8 https://doi.org/10.1093/bioinformatics/17.8.721	journal	August 2001
Multiple reference genomes and transcriptomes for Arabidopsis thaliana Gan, Xiangchao; Stegle, Oliver; Behr, Jonas Nature, Vol. 477, Issue 7365 https://doi.org/10.1038/nature10414	journal	August 2011
SNP discovery in black cottonwood ( Populus trichocarpa ) by population transcriptome resequencing : SNP DISCOVERY: NEXT GENERATION SEQUENCING Geraldes, Armando; Pang, Johnson; Thiessen, Nina Molecular Ecology Resources, Vol. 11 https://doi.org/10.1111/j.1755-0998.2010.02960.x	journal	February 2011
Aldo (and Keto) Hexoses and Uronic Acids Feingold, D. S. Plant Carbohydrates I https://doi.org/10.1007/978-3-642-68275-9_1	book	January 1982
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
The structure, function, and biosynthesis of plant cell wall pectic polysaccharides Caffall, Kerry Hosmer; Mohnen, Debra Carbohydrate Research, Vol. 344, Issue 14 https://doi.org/10.1016/j.carres.2009.05.021	journal	September 2009
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n -peptide compositions Yu, Chin-Sheng; Lin, Chih-Jen; Hwang, Jenn-Kang Protein Science, Vol. 13, Issue 5 https://doi.org/10.1110/ps.03479604	journal	May 2004
Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside Seifert, Georg J. Current Opinion in Plant Biology, Vol. 7, Issue 3 https://doi.org/10.1016/j.pbi.2004.03.004	journal	June 2004
Biosynthesis and functions of the plant sulfolipid Shimojima, Mie Progress in Lipid Research, Vol. 50, Issue 3 https://doi.org/10.1016/j.plipres.2011.02.003	journal	July 2011
INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence: GENOME SCANS AND ADAPTIVE POPULATION DIVERGENCE Storz, Jay F. Molecular Ecology, Vol. 14, Issue 3 https://doi.org/10.1111/j.1365-294X.2005.02437.x	journal	January 2005
The Pathway Tools software Karp, P. D.; Paley, S.; Romero, P. Bioinformatics, Vol. 18, Issue Suppl 1 https://doi.org/10.1093/bioinformatics/18.suppl_1.S225	journal	July 2002
Production of Complex Multiantennary N -Glycans in Nicotiana benthamiana Plants Nagels, Bieke; Van Damme, Els J. M.; Pabst, Martin Plant Physiology, Vol. 155, Issue 3 https://doi.org/10.1104/pp.110.168773	journal	January 2011
Plant Nucleotide Sugar Formation, Interconversion, and Salvage by Sugar Recycling* Bar-Peled, Maor; O'Neill, Malcolm A. Annual Review of Plant Biology, Vol. 62, Issue 1 https://doi.org/10.1146/annurev-arplant-042110-103918	journal	June 2011
Enzymatic Synthesis and Purification of [3H]Uridine Diphosphate Galacturonic Acid for Use in Studying Golgi-Localized Transporters Orellana, Ariel; Mohnen, Debra Analytical Biochemistry, Vol. 272, Issue 2 https://doi.org/10.1006/abio.1999.4159	journal	August 1999
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis Ostlund, G.; Schmitt, T.; Forslund, K. Nucleic Acids Research, Vol. 38, Issue Database https://doi.org/10.1093/nar/gkp931	journal	November 2009
Prediction of protein subcellular localization Yu, Chin-Sheng; Chen, Yu-Ching; Lu, Chih-Hao Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 3 https://doi.org/10.1002/prot.21018	journal	June 2006
KEGG for representation and analysis of molecular networks involving diseases and drugs Kanehisa, Minoru; Goto, Susumu; Furumichi, Miho Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp896	journal	October 2009
Biosynthesis of UDP-Xylose. Cloning and Characterization of a Novel Arabidopsis Gene Family, UXS , Encoding Soluble and Putative Membrane-Bound UDP-Glucuronic Acid Decarboxylase Isoforms Harper, April D.; Bar-Peled, Maor Plant Physiology, Vol. 130, Issue 4 https://doi.org/10.1104/pp.009654	journal	December 2002
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology Karp, P. D.; Paley, S. M.; Krummenacker, M. Briefings in Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1093/bib/bbp043	journal	December 2009

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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

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