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Plant Metabolic Network
PMN Project OverviewPMN: Plant Metabolic Network
The central goal of the Plant Metabolic Network (PMN) is to bring together biochemical pathway databases and research communities focused on plant metabolism.
PMN, first made public in June 2008, draws upon the work of many individuals with expertise in annotating genomes, generating metabolic pathway databases, curating biochemical information from the literature, and forming extensive network of collaborations with biological databases and biochemistry researchers.
Global Vision and MissionAs the worldwide demand for production of food, animal feed, biofuels, industrial inputs, and new medicines continues to grow, there is an increasingly urgent need to develop new technologies using plants. The long-term goal of developing these technologies has prompted the sequencing of plant genomes and gene complements. There is a growing need to place the sequenced and annotated genomes in a biochemical context in order to facilitate discovery of enzymes and engineering of metabolism. PMN will generate an infrastructure for drawing together diverse sources of plant metabolism information.
PlantCycAt the center of the PMN is PlantCyc, a database containing pathways and their catalytic enzymes and genes, as well as compounds from many plant species. The majority of pathway diagrams in PlantCyc were manually extracted from the plant literature. They are either supported by experimental evidence or are based on expert hypotheses. A small portion of the pathways were computationally predicted. These pathways are known to exist in other non-plant organisms, but have not been found in plants. However, some hints indicate that plants may utilize the same pathway or similar routes. Both experimentally-verified and computationally-predicted enzymes and genes are assigned to pathways. Evidence codes are attached to pathways and to the assignments of genes/enzymes to provide information about data quality.
In addition to new pathways curated in-house, the first release of PlantCyc also contains all pathways from AraCyc, all plant pathways from MetaCyc, and a number of curated pathways from other plant pathway databases including RiceCyc and MedicCyc. We also integrated computational assignments of enzymes and genes from other plant pathway databases including AraCyc, RiceCyc, MedicCyc, and SolCyc. Thus, PlantCyc brings together information about over 800 pathways in more than 300 plant species (See Database Statistics). The content of PlantCyc is expected to grow rapidly as more plant genomes are sequenced and annotated and new biochemical data are published. Curated plant pathway data from MetaCyc and other resources will be continuously added to augment the in-house data. Semi-annual releases will be made to provide the most up-to-date information to the public.
Species-specific Metabolic Pathway DatabasesPMN will generate metabolic pathway databases for a number of other plant organisms. Our choices were based on criteria including the available number of genome/EST sequences, the utility and agronomical value of the individual species, as well as taxonomic interest. The new databases will include, but are not limited to, wheat, sugarcane, moss, and papaya. To build each database, putative enzyme sequences will first be identified for each organism using our in-house-developed annotation methods. The Pathway Tools software will then be used in the initial pathway prediction using PlantCyc and MetaCyc as reference databases. The predicted pathways and enzymes will be further curated with literature information. It is a daunting task. We thus ask for contributions from the plant research community. An entire new database may be adopted for curation and maintenance. Please contact us if your group is interested.
Curation and Community CollaborationThe Plant Metabolic Network aims to foster cooperation and sharing of resources and expertise among many different members of the research community. PMN will rely heavily on the work of curators at the PMN, but will also depend upon contributions from the curation teams at other databases interested in different species. Currently we are collaborating with MetaCyc, MaizeGDB, SolCyc, RiceCyc, and MedicCyc for data exchange. Biochemistry experts on the PMN Editorial Board will review the pathways related to their field of expertise. Moreover, all other researchers who are interested in specific domains of metabolism are encouraged to provide new data, feedback, suggestions, and corrections to improve the content of PlantCyc and the other species-specific databases. Plus, scientists can contribute information directly to curators at major scientific meetings and during fun-filled curatorial jamborees. In addition, PMN members work closely with the Bioinformatics Research Group at SRI International. This group provides the Pathway Tools software that is used to predict, display, and search the PMN databases and other related metabolic pathway databases.
Enhancing Metabolic Research EffortsMetabolic databases built from this project will address the need of the scientific community to analyze and display the growing body of data that is emerging from both conventional biochemistry and high-throughput/large-scale data experiments. The proposed network of databases will facilitate the discovery of new enzymes and pathways, and the engineering of metabolic pathways. In addition, researchers studying individual genes and mutants will be able to put their findings in the context of overall metabolic scheme of an organism, thereby deepening their understanding of the roles played by their genes of interest.
PMN and EducationThe Plant Metabolic Network of databases will not only facilitate research, but also provide an up-to-date, easily accessible set of teaching and educational resources for students. In addition to providing biochemical reaction diagrams, organism-specific metabolic maps, detailed descriptions of enzymes and pathways, and links to other resources, the PMN website will house tutorials to help guide teachers and students as they learn more about the valuable bioinformatic data and analysis tools that are crucial elements of modern biological research.
PMN SupportThe PMN is supported by the National Science Foundation (Grant #: 1026003 and 0640769), as well as by the Department of Energy (BER Grant #: ER65472 ). The PMN is based at the Department of Plant Biology at the Carnegie Institution for Science
Editorial Board
The Plant Metabolic Network editorial board is an international assemblage of some of the world-class experts and leaders in varied domains of plant primary and secondary metabolism.
Our board provides overall vision and guidance to the PMN project and plays an active role in ensuring the high quality of the information present in the PMN.
More specifically, editors may review curated pathways for their accuracy and coverage before they are published online, either directly or via solicitation to other experts. They may also identify missing pathways and enzymes and inform curators of literature references to be used for curating new pathways or updating existing pathways.
Primary Metabolism
Amines and Polyamines
Markus Piotrowski - Ruhr University Bochum, Germany
Amino Acids
Thomas Leustek - Rutgers University, USA
Carbohydrates
Maor Bar-Peled - Complex Carbohydrate Research Center, University of Georgia, USA
Cofactors, Prostethic Groups, and Electron Carriers
Tadhg Begley - Texas A&M University, USA
Dean Dellapenna - Michigan State University, USA
Nick Smirnoff - University of Exeter, UK
Alison Smith - University of Cambridge, UK
Takashi Hashimoto - Nara Institute of Science and Technology, Japan
Fatty Acids and Lipids
Ed Cahoon - University of Nebraska-Lincoln, USA
Jan Jaworski - Donald Danforth Plant Science Center, USA
Basil Nikolau - Iowa State University, USA
Ruth Welti - Kansas State University, USA
Hormones and Regulators
Sue Abrams - National Research Council-Plant Biotechnology Institute, Canada
Jerry Cohen - University of Minnesota, USA
Mary Wildermuth - University of California, Berkeley, USA
Nucleosides and Nucleotides
Rita Zrenner - Max Planck Institute of Molecular Plant Physiology, Germany
Secondary Metabolism
Alkaloids
Peter Facchini - University of Calgary, Canada
Flavonoids
Erich Grotewold - Ohio State University, USA
Lloyd Sumner - The Samuel Roberts Noble Foundation, USA
Brenda Winkel - Virginia Tech, USA
Oliver Yu - Donald Danforth Plant Science Center, USA
Phenylpropanoids
Clint Chapple - Purdue University, USA
David Gang - University of Arizona, USA
Plant Volatiles
Eran Pichersky - University of Michigan, USA
Terpenoids
Jonathan Page - National Research Council-Plant Biotechnology Institute, Canada
Mark Lange - Washington State University, USA
Transporters
Wolf Frommer - Carnegie Institution for Science, USA
We are grateful to these distinguished individuals for their contributions!
Emeriti board members
In Memoriam - Joachim Schroeder - University of Freiburg, Germany
We thank Dr. Schroeder for his advice on polyketides. He passed away in March of 2011.
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