1. Bienvenidos al PMN! Kate Dreher curator PMN/TAIR

2. PMN = The Plant Metabolic Network Created in 2008 Funded by the National Science Foundation What is the PMN? How can the PMN help researchers? How does the PMN grow? Introduction to the PMN Sue Rhee (PI) Peifen Zhang (Director)

3. Plants provide crucial benefits to the ecosystem and humanity A better understanding of plant metabolism may contribute to: More nutritious foods New medicines More pest-resistant plants Higher photosynthetic capacity and yield in crops Better biofuel feedstocks Improved industrial inputs (e.g. oils, fibers, etc.)... many more applications How can the PMN help? Why study plant metabolism?

4. More nutritious foods vitamin A biosynthesis, folate biosynthesis... Medicines morphine biosynthesis, taxol biosynthesis... More pest-resistant plants maackiain biosynthesis, capsidiol biosynthesis... Higher photosynthetic capacity and yield in crops chlorophyll biosynthesis, Calvin cycle... Better biofuel feedstocks cellulose biosynthesis, lignin biosynthesis... Many additional important applications ethylene biosynthesis, resveratrol biosynthesis... The PMN provides information about biochemical pathways related to...

5. What is the PMN? A Network of Plant Metabolic Pathway Databases and Communities Major goals: Create metabolic pathway databases to catalog all of the biochemical pathways present in specific species Create PlantCyc – a comprehensive metabolic pathway database that brings together data from diverse plants Create a pipeline to take new plant DNA sequence data and to predict the set of metabolic pathways present in diverse species Create a website to bring together researchers working on plant metabolism PMN website: www.plantcyc.orgwww.plantcyc.org

6. Pathway Enzyme Gene Reaction Compound Evidence Code Whats in the metabolic pathway databases in the PMN?

8. Pathway Enzyme Gene Reaction Compound Evidence Code

9. Whats in the metabolic pathway databases in the PMN? Compound: CDP-choline Synonyms Appears as Product Classification(s) Molecular Weight / Formula Appears as Reactant

10. Whats in the metabolic pathway databases in the PMN? Pathway Enzyme Gene Reaction Compound Evidence Code

11. Whats in the metabolic pathway databases in the PMN? Arabidopsis Enzyme: phosphatidyltransferase Multifunctional protein * *

12. Whats in the metabolic pathway databases in the PMN? Reaction Pathway(s) Summary References Inhibitors, Kinetic Parameters, etc. Arabidopsis Enzyme: phosphatidyltransferase

13. Whats in the metabolic pathway databases in the PMN? Pathway Enzyme Gene Reaction Compound Evidence Code To TAIR...

14. Whats in the metabolic pathway databases in the PMN? Contain detailed information about: Genes Enzymes Compounds Reactions Pathways Generated and displayed using Pathway Tools software Peter Karp, SRI International Include pathways generated through Manual curation when a curator reads scientific literature Computational predictions made by the Pathologic software

15. There are two types of databases in the PMN Single-species databases collections of pathways, enzymes, reactions, etc. for one species include metabolic pathway overview and data overlay tools AraCyc founding member of the PMN focuses on Arabidopsis thaliana first created in 2002

16. Single species databases in the PMN PGDBPlantHostStatus AraCycArabidopsisTAIR/PMNSubstantial curation PoplarCycPoplarTAIR/PMNComing soon... RiceCycRiceGrameneSome curation SorghumGrameneNo curation MedicCycMedicagoNoble Foundationsome curation LycoCycTomatoSGNsome curation PotatoSGNNo curation PepperSGNNo curation TobaccoSGNNo curation PetuniaSGNNo curation CoffeeSGNNo curation SoyCycSoybeanSoybaseComing next year...

17. Multi-species databases in the PMN Multi-species databases collections of pathways, enzymes, reactions, etc. for multiple species Vary by taxonomic range: Broad: PlantCyc Includes data from all the species found in the PMN Narrow PoplarCyc Initially this will be a single species database – Populus trichocarpa Later, enzymes from other Populus species will be added Vary by metabolic range: Broad PlantCyc Includes wide breadth of pathways and compounds from all metabolic domains Narrow BIACyc Only includes pathways and compounds related to a specific metabolic domain: benzyl isoquinoline alkaloids

18. How can researchers use the PMN? Learn background information about particular metabolic pathways Use enzymes present in the database to search for homologous enzymes in another species Predict papaya linalool synthases using Arabidopsis and Clarkia breweri linalool synthases in PlantCyc Analyze experimental data in a metabolic context Easily identify which metabolic pathways are most affected in response to a stress, in a particular mutant, etc. Create new metabolic pathway database to meet their research needs Create WheatCyc, PapayaCyc, etc.

19. More details about the PMN content...

20. What is the current size of the PMN? July 2009 Single species databases linked to the PMN: 11 AraCyc, RiceCyc, LycoCyc, et al Multi-species databases linked to the PMN: 1 PlantCyc 581 pathways 2501 reactions 8558 enzymes 1925 with experimental evidence 2464 compounds 250+ species 4971 references

21. What species are in the PMN? Over 250 species Vast majority are plant species Other species A few other photosynthetic organisms are included Synechocystis (cyanobacteria) A few fungal symbionts from lichen are included Alectoria, Cladonia, Evernia, Lecanora, Ramalina, Unsea

22. What metabolites are in the PMN? Over 2300 compounds Includes primary and secondary metabolites Focuses on small compounds

23. What metabolites are in the PMN? Primary metabolites (essential) sugars glucose, fructose,... amino acids tryptophan, glutamine,... lipids waxes, phosphatidylcholine,... vitamins A, E, K, C, thiamine, niacin,... hormones auxin, brassinosteroids, ethylene...

24. What metabolites are in the PMN? Secondary metabolites (important, but not essential) terpenoids orzyalexin, menthol,... organosulfur compounds glucosinolates, camalexin... isoflavonoids glyceollin, daidzein... alkaloids caffeine, capsaicin,... polyketides aloesone,... many more...

25. What metabolites are in the PMN? Focus on small molecule metabolism Small No strict standards Generally exclude: Macromolecules that are built using templates by huge, multi-subunit enzyme complexes Not in the PMN: chromosomes, proteins, mRNA transcripts... but the building blocks are included Nucleotides and amino acids are in the PMN In the PMN: cellulose and rubber

26. What enzymes are in the PMN? Enzymes that build or transport small metabolites Not in the PMN: DNA ligase, DNA polymerase DNA modifying enzymes DNA methytransferases Ribosomal proteins Protein modifying enzymes serine/threonine kinases, histone acetyltransferases In the PMN All other classes of enzymes that act on small metabolites

27. What enzymes are in the PMN? The majority of enzymes with experimental support come from a limited number of species Arabidopsis thaliana (~952) Glycine max (~75) Large computationally predicted enzyme sets have been brought into PlantCyc from three species: Medicago truncatula Oryza sativa Solanum lycopersicon New computationally predicted enzyme sets are on their way... Populus trichocarpa (coming soon!!!) Glycine max (many more due in 2010) and wed be happy to add your favorite species if youd like to help...

28. How will the PMN grow in the future? Manual curation New metabolic pathways are discovered Curators update multi- and/or single-species databases Enter new data Compound structures Enzymatic activity parameters Pathway diagram etc. Write summaries

29. How will the PMN grow in the future? Computational predictions New sets of DNA sequences become available Unigene builds are generated Genomes are sequenced Large EST data sets are created Set of DNA sequences -> set of predicted enzyme functions Performed using computer algorithms The PMN is working to develop better algorithms to increase the accuracy of the predictions Set of predicted enzyme functions -> set of predicted metabolic pathways The PathoLogic program uses a reference database to predict the metabolic pathways for the enzyme sets Set of predicted metabolic pathways -> set of validated metabolic pathways Curators remove incorrect information and add additional data

30. PathoLogic ANNOTATED GENOME Pv1234.56.a chorismate mutase prephenate aminotransferase arogenate dehydratase chorismateprephenateL-arogenateL-phenylalanine 5.4.99.5 2.6.1.79 4.2.1.91 Gene calls Gene functions DNA sequences Pv1234.56.a chorismate mutase PlantCyc / MetaCyc Single species database PhaseolusCyc Phaseolus vulgaris How will the PMN grow in the future? + validation

31. How will the PMN grow in the future? Increased participation!

32. Who uses the PMN?: June 4 – July 4, 2009

33. 1000 2010:

34. A few reasons to start using the PMN... Obtain reference information How is ________ synthesized in different organisms? I study a __________ enzyme; what pathway is it part of? My mutant has defective _______ synthesis What enzymes are involved in this metabolic pathway? What compounds are upstream and downstream of my target compound? What are the putative plant orthologs of the _______ enzyme? Visualize microarray, proteomic, and metabolomic data Use the OMICS viewer Quickly identify pathways that are up-regulated or down-regulated in response to stress, in a mutant, etc. Transcript changes following wounding

35. We are here to help: www.plantcyc.org Please use our data Please use our tools Please help us to improve our databases! Please contact us if we can be of any help! Make an appointment to meet with me during my visit (Puedo tratar de hablar en español) curator@plantcyc.org www.plantcyc.org

36. PMN Acknowledgements Current Curators: - A. S. Karthikeyan (curator) Recent Past Contributors: - Christophe Tissier (curator) - Hartmut Foerster (curator) Collaborators: - Peter Karp (SRI) - Ron Caspi (SRI) - SRI Tech Team - Lukas Mueller (SGN) - Anuradha Pujar (SGN) - Gramene and MedicCyc Peifen Zhang (Director) Sue Rhee (PI) Eva Huala (Co-PI) Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Administrator) - Raymond Chetty - Anjo Chi - Vanessa Kirkup - Cynthia Lee - Tom Meyer - Shanker Singh - Chris Wilks

37. We are here to help: www.plantcyc.org Please use our data Please use our tools Please help us to improve our databases! Please contact us if we can be of any help! Make an appointment to meet with me during my visit (Puedo tratar de hablar en español) curator@plantcyc.org www.plantcyc.org

38. How does the PMN grow? Validation improves predicted databases Remove incorrect pathways Create or import relevant pathways that were not predicted Add references, data, and evidence codes

39. Who are the communities in the PMN? Many groups can work together to build and improve the PMN Researchers Perform experiments and publish the results Directly provide data to the PMN Review new and existing pathways Bioinformaticians Develop better algorithms for predicting enzyme functions Software providers and Tech Team members Improve display Provide new tools for data visualization and analysis Enhance pathway prediction program Curators Mine scientific literature to enter metabolic data Interact with all other community groups to ensure the quality of the database Share data between different databases Teach researchers how to take advantage of the PMN Many researchers can use the PMN to assist their studies

40. How does the PMN grow? In the future... New single species databases are created New data can be imported into PlantCyc PlantCyc is expanded and improved Allows better predictions of future single-species databases The Cycle continues at the Plant Metabolic Network ¡Queremos su participación!