bienvenidos al pmn! kate dreher curator pmn/tair
TRANSCRIPT
Bienvenidos al PMN!
Kate Dreher
curator
PMN/TAIR
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)
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?
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. . .
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.org
Pathway
EnzymeGene
ReactionCompound
Evidence Code
What’s in the metabolic pathway databases in the PMN?
What’s in the metabolic pathway databases in the PMN?
What’s in the metabolic pathway databases in the PMN?
Pathway
EnzymeGene
ReactionCompound
Evidence Code
What’s in the metabolic pathway databases in the PMN?
Compound: CDP-choline
Synonyms
Appears as Product
Classification(s)
Molecular Weight / Formula
Appears as Reactant
What’s in the metabolic pathway databases in the PMN?
Pathway
EnzymeGene
ReactionCompound
Evidence Code
What’s in the metabolic pathway databases in the PMN?
Arabidopsis Enzyme: phosphatidyltransferase
Multifunctional protein
**
What’s in the metabolic pathway databases in the PMN?
Reaction
Pathway(s)
Summary
References
Inhibitors, Kinetic Parameters, etc.
Arabidopsis Enzyme: phosphatidyltransferase
What’s in the metabolic pathway databases in the PMN?
Pathway
EnzymeGene
ReactionCompound
Evidence Code
To TAIR . . .
What’s 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
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
Single species databases in the PMN
PGDB Plant Host Status
AraCyc Arabidopsis TAIR/PMN Substantial curation
PoplarCyc Poplar TAIR/PMN Coming soon . . .
RiceCyc Rice Gramene Some curation
Sorghum Gramene No curation
MedicCyc Medicago Noble Foundation some curation
LycoCyc Tomato SGN some curation
Potato SGN No curation
Pepper SGN No curation
Tobacco SGN No curation
Petunia SGN No curation
Coffee SGN No curation
SoyCyc Soybean Soybase Coming next year . . .
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
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.
More details about the PMN content . . .
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
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
What metabolites are in the PMN?
Over 2300 compounds
Includes primary and secondary metabolites
Focuses on “small” compounds
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 . . .
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 . . .
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
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
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 we’d be happy to add your favorite species if you’d like to help. . .
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
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
PathoLogic
ANNOTATED GENOME
Pv1234.56.achorismate mutase
chorismate mutase
prephenate aminotransferase
arogenate dehydratase
chorismate prephenate L-arogenate L-phenylalanine5.4.99.5 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
How will the PMN grow in the future?
Increased participation!
Who uses the PMN?: June 4 – July 4, 2009
Who uses the PMN?: June 4 – July 4, 2009
10002010:
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
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)
www.plantcyc.org
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
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)
www.plantcyc.org
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
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
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!