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MICROME training workshop

MICROME training workshop. Curation of GPR using MicroScope platform. 03/28/2012 Marseille. MicroScope Metabolic Databases. Relational DataBase PkGDB (Prokaryotic Genome DataBase). EC / reaction correspondence. • Experimentally elucidated metabolic pathways.

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MICROME training workshop

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  1. MICROME training workshop Curation of GPR using MicroScope platform 03/28/2012 Marseille

  2. MicroScope Metabolic Databases Relational DataBase PkGDB (Prokaryotic Genome DataBase) EC / reaction correspondence • Experimentally elucidated metabolic pathways • 1800 pathways from 2216 organisms (P. Karp, SRI, USA) Pathway Tools A metabolic database is built for each annotated microbial genome PGDB = Pathway/Genome Database(orgname_Cyc) http://www.genoscope.cns.fr/agc/microcyc Today: 1233 organisms (of which 676 public genomes), 41 Go PkGDB Mapping on the KEGG metabolic maps (http://www.kegg.jp/)

  3. www.genoscope.cns.fr/agc/microscope MicroScope Web site • More than 30 tools are made available to the community «guest» access «guest» access Since 2005, more than 50.000 expert annotations per year

  4. Microscope GPR editor • GPR curation interface: The gene curation interface of Microscope allows the validation of Gene-Reaction associations based on curated gene annotations. Two reference reaction resources availables, MetaCyc (functional) and RHEA (under development): • Automatic retrieval of Metacyc/Rhea reactions based on • EC number • Keyword search 4.1.3.27, 2.4.2.18

  5. MicroScope Pathway validation interface This tool allows users to curate the prediction of Pathologic algorithm by assigning different status : • predicted: predicted by the BioCyc pathologic algorithm (default one). • validated: curated as a functional pathway. • variant needed: the predicted pathway is not completely correct for the organism. A new variant must be defined. • unknown: not enough evidence to declare the pathway as functional. • non functional: the pathway has been lost in the organism and is no more functional (gene loss, pseudogenization). • deleted: curated as a false positive prediction.

  6. MicroScope Pathway validation interface Organism to curate Current state of curation Add new MetaCyc pathway Predicted and curated Pathway list

  7. CanOE strategy: genomic and metabolic contexts Integrating conserved Metabolons over n organisms => Candidate genes for Orphan Enzymes

  8. CanOE strategy: genomic and metabolic contexts Integrating conserved Metabolons over n organisms => Candidate genes for Orphan Enzymes Gene family integration using MCL Generation of potential associations between gap genes and orphan reactions

  9. CanOE strategy: scores and ranks Gene Family/ReactionAssociations Ranking strategy using: Score F->R and Score R->F

  10. CanOE: Allantoin degradation metabolon in E. coli K-12 Oxamatecarbamoyltransferase is a global orphan reaction www.genoscope.cns.fr/agc/microscope/metabolism/canoe.php Smith AAT, Belda E., Viari A., Médigue C., and Vallenet D. “The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes” (Plos Computational Biology, In revision)

  11. MicroScope and Microme • Development of web-services to provide Microme central repository with curated Gene-Reaction associations from Microscope platform Curation tool microcyc PkGDB Reconstruction Each night Web-services

  12. Test-case: Bacillus subtilis168re-annotation • Second most intensively studied bacterium after Escherichia coli, being a model organism for Gram-positive bacteria • Genome sequenced in 1997. 4,214 Megabases, 4000 CDSs Nature 1997 Nov 20;390(6657):249-56 • Re-sequencing and first re-annotation of the genome in 2009 Microbiology (2009), 155, 1758-1775 • Re-annotation of the genome in the context of Microme project with special focus in the curation of Gene-Reaction associations by using Microscope metabolic tools and curation interface. Collaborative work LABGeM (CEA)- SIB (A. Morgat) - AMAbiotics (A. Danchin)

  13. Test-case:Bacillus subtilis168re-annotation • Stats of curation Gene-Reaction associations in Microscope Nº reactions Nº CDS Nº Gene-Reaction associations 105 CDS without automatically predicted reaction in initial projections • 147 new reactions added (not originally predicted) • 184 originally predicted reactions removed

  14. Test-case:Bacillus subtilis 168 re-annotation • 17 possible updates of SwissProt annotations • 6 possible new EC numbers Reported to SwissProt/IUBMB curators • 14 possible new metabolic pathways/pathway variants not presents in MetaCyc • Biotin biosynthesis pathway variant • Lipoate biosynthesis pathway variant • Myoinositol catabolism pathway variant • Rhamnogalacturonan type I degradation pathway variant • Acetoin dehydrogenase pathway variant • Methionin salvage pathway variant • Bacillaene biosynthesis pathway • Aerobic respiration pathway variants New pathway variants Addition to Microme central repository (Next MICROME release) • Aromatic polyketide biosynthesis pathway • 2-methylthio-N6-threocarbamoyladenosine biosynthesis • Bacilysocin biosynthesis • Archaeal-type ether lipid biosynthesis • Bacillaene biosynthesis pathway • Methionine-Cysteine interconversion New metab. pathways

  15. Test-case: Bacillus subtilis 168 re-annotation • Biotin biosynthesis pathway variant: Update of DAP aminotransferase pathway variant (EC:2.6.1.62) KEGG pathway (map00780) MetaCyc pathway (PWY-5005) S-Adenosyl-L-methionine as amino group donor L-lysine instead S-adenosyl-Methionine as amino group donor in Bacillus subtilis BioA enzyme

  16. Demo: Bacillus subtilisdTDP-L-rhamnosebiosynthesis I http://www.genoscope.cns.fr/agc/microscope

  17. Exercise 1: Lysine biosynthesis in A. baylyiADP1 • Using UniPathway find the missing reaction(s) in AcinetobacterbaylyiADP1 for the Lysine biosynthesis DAP pathway http://www.grenoble.prabi.fr/zeo4/obiwarehouse/unipathway/upa?upid=UPA00034 • Using MicroScope A. baylyiADP1 training version (AcinetoTP), find and annotate the candidate gene for aspartate kinase. • URL: http://www.genoscope.cns.fr/agc/microscope • Login: aciadTP • Password: bonjour • Organism: AcinetoTP • Tool: Search by keywords with datasets SwissProt and PRIAM

  18. Exercise 2: Lysine in FusobacteriumnucleatumATCC 25586 • Using UniPathway and MicroScope search for lysine biosynthesis pathway* • Is the pathway functional in F. nucleatum ? Confirm your conclusions by bibliographical evidences. • http://www.grenoble.prabi.fr/zeo4/obiwarehouse/unipathway/upa?upid=UPA00034 • MicroScope->Metabolic Profiles tool • Pubmed

  19. Exercise 3: Lysine biosynthesis in B. pseudomalleiK96243 • Using UniPathway find the missing reaction(s) in BurkholderiapseudomalleiK96243 for the Lysine biosynthesis DAP pathway http://www.grenoble.prabi.fr/zeo4/obiwarehouse/unipathway/upa?upid=UPA00034 • Using MicroScope CanOE tool, find the candidate gene for UER00020 (EC: 2.6.1.17, MetaCyc: SUCCINYLDIAMINOPIMTRANS-RXN). • URL: http://www.genoscope.cns.fr/agc/microscope/metabolism/canoe.php • Search reaction by keyword • Get CanOE Reaction Details • Check details of the Gene Family 953 • Check details of GF593-SUCCINYLDIAMINOPIMTRANS-RXN associations • Open the predicted metabolon in B. pseudomallei • Open the Gene window and get other evidences supporting the annotation of the candidate gene for the reaction UER00020

  20. Exercise 4: Lysine biosynthesis ULS00008 • Using UniPathway, in which organism the ULS00008 is complete? List the organisms which may have this pathway variant. • http://www.grenoble.prabi.fr/zeo4/obiwarehouse/unipathway/upa?upid=UPA00034 • Using MicroScope, find the candidate genes for the missing reactions of the ULS00008 in other Bacillus. • URL: http://www.genoscope.cns.fr/agc/microscope • MaGe->Genome browser • Select Bacillus subtilisas reference genome and explore the genomic contexts of the the gene BSU14000 within other bacillus genomes included in UniPathway reference organism list.

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