Title メタボローム技術で得られる代謝経路不明な多数の化合物の組み合わせから経路を予測する手法の開発 Author(s) 小寺, 正明 Citation2010 年度科学技術振興機構 ERATO 湊離散構造処理系プロジェクト講究録. p.193-203. Issue Date 2011-06 Doc URL http://hdl.handle.net/2115/48442 Type conference presentation Note ERATO セミナ 2010 : No.32. 2011 年 1 月 21 日 File Information 32_all.pdf Instructions for use Hokkaido University Collection of Scholarly and Aca
ERATO 2010 - No. 32 2011/1/21 orphan metabolites orphan metabolites EC KEGG orphan metabolites 77% EC random-forest 98% 193
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2010 年度 ERATO 湊離散構造処理系プロジェクト講究録 Elicitation of possible enzyme reaction equations involving orphan metabolites found in metabolomic study. 0 Masaaki KOTERA 1 2004 E-zyme 2008 GREP 2008 Genome, Transcriptome Proteome Metabolome Fluxome 2 Phenome http://www.genome.jp/kegg/pathway/map/map01100.html 3 1. GC HPLC CE 2. MS NMR TLC 1. 2. 4 Penicillin, antibiotics from Penicillium notatum Tetrahydrocannabinol, present in Cannabis sativa, protecting the plant from harmful UV- radiation. Cocaine, present in Erythroxylon coca the Coca plant Tetrodoxin, a potent neurotoxin present in certain kinds of fish 5 195
Orphan metabolites 8 KEGG orphan metabolites 206 sesquiterpene lactones 124 isoquinoline alkaloids 122 indole alkaloids 107 diterpenoids 106 sesquiterpenoids 92 flavones and flavonols 89 quinones etc. (3108 compounds in total) (2008 ) 9 EC (EC number) IUM1961 ID 10 11 (ioinformatics) 12 13 196
2004 E-zyme 2008 GREP 2008 14 15 16 17 2004 E-zyme 2008 GREP 2008 18 19 197
Orphan metabolites Masaaki Kotera, Andrew G. McDonald, Sinead oyce, Keith F. Tipton. Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites. J. Chem. Inf. Model. 2008, 20 48(12):2335-2349. EC x.x.x.x 21 GREP Generator of Reaction Equations & Pathways (Kotera et al., 2008) A D-glucose Pair 1 Pair 1 + Pair 2 A + C = C A + C + ATP = + AMP + PPi 14,000 2008 etanidin Pair 2 EC EC6.-.-.- (Ligase) 22 14,000 x 14,000 / 2 = 98,000,000 23 Unreported pairs Proposed pairs Reactant pair Reactant pair 24 Reactant pairs = Reported pairs 25 198
Number of pairs / total pairs (Pairs with less than 3 overlapped atoms are omitted.) Tanimoto Reported / Unreported pairs Number of pairs / total pairs Reported pair (Pairs with less than 3 overlapped atoms are omitted.) Reported / Unreported 26 Reported / Unreported 27 Number of pairs / total pairs (Pairs with less than 3 overlapped atoms are omitted.) Reported / Unreported pairs Reported / Unreported ROC 2, 5, 6 Reported / Unreported 28 29. 2,.3 4. EC x.x.x.x 30 A Pair 1 D-glucose C Pair 2 etanidin 31 199
EC H2 NADH:NAD CH2 S-Adenosyl-L-methionine:S-Adenosyl-L-homocysteine NH3:O H2O+O2:NH3+H2O2 etc 32 33 EC etc 34 35 1. reported pairs 95% 5% reported pairs EC reported pairs 2. unreported pairs % EC99EC unreported pairs EC99% 3. 4. 13 100 36 XY reported pair EC1 = 0.125 EC2 = 0.875 EC99 = 0.000 DQ reported pair EC1 = 0.125 EC2 = 0.000 37 EC99 = 0.875 200
EC99 ROC etanidin EC99 ROC EC99=5% EC99=1% 38 39 8-(3,3-DMA)galangin + Polyisopentenyldiphosphate = Geranyl diphosphate + 3,5,7-Trihydroxyflavone Example EC2.2.1 2-Isopentenyl diphosphate + 3,5,7-Trihydroxyflavone = 8-(3,3-DMA)galangin + Diphosphate / 40 41 3108 orphan metabolites 199 490 EC 42 43 201
2004 E-zyme 2008 GREP 2008 GREP A D-glucose C Pair 1 Pair 1 + Pair 2 A + C = A + C + ATP = + AMP + PPi 44 etanidin Pair 2 EC EC6.-.-.- (Ligase) 45 ATOM () OND () - VICI () RING () SKEL () 46 47 KEGG 16,372 16372 100 Atom = 216 ID 216 1. Atom_C 14001 2. ond_cc 13861 3. Atom_O 13247 4. ond_co 12955 5. Vici_OC 12371 6. Vici_CCC 11878 7. Vici_CCCO 10068 8. Vici_CCCC 9250 9. Ring_CCCCCC 8153 10. Vici_CC 7724 : 183. Ring_CCNCO 106 184. Skel_C2C2C2C2 100 185. Ring_CCCCCCCCCCCCCCCCCCCO 100 186. Atom_* 95 187. Atom_Na 78 : 215. Atom_Cu 2 216. Atom_Cd 2 16,732 + 16,732 x 16,732 / 2 = 139,996,644 48 ID+ID 216 139,996,644 49 202
Sketchsort 139,996,644 : (Tabei et al., 2010) 50 GREP A D-glucose C etanidin Pair 1 Pair 1 + Pair 2 A + C = A + C + ATP = + AMP + PPi Pair 2 EC6.-.-.- (Ligase) EC 51 52 53 203