1, StarOmics course,Lausanne, Monday November 19 th Training agenda Chemicals Reactions Enzymes Pathways

2, StarOmics course,Lausanne, Monday November 19 th Outline Part I: Introduction Data model L-lysine biosynthesis Pathway resources UniPathway, KEGG, MetaCyc, Reactome, GO Part II: UniPathway tutorial

3, StarOmics course,Lausanne, Monday November 19 th  Gene Ontology: biological process  KEGG  MetaCyc  Reactome  UniPathway … Metabolic pathway resources 3

4, StarOmics course,Lausanne, Monday November 19 th – Dealing with the metabolic network as a whole is complex, and usage consists in decomposing the network into sub-parts, called metabolic pathways. Beside this pragmatic reason, another reason is that these pathways may be considered as elementary functional "modules" or building blocks. They can be combined, may have been conserved through evolution or may have evolved independently. Metabolic pathways 4

5, StarOmics course,Lausanne, Monday November 19 th – Dealing with the metabolic network as a whole is complex, and usage consists in decomposing the network into sub-parts, called metabolic pathways. Beside this pragmatic reason, another reason is that these pathways may be considered as elementary functional "modules" or building blocks. They can be combined, may have been conserved through evolution or may have evolved independently. – A metabolic pathway can be common to several organisms, meaning that the same set of reactions and enzyme families occurs in these organisms. However, some deviations (alternative reactions) can be observed for a specific organism (or a group of organisms), leading to the notion of "variants”. Metabolic pathways 5

6, StarOmics course,Lausanne, Monday November 19 th Variations in the biosynthesis of L-lysine Yuchen Liu et al. J Bacteriol. 2010, 192: DAP pathway Torruella et al. J Mol. Evol. 2009, 69: AAA pathway

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8, StarOmics course,Lausanne, Monday November 19 th L-lysine biosynthesis via DAP pathwayL-lysine biosynthesis via AAA pathway L-alpha-aminoadipate from 2-oxoglutarate LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (acetylase route) LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route) LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route) L-lysine from DL-2,6 diaminopimelate (S)-tetrahydrodipicolinate from L-aspartate DL-2,6-diaminopimelate from LL-2,6diaminopimelate DL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate L-alpha-aminoadipate from 2-oxoglutarate L-lysine from L-alpha- aminoadipate (fungal route) L-lysine from L- alpha-aminoadipate (Thermus route) L-lysine biosynthesis 8

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10, StarOmics course,Lausanne, Monday November 19 th DAP pathway AAA pathway L-Lysine 10

11, StarOmics course,Lausanne, Monday November 19 th variantIIIIIIIVVVI I II III7005 IV950 V100 VI7 Individual Amino Acids Biosynthesis Lysine biosynthesis Lysine biosynthesis I Lysine biosynthesis II Lysine biosynthesis III Lysine biosynthesis IV Lysine biosynthesis V Lysine biosynthesis VI a AAA pathway (2 variants) DAP pathway (4 variants) V IV IIIIII VI c 11

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13, StarOmics course,Lausanne, Monday November 19 th  Gene Ontology: biological process  KEGG  MetaCyc  Reactome  UniPathway … Metabolic pathway resources 13

14, StarOmics course,Lausanne, Monday November 19 th L-lysine biosynthesis via DAP pathwayL-lysine biosynthesis via AAA pathway L-alpha-aminoadipate from 2-oxoglutarate LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (acetylase route) LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route) LL-2,6 diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route) L-lysine from DL-2,6 diaminopimelate (S)-tetrahydrodipicolinate from L-aspartate DL-2,6-diaminopimelate from LL-2,6diaminopimelate DL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate L-alpha-aminoadipate from 2-oxoglutarate L-lysine from L-alpha- aminoadipate (fungal route) L-lysine from L- alpha-aminoadipate (Thermus route) L-lysine biosynthesis 14

15, StarOmics course,Lausanne, Monday November 19 th UniPathway concepts 15

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17, StarOmics course,Lausanne, Monday November 19 th UCR03444: Left-to-Right direction is used in UER00029 UCR04371: Right-to-Left direction is used in UER00029 UER00028 (EC ) = UCR00271 [LR] UER00029 (EC ) = UCR03444 [LR] + UCR04371 [RL] + ULS00012 L-a-aminoadipate from 2-oxoglutarate UCR00271: Left-to-Right direction is used in UER

18, StarOmics course,Lausanne, Monday November 19 th Protein-Reaction curation is performed in UniProt UniPathway provides a structured controlled vocabulary for the annotation of pathway information within UniProtKB protein records. 18

19, StarOmics course,Lausanne, Monday November 19 th L-lysine biosynthesis via AAA pathway UniPathway : label construction An enzymatic reaction is labelled by its relative position in the sub-pathway : step n/m step 1/4 step 2/4 step 3/4 step 4/4 L-alpha aminoadipate from 2- oxoglutarate A sub-pathway is labelled by its terminal compounds : product from substrate A pathway is labelled by its terminal compound(s) “product biosynthesis” | “substrate degradation” [via xxx pathway] 19

20, StarOmics course,Lausanne, Monday November 19 th CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA CC pathway; L-lysine from L-alpha-aminoadipate (Thermus route): step CC 5/5. Acetyl-lysine deacetylase (T.thermophilus) (LYSK_THET2; Q8VUS5) UniProt Headlines UPA00033 L-lysine via AAA pathway UPA00402 Amino-acid biosynthesis ULS00014 L-lysine from L-alpha-aminoadipate (Thermus route) UER00039 step 5/5 CC-!-PATHWAY: super-pathway; pathway; sub-pathway: enzymatic-reaction. UniPathway : label construction

21, StarOmics course,Lausanne, Monday November 19 th General annotation : Pathway  link to UniPathway web site 21

22, StarOmics course,Lausanne, Monday November 19 th Pathway exploration 22

23, StarOmics course,Lausanne, Monday November 19 th Chemical view Taxonomy view Protein view P1 P2 glutamineglutamate + pyruvate anthranilatechorismate Molecular enzyme :TrpED Enzyme classification : EC Anthranilate synthase How a given pathway is distributed into kingdoms, species,…? Genomic view gene a gene b How genes coding for the enzymes of a metabolic pathway are distributed into the genome? 23

24, StarOmics course,Lausanne, Monday November 19 th OBI Warehouse TrEMBL reference proteomes TrEMBL reference proteomes Swiss-Prot UniPathway Calculation NCBI. RefSeq genomes GeneOntology Enzyme /IntEnz Taxonomy. NCBI Taxonomy. NCBI Data update: sync. with UniProt releases UniProtKB (part.) RhEA BioCyc Eco/MetaCyc KEGG LIGAND ChEBI 24

25, StarOmics course,Lausanne, Monday November 19 th UniProt complete proteomes Protein view Chemical view Ontology view Pathway Sub-pathway Enz-reaction Genomic view Taxonomy view 25

26, StarOmics course,Lausanne, Monday November 19 th UniPathwa y tutorial

27, StarOmics course,Lausanne, Monday November 19 th UniPathway short tour

28, StarOmics course,Lausanne, Monday November 19 th The home page is organized in 8 sections accessible through tabs List of pathways for a given species List of compounds used in UniPathway List of pathways in UniPathway Search UniPathway

29, StarOmics course,Lausanne, Monday November 19 th Quick search: lysine Linear Sub-pathway: ULS Pathway: UPA Enzymatic-Reaction: UER Action: Click on Quick search tab then enter lysine in the UniPathway text field then click on Go button

30, StarOmics course,Lausanne, Monday November 19 th Browse pathway – compound - organism

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32, StarOmics course,Lausanne, Monday November 19 th Table widget: known bug  if you encounter this error message  just reload the web page

33, StarOmics course,Lausanne, Monday November 19 th Browse organism Action: Enter ECOL then select ECOLI then click on Go button

34, StarOmics course,Lausanne, Monday November 19 th Browse organism provides the list of metabolic pathways for a selected organism oscode=ECOLI UniProtKB/S wiss-Prot annotation (reviewed)

35, StarOmics course,Lausanne, Monday November 19 th Action: Click again on Quick search then click on UPA00034 (L-lysine biosynthesis via DAP pathway) Browse one pathway

36, StarOmics course,Lausanne, Monday November 19 th UniPathway: Pathway: Overview tabs sections Action: Click on map00300 to open the KEGG map with highlighted reactions upid=UPA00034

37, StarOmics course,Lausanne, Monday November 19 th Lysine biosynthesis via DAP pathway in Acinetobacter Click on ACIAD (Acinetobacter) – the scientific name is given in the tooltip

38, StarOmics course,Lausanne, Monday November 19 th UniPathway:Pathway: Genome view

39, StarOmics course,Lausanne, Monday November 19 th Thank you for your attention!