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ShewCyc and BeoCyc : discovery platforms for environmental and bioenergy research

ShewCyc and BeoCyc : discovery platforms for environmental and bioenergy research. Tatiana Karpinets, Gretta Serres , and Michael Leuze Oak Ridge National Lab, Marine Biological Laboratory. Pathway Tools Workshop 2010. ShewCyc and Shewanella Knowledgebase.

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ShewCyc and BeoCyc : discovery platforms for environmental and bioenergy research

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  1. ShewCycand BeoCyc: discovery platforms for environmental and bioenergy research Tatiana Karpinets, GrettaSerres, and Michael Leuze Oak Ridge National Lab, Marine Biological Laboratory Pathway Tools Workshop 2010

  2. ShewCycand Shewanella Knowledgebase http://shewanella-knowledgebase.org:8080/Shewanella/

  3. Manually curated PGDB for ShewanellaoneidensisMR1

  4. Manual reannotation • Localization prediction • Regulon predictions (http://regprecise.lbl.gov/RegPrecise/) • Capture information from literature, gene expression data, proteomics

  5. Yang et al. J Biol Chem. 281:29872-85

  6. Crp Fur ArgR Fnr

  7. ShewanellaoneidensisMetabolic Pathway Viewer developed by Erich Baker , Baylor University, TX http://watson.ecs.baylor.edu/4360/

  8. Multi-Genome Annotation Solution:Ortholog Editor in Combination with Genome Editors Manual Curation Improved Individual Genome Editors

  9. Ortholog Table Tools Sort Search Table Overview Edit View Evidence View Alignments View Consistency Check View Download

  10. Edit View

  11. Alignment View MUSCLE (3.6) multiple sequence alignment Sfri_3956 MKIRVLISLATAFFMLNTSSAFAKDPADTAVQPLLVKPKVIIFDVNETLLDLENMRASVG Swoo_1992 ---------------------MTLELRDTSIIKDF--PKAVIFDTDNTLYPYHYSHQQAS :: : **:: : **.:***.::** . ... Sfri_3956 KALNGREDLLPLWFSTMLHHSLVVSATGDYQTFGSIGVA---------SLQMVAEINGIA Swoo_1992 LAVQQKAEKILGIKQSRFSDALKISKREIKERLGETASSHSRLLYFQRTIELLGLKTQIM *:: . : : .: : :* :* : :*. . : :::::. . * Sfri_3956 ITPEQAKTAILTPLRSLPAHPDVAEGLAKLKAQGYKLVTLTNSSLEGVTLQLKNANLSQY Swoo_1992 TTLDLEQTYWRTFLTNSQLFPEMHEFLHDLRAHGIQSAVVTDLTAQIQFRKLVYFGLHEA * : :* * * . .*:: * * .*.*:* : ..:*: : : :* .* : Sfri_3956 FDANLSIESVGVFKPHLKTYQWAIKDLGVNADEAL-MVAAHGW-DIAGADKAGLQTAFIR Swoo_1992 FDYIVTTEEAGADKPNPLPFQLARSKLGLEKGDNLWMIGDHPVKDIQGAKKT-LGAITLQ ** :: *..*. **: .:* * ..**:: .: * *:. * ** **.*: * : :. Sfri_3956 RQGKVLFPLAAQPDYNVL--DVNELASTLAKFN----- Swoo_1992 KNHKDVKVLKGKEGPDILFDKYSELRELLGEISSNKGK .: * : * .: . ::* . .** . *.::.

  12. Evidence View

  13. Consistency Check View Group annotation Protein length consistency Original annotations Domain consistency Automatic identification of bad grouping • Protein Length Consistency • Domain Consistency

  14. ShewCyc

  15. Probing Intergenic Regions (IGs) in S. oneidensisusing microarray Experimental data (Many Microbe Microarrays Database): CRP mutant vs wild type MR1 (various time points during the transition from aerobic growth with lactate to anaerobic growth with lactate and fumarate. Affymetrix microarray was designed to probe transcripts derived from both genes and IGs Examples: IG SO0016_SO0022; IG SO0017-SO0015

  16. A regulatory effect of the IG transcription Down-stream gene IG Up-stream gene Subset I: IG regions with the same direction of change in gene expression as their neighboring genes (1466) Subset A: IG regions with directions of changes in gene expression that are opposite to upstream genes (805) Subset B: IG regions with directions of changes in gene expression that are opposite to downstream genes (820)

  17. Revealing a biological role of Intergenic Regions transcription using Pathway Tools IG (SO2490_SO2491) SO2490 (HexR) Enzymes of the Entner–Doudoroff(ED) pathway SO2491 (PykA) HexR PykA

  18. BioEnergy research Science Center(BESC) Breakdowninto sugars Fuel(s) Sugar Fermentation Cellulosic biomass BESC’s approach: • designing plant cell walls for rapid deconstruction and • engineering microbes for converting plants into biofuel in a single step (consolidated bioprocessing)

  19. BESC knowledgebase: a discovery platform for bioenergy research Manually curated (NREL, UGA) pathway genome database for Populustrichocarpa Usage Summary http://besckb.ornl.gov • Genomes comparison, analysis and visualization tools: • Genome browsers • Comparative chromosome maps (CMAP) • Metabolic maps • Omic Viewers • and more Metabolic reconstructions for BESC relevant microorganisms (BeoCyc) Integrating Experimental Data from LIMS and external resources: Microbial Phenotypes comparison toolkit • Computational predictions: • Orthologs/Inparalogs • Protein Domains • Protein Localization • Metabolic enzymes and pathways • Carbohydrates Active Enzymes • and more Analysis Framework

  20. CAZYmes Analysis Toolkit (CAT) Novel approach based on the association analysis to discover links between CAZy families and pfam domains Web site: http://cricket.ornl.gov/cgi-bin/cat.cgi Find conserved associations between CAZy families and pfam domains Assign carbohydrates activity to unknown protein domains Find CAZymes among hypothetical proteins Assign CAZy families to a sequence with high specificity and sensitivity Suggest novel CAZy families

  21. Private BeoCychosts a • P. trichocarpa PGDB manually curated by NREL team GDP-mannose biosynthesis II, GDP-L-fucose biosynthesis I (from GDP-D-mannose), GDP-L-fucose biosynthesis II (from L-fucose), UDP-D-galactose biosynthesis, UDP-D-galacturonate biosynthesis I (from UDP-D-glucuronate), UDP-D-galacturonate biosynthesis II (from D-galacturonate), UDP-D-glucose biosynthesis (from sucrose), UDP-D-glucuronate biosynthesis (from myo-inositol), UDP-D-xylose biosynthesis (compartmentalized), UDP-L-arabinose biosynthesis I (from UDP-xylose) in Endoplasmic Reticulum, UDP-L-arabinose biosynthesis I (from UDP-xylose) in Cytosol, UDP-L-arabinose biosynthesis I (from UDP-xylose) in Golgi lumen, UDP-L-arabinose biosynthesis II (from L-arabinose) in Cytosol

  22. BeoCyc and BESC knowledgebase http://bobcat.ornl.gov/besc/index.jsp

  23. Arabidopsis Populus EC numbers EC numbers Genes Genes Blast Ortholog search Sequences Sequences Kyoto Encyclopedia of Genes and Genomes genomic and molecular information Improving PopulusTrichocarpa genome annotation • Poor annotation of the poplar genome (gene models and predicted enzymes) • Poor representation of the cell wall biosynthesis and related pathways in the reference databases (MetaCyc, KEGG, and PlantCyc) Future!!! RESD & PESD

  24. Refine the PGDBs RefSeq files from the NCBI Create MySQL tables Pathway Genome Databases Supplement databases by additional annotations Input files for Pathologic Enzyme information KEGG, CAZy Compare phenotypes of the organisms In terms of their genomic and metabolic characteristics Integration of the metabolic reconstructions into BESC knowledgebase

  25. Arabidopsis Populus EC numbers EC numbers Genes Genes Ortholog search Sequences Sequences Challenge : automatic PGDB generation for draft genomes using one table for orf predictions fastAcontigs !!! Predict automatically TU, complexes, transporters for each contig >C0 ATAAAGACGAAAAGCACCGGATCGAACACCGCCACTTCGAAAACTTCGAACGTCTACGG …. >C1r AGTGCGGCTAGGCCGTCGATGGAGCTAGGCCGTCGA …. >C3r GACGAAAAGCAGACGAAAAGCAGACGAAAAGCAGCT…. ….

  26. Involvement of Single-Genotype Consortia in Degradation of Aromatic Compounds by Rhodopseudomonaspalustris p-Coumarate - - anoxygenic photosynthesis Benzoate - aerobic or anaerobic respiration and fermentation - fixation of nitrogen gas - utilization of carbon through CO2 reduction using H2 as an electron donor

  27. Average log2 ratio of the expression of nitrogenases with different cofactors in the growth on p-coumarate and benzoate versus succinate • Transpoters • Chemotaxesoperons • Curli formation operon

  28. Expression of R. palustrisphenotypes under p-coumarate (black columns) and benzoate (white columns) degrading conditions if compared with growth on succinate. p-Coumarate - Benzoate

  29. Structures of R. palustris consortia mediating anaerobic growth on p-coumarate (A) and on benzoate (B)

  30. Putative electron donor and electron acceptor reactions under different modes of the Rhodopseudomonaspalustrisgrowth

  31. Changes in total nitrogen, ammonium and dissolved nitrogen gas during the benzoate degradation as functions of OD660

  32. Acknowledgements ShewCyc and Shewanella Knowledgebase PNNL: Margaret Romine Marine Biological Laboratory: Margrethe Serres ORNL: Denise Schmoyer Guruprasad Kora Mustafa Syed Erich Baker Hoony Park Nagiza Samatova and Edward Uberbacher BeoCyc and BESC Knowledgebase NREL: Ambarish Nag Christopher Chang UGA: Maor Bar-Peled ORNL: Mustafa Syed Hoony Park Morrey Parang Denise Schmoyer and Edward C. Uberbacher

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