Intro       GC      Protein detection          Nitrilases   NHases   PKS   THM




        Computational analysis of metag...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro         GC       Protein detection   Nitrilases   NHases        PKS       THM




        For the microbial ecologis...
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM
Intro        GC       Protein detection   Nitrilases   NHases   PKS   THM




        Great plate count anomaly
        Le...
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM




                          Metagenomics
              ...
Intro   GC   Protein detection   Nitrilases   NHases   PKS   THM

 Workflow of metagenomics sequencing
Intro   GC    Protein detection   Nitrilases   NHases   PKS   THM

 Selected metagenomic data sets
Intro   GC       Protein detection   Nitrilases   NHases   PKS   THM

 Challenges




        Usually a low coverage
     ...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro    GC        Protein detection   Nitrilases   NHases   PKS   THM

 GC analysis




        GC content = percentage o...
Intro   GC    Protein detection             Nitrilases     NHases   PKS   THM

 GC analysis - huge difference between soil ...
Intro   GC    Protein detection          Nitrilases   NHases   PKS   THM

 GC analysis - further data confirms statement


...
Intro   GC        Protein detection   Nitrilases   NHases   PKS   THM

 GC analysis - possible influencing factors




    ...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro   GC        Protein detection   Nitrilases   NHases   PKS   THM

 Metagenomics data sets as resources of biotech enz...
Intro   GC     Protein detection   Nitrilases   NHases   PKS   THM

 Protein detection and classification workflow
Intro    GC         Protein detection    Nitrilases    NHases    PKS   THM

 Nitrilases




        Nitrile + water       ...
Intro   GC    Protein detection          Nitrilases   NHases   PKS   THM

 Nitrilases - new members and subfamilies found
...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro    GC        Protein detection    Nitrilases   NHases   PKS   THM

 NHases




        Nitril hydratases (NHases)
  ...
Intro   GC    Protein detection             Nitrilases     NHases   PKS   THM

 NHases - tree of the α domain




        ...
Intro   GC    Protein detection   Nitrilases   NHases   PKS   THM

 NHases - Monosiga brevicollis’ taxomony
Intro   GC     Protein detection             Nitrilases     NHases   PKS   THM

 NHases - in Monosiga brevicollis




    ...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro     GC       Protein detection   Nitrilases   NHases      PKS   THM

 PKS I




         Polyketide synthases (PKS) ...
Intro       GC        Protein detection              Nitrilases       NHases   PKS   THM

 PKS I - polyketide synthesis st...
Intro       GC         Protein detection       Nitrilases   NHases       PKS       THM

 PKS I - examples of polyketides

...
Intro   GC    Protein detection             Nitrilases     NHases   PKS   THM

 PKS I - tree of the AT domain HMM hits



...
Intro   GC     Protein detection             Nitrilases     NHases   PKS   THM

 PKS I - tree overview




               ...
Intro   GC      Protein detection             Nitrilases     NHases   PKS   THM

 PKS I - hit distribution




           ...
Intro   GC   Protein detection             Nitrilases     NHases   PKS   THM

 PKS I - PKSs per genome




               ...
Intro          GC          Protein detection   Nitrilases   NHases   PKS   THM

 Table of content


        1   Introducti...
Intro        GC        Protein detection   Nitrilases   NHases   PKS       THM

 Take home messages




        Metagenomi...
Intro   GC          Protein detection   Nitrilases   NHases   PKS   THM

 Acknowledgements



        Peer Bork
        Th...
Intro    GC              Protein detection            Nitrilases            NHases              PKS            THM

 Image...
Intro    GC            Protein detection           Nitrilases         NHases           PKS            THM

 Image sources/...
Intro   GC   Protein detection            Nitrilases           NHases       PKS   THM

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Computational analysis of metagenomic data: delineation of compositional features and screens for desirable enzymes

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PhD defense / Promotionsverteidigung, 2009, February 4th, Würzburg, Germany

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Computational analysis of metagenomic data: delineation of compositional features and screens for desirable enzymes

  1. 1. Intro GC Protein detection Nitrilases NHases PKS THM Computational analysis of metagenomic data: delineation of compositional features and screens for desirable enzymes Konrad U. F¨rstner o Bork Group, EMBL Promotionskolloquium 04. Februar 2009
  2. 2. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  3. 3. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  4. 4. Intro GC Protein detection Nitrilases NHases PKS THM For the microbial ecologist, what can be cultured is the basis of his conception of what exists. This is exactly like learning about animals from visiting zoos. Carl Woese
  5. 5. Intro GC Protein detection Nitrilases NHases PKS THM
  6. 6. Intro GC Protein detection Nitrilases NHases PKS THM
  7. 7. Intro GC Protein detection Nitrilases NHases PKS THM
  8. 8. Intro GC Protein detection Nitrilases NHases PKS THM
  9. 9. Intro GC Protein detection Nitrilases NHases PKS THM Great plate count anomaly Less than 1% of the microbes can be cultured under standard conditions.
  10. 10. Intro GC Protein detection Nitrilases NHases PKS THM Metagenomics = culture independent approaches
  11. 11. Intro GC Protein detection Nitrilases NHases PKS THM Workflow of metagenomics sequencing
  12. 12. Intro GC Protein detection Nitrilases NHases PKS THM Selected metagenomic data sets
  13. 13. Intro GC Protein detection Nitrilases NHases PKS THM Challenges Usually a low coverage Dominant species Short sequences Data size ⇒ storage/memory/CPU intensive ⇒ software not developed for that No standard protocols ⇒ hard to compare
  14. 14. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  15. 15. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis GC content = percentage of Guanine-Cytosine bp in the DNA/RNA influences a.o. Melting temperature of DNA/RNA Codon usage
  16. 16. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis - huge difference between soil and ocean water Foerstner et al., 2005
  17. 17. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis - further data confirms statement Raes et al., 2007
  18. 18. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis - possible influencing factors Nitrogen availability Genome size Ultraviolet light exposure and repair mechanism Codon usage of pioneers
  19. 19. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  20. 20. Intro GC Protein detection Nitrilases NHases PKS THM Metagenomics data sets as resources of biotech enzymes Many microbial enzymes are essential tools in e.g. the chemical, pharma and food industries Searching in metagenomic data sets might reveal new potent members of known enzymes classes
  21. 21. Intro GC Protein detection Nitrilases NHases PKS THM Protein detection and classification workflow
  22. 22. Intro GC Protein detection Nitrilases NHases PKS THM Nitrilases Nitrile + water carboxylic acids + ammonia One protein Application in the chemical industry Stereo- and regio-specific conversion of nitriles
  23. 23. Intro GC Protein detection Nitrilases NHases PKS THM Nitrilases - new members and subfamilies found Raes et al., 2007
  24. 24. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  25. 25. Intro GC Protein detection Nitrilases NHases PKS THM NHases Nitril hydratases (NHases) Nitrile + water amide Two domains Application in the chemical industry Acrylamide >30,000 tons/year Nicotinamide >3500 tons/year Waste water treatment
  26. 26. Intro GC Protein detection Nitrilases NHases PKS THM NHases - tree of the α domain Foerstner et al., 2008
  27. 27. Intro GC Protein detection Nitrilases NHases PKS THM NHases - Monosiga brevicollis’ taxomony
  28. 28. Intro GC Protein detection Nitrilases NHases PKS THM NHases - in Monosiga brevicollis Foerstner et al., 2008
  29. 29. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  30. 30. Intro GC Protein detection Nitrilases NHases PKS THM PKS I Polyketide synthases (PKS) create a heterogeneous group of secondary metabolites The synthesis is similar to the fatty acid synthesis Multiple domains We focused on polyketide synthases type I (PKS I)
  31. 31. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - polyketide synthesis steps This picture of this slide is removed due to copyright restriction. Jenke-Kodama et al., 2005
  32. 32. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - examples of polyketides Erythromycin Oleandomycin Aflatoxin B1
  33. 33. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - tree of the AT domain HMM hits Foerstner et al., 2008
  34. 34. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - tree overview Foerstner et al., 2008
  35. 35. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - hit distribution Foerstner et al., 2008
  36. 36. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - PKSs per genome Foerstner et al., 2008
  37. 37. Intro GC Protein detection Nitrilases NHases PKS THM Table of content 1 Introduction 2 GC content analysis 3 Protein detection workflow 4 Nitrilases 5 Nitril hydratases 6 Polyketide synthases I 7 Take home messages
  38. 38. Intro GC Protein detection Nitrilases NHases PKS THM Take home messages Metagenomics ... ... might help us to explore the complete microbial world ... still has many technical challenges ... can reveal the environmetal influence on genomic features ... can help discover new enzymes
  39. 39. Intro GC Protein detection Nitrilases NHases PKS THM Acknowledgements Peer Bork Thomas Dandekar Lars Steinmetz Toby Gibson The whole Bork group esp. Jeroen Raes and Takuji Yamada Christian von Mering Melly My friends and family
  40. 40. Intro GC Protein detection Nitrilases NHases PKS THM Image sources/attribution - part 1/2 Orangutan Houston Zoo http://flickr.com/photos/billtex48/2178056762/ by (Bill and Mavis) - B&M Opel Zoo 07.07.2007 http://flickr.com/photos/lamberty/754218458 by frijolito75 Giraffe http://flickr.com/photos/abelle/280246250/ by A.Bell Snuggling http://flickr.com/photos/buckwoo/2421562192/ by Ken W! Delicious Dead Bee and Hungry Ants http://flickr.com/photos/hamed/176176998/ by Hamed Saber hundreds of fish swarm a soft coral head http://flickr.com/photos/g-na/370131126/ by g-na hunt is on http://flickr.com/photos/doug88888/2930690305/ by doug88888 Long-billed Curlew http://flickr.com/photos/mikebaird/3011987508/ by mikebaird 145ps 01087.jpg http://flickr.com/photos/ricephotos/2679758872/ by IRRI Images Polymicrobic biofilm epifluorescence http://commons.wikimedia.org/wiki/File:Polymicrobic_biofilm_epifluorescence.jpg The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. PLoS Biology Vol. 5, No. 3, e77 doi:10.1371/journal.pbio.0050077 green farm http://flickr.com/photos/nakae/204037619/ by nakae Acid Mine Drainage http://flickr.com/photos/savethewildup/400614071/ by savethewildup blue ocean http://flickr.com/photos/coolskipper/27242821/ by coolskipper Digestive system http://commons.wikimedia.org/wiki/File:Digestive_system_whitout_labels.svg by Mariana Ruiz Villarreal Pg166 bioreactor http://commons.wikimedia.org/wiki/File:Pg166_bioreactor.jpg
  41. 41. Intro GC Protein detection Nitrilases NHases PKS THM Image sources/attribution - part 2/2 Big Drop-Off [...] http://flickr.com/photos/ctsnow/113339176/ by ctsnow Sphaeroeca-colony http://commons.wikimedia.org/wiki/File:Sphaeroeca-colony.jpg by Dhzanette Ocean view http://flickr.com/photos/provoost/399669002/ by Sjors Provoost The hurdles http://flickr.com/photos/29621494N02/3060466344/ by paula fisher Erythromycin http://de.wikipedia.org/w/index.php?title=Datei:Erythrommycin_A_B_C.svg by Yikrazuul Aflatoxin B1 http://de.wikipedia.org/w/index.php?title=Datei: Aflatoxin_B1.svg&filetimestamp=20070113042046 by Bryan Derksen Oleandomycin http://en.wikipedia.org/wiki/File:Oleandomycin.png by Edgar181 Tool rack http://en.wikipedia.org/wiki/File:Oleandomycin.png by L. Marie Collaboration http://flickr.com/photos/fncll/145149313/ ChrisL AK Base pair AT http://commons.wikimedia.org/wiki/File:Base_pair_AT.svg Base pair GC http://commons.wikimedia.org/wiki/File:Base_pair_GC.svg
  42. 42. Intro GC Protein detection Nitrilases NHases PKS THM About this document A Created in L TEX using the beamer class, TeX Live and Emacs. All these programs run on OpenBSD. http://www.latex-project.org http://latex-beamer.sourceforge.net http://www.tug.org/texlive/ http://www.gnu.org/software/emacs http://www.gimp.org/ http://www.openbsd.org Published under the Creative Commons Attribution 3.0 License http://creativecommons.org/licenses/by/3.0/ Document version 1.0 2009/02/04

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