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

Promotionskolloquium - PhD defence

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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¨ orstner Bork Group, EMBL Promotionskolloquium 04. Februar 2009
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. 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. 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. Intro GC Protein detection Nitrilases NHases PKS THM
6. Intro GC Protein detection Nitrilases NHases PKS THM
7. Intro GC Protein detection Nitrilases NHases PKS THM
8. Intro GC Protein detection Nitrilases NHases PKS THM
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. Intro GC Protein detection Nitrilases NHases PKS THM Metagenomics = culture independent approaches
11. Intro GC Protein detection Nitrilases NHases PKS THM Workflow of metagenomics sequencing
12. Intro GC Protein detection Nitrilases NHases PKS THM Selected metagenomic data sets
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. 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. 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. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis - huge difference between soil and ocean water Foerstner et al., 2005
17. Intro GC Protein detection Nitrilases NHases PKS THM GC analysis - further data confirms statement Raes et al., 2007
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. 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. 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. Intro GC Protein detection Nitrilases NHases PKS THM Protein detection and classification workflow
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. Intro GC Protein detection Nitrilases NHases PKS THM Nitrilases - new members and subfamilies found Raes et al., 2007
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. 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. Intro GC Protein detection Nitrilases NHases PKS THM NHases - tree of the α domain Foerstner et al., 2008
27. Intro GC Protein detection Nitrilases NHases PKS THM NHases - Monosiga brevicollis’ taxomony
28. Intro GC Protein detection Nitrilases NHases PKS THM NHases - in Monosiga brevicollis Foerstner et al., 2008
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. 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. 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. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - examples of polyketides Erythromycin Oleandomycin Aflatoxin B1
33. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - tree of the AT domain HMM hits Foerstner et al., 2008
34. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - tree overview Foerstner et al., 2008
35. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - hit distribution Foerstner et al., 2008
36. Intro GC Protein detection Nitrilases NHases PKS THM PKS I - PKSs per genome Foerstner et al., 2008
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. 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. 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. 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. 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. Intro GC Protein detection Nitrilases NHases PKS THM About this document Created in L ATEX 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