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Center for Biological Sequence Analysis The Technical University of Denmark DTU. Comparative Microbial Genomics Group. title. Comparative Genomics of five Clostridium species. A DNA-Centric View. Adv. Bioinformatics Lekture, 21 November, 2003.

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  1. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group title Comparative Genomics of five Clostridium species A DNA-Centric View Adv. Bioinformatics Lekture, 21 November, 2003 DIAGNOSIS, EPIDEMIOLOGY AND ANTIBIOTIC RESISTANCE OF THE GENUS CLOSTRIDIUM 17-18 October, 2003 - Parma, Italy

  2. Comparative Microbial Genomics Group Center for Biological Sequence Analysis The Technical University of Denmark DTU overview OVERVIEW 1. Comparison of five Clostridium genomes 2. Local View: DNA Structures and Clostridium Promoters 3. Global View: oligomer bias in Clostridium genomes Parma, 2003

  3. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cp 100 genomes How do you compare more than 100 bacterial genomes? Parma, 2003

  4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group AT content Parma, 2003

  5. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group AT content Parma, 2003

  6. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Global Repeats Parma, 2003

  7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Local Repeats Parma, 2003

  8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Purine stretches Parma, 2003

  9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cp. rRNAs Parma, 2003

  10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cp. protein Parma, 2003

  11. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group All paralogs Parma, 2003

  12. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group firmicutes Parma, 2003

  13. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.tetani plasmid Parma, 2003

  14. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.tet zoom Parma, 2003

  15. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter Structural profile Promoter structures -35 -10 “TATA box” Parma, 2003

  16. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Campy pVir zoom Parma, 2003

  17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter structure -35 -10 TATA J. Mol. Biol., 326:1361-1372, (2003). Parma, 2003

  18. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Translation start aligned J. Mol. Biol., 299:907-930, (2000). Parma, 2003

  19. cruciform -35 -10 +1 rigid melts DNA curvature, flexibility important here CDS mRNA +1 -10 -35 b / b’ s a Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter Structural profile Promoter structures CDS Parma, 2003

  20. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Information Depends on Context….. context Parma, 2003

  21. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group sigmas Parma, 2003

  22. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Sigma70s with colour Clostridium ’s C. acetobutylicum C. perfringens C. tetani spoI RpoH FliA RpoS SpoII RpoD

  23. Center for Biological Sequence Analysis The Technical University of Denmark DTU “RpoD like” RpoD RpoS Sig70 tree 70 sigE sporulation iniation RpoH Actinobacteria Chlamydia RpoF flagella Cyanobact. sigF sporulation Firmicutes “other phyla” sigG sporulation sigH Proteobacteria

  24. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group sigmas Parma, 2003

  25. -35 -10 +1 b / b’ 300 mM salt s a 37 deg C +1 50 mM salt DNA curvature, flexibility important here -10 -35 20 deg C b / b’ s a Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Environmental influence Parma, 2003

  26. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Information Depends on Context….. Context 2 Parma, 2003

  27. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. acetobutylicum Parma, 2003

  28. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. botulinum Parma, 2003

  29. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.difficile Atlas Parma, 2003

  30. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.tetani genome Parma, 2003

  31. Toxin tetanospasmin • Anaerobic conditions allow germination of spores and production of toxins. • The tetanus toxin is a 150 KDa protein, which is cleaved extra cellular, to a 100 Kda and a 50 Kda, that are binded with a sulfur bridge. • Toxin binds in central nervous system • Interferes with neurotransmitter release to block inhibitor impulses. • Leads to unopposed muscle contraction and spasm.

  32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.perfringens Parma, 2003

  33. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C.perf. skew Parma, 2003

  34. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group LEADING STRAND, Oligomer bias (up to 8mers) Origin position: 0 Strand difference(bits): 4105557 Oligo bits G 92292 GA 81583 AG 64095 AGA 60700 GG 46169 GAG 34200 GAA 33918 A 31417 GGA 31259 AA 25862 AGG 25340 AAG 24943 AGAG 24464 AGAA 23535 AAGA 23005 GAAA 18825 GAGA 18448 ATG 18129 GAT 17623 GGG 17200 oligomers LAGGING STRAND, Oligomer bias Terminus position: 1361000 Strand difference(bits): 3977053 Oligo bits C 93908 TC 82712 CT 62349 TCT 57477 CC 47113 TTC 35786 CTC 32995 TCC 32250 T 29779 CCT 24636 TT 23842 TTCT 23751 CTCT 22962 CTT 22661 TCTT 21517 TTTC 19334 CCC 18554 CAT 18537 TCTC 17833 ATC 17657

  35. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. Perf skew2

  36. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Organisms S/N

  37. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Signal/Noise plot

  38. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group summary Summary 1. DNA sequence  DNA structure  Function 2. Clostridium difficile is more likely to be variable. 3. Clostridium DNA is different!

  39. Parma, 2003 Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Acknowledgements Acknowledgements • Jakob Bondo • Jimmy Hoffmann Hansen • Paiman Khorsand-Jamal • Anne Egholm Pedersen • Maria Seier Petersen • Peter Hallin www.cbs.dtu.dk • Hans-Henrik Stærfeldt • Lars Juhl Jensen • Carsten Friis • Marie Skovgaard • Peder Worning • Thomas Scheritz Pontén • Søren Brunak The Danish Research Foundation Dave@cbs.dtu.dk

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