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Center for Biological Sequence Analysis The Technical University of Denmark DTU. Comparative Microbial Genomics Group. title. DNA Atlases for Campylobacter, Helicobacter, and Related Organisms. Sunday, 6 September, 2003. CHRO2003.

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  1. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group title DNA Atlases for Campylobacter, Helicobacter, and Related Organisms Sunday, 6 September, 2003 CHRO2003

  2. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group overview OVERVIEW Introduction to CHROs DNA Atlases - “whole genome maps” Proteome comparison CHRO2003

  3. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Phylogenetic tree  Ectosymbiont of shrimp Symbiont of lugworm Wolinella succinogenes Lawsonia intracellularis Helicobacter pylori  Helicobacter hepaticus Sutterella wadsworthensis  proteobacteria Arcobacter nitrofigilis  Sulfurospirillum deleyianum Aquaspirillum polymorphum Anaerobiospirillum succiniciproducens  Campylobacter curvus Campylobacter jejuni Campylobacter fetus subsp. fetus Modified from "Taxonomy of Campylobacter, Arcobacter, Helicobacter and related bacteria", by S.On, Journal of Applied Microbiology, 90, 1S-15S, (2001). CHRO2003

  4. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Phylogenetic tree Wolinella succinogenes Helicobacterpylori Helicobacter hepaticus Arcobacter nitrofigilis Sulfurospirillum deleyianum Campylobacter curvus Campylobacter fetus subsp. fetus Campylobacterjejuni Related Organisms CHRO2003

  5. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Nice H.pylori pix H. pylori image courtesy of Luke Marshall Concrete Bob Software(www.ConcreteBob.com) CHRO2003

  6. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Stamp collecting “All Science is either physics or Stamp Collecting.” - T. Rutherford CHRO2003

  7. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Epsilons sequenced How do you compare more than 100 bacterial genomes? CHRO2003

  8. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group AT content W.succinogenes CHRO2003

  9. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Intro. The DNA sequence contains information. But what kind of information? CHRO2003

  10. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group >gi|24115631|gb|AF226280.2| Campylobacter jejuni 81-176 virulence plasmid pVir, complete sequence ATGGCTTTTATTGACGATAAAAAAGATCCAAATTTTATATTTCAACTTGAGAGAAATATAAAAGCGTATATGCTATACATTATTATAGCTTTAACTACGATTGTAGTTTCTCTTGCTATTGCCATTACTTTTCTTGCCCCTTTTAAAGAAGTAAAGCCTTATTTAGTATTTTTTTCAGACGGCGAAACTAATTTTGTAAAGGTAGAACAAGCAGGAATGGATATGAGAGCCGATGAGAATTTATTAAAATCAATTCTCGCAGGCTATGTTAAAAAACGCGAAACGATAAATCGTGTCGATGATAGTGAGAGATACGAAGAGATCAGACTTCAATCTCAAAAAAATGTGTGGGAAACATTCTCAAACTTAGTAAAAGCTCCAAATTCTATTTATACAACGCAAGGAGTTTTTAGAAGCATTGAAATTATCAATGTTTCAATTTTTAATAAAAATGTAGCTACGATCGATTTTATAGCAAAAATAACTAATAGAGATGGTAGTGAGAACCATTTAAAAAAATATCGTGCCACATTATTTTTTGATTTTATACCAATGGAGCTTACTTATAATTCAGTTCCAAAAAATCCTACAGGCTTTATTGTCAAACAATATTCAATTACAGACATTATTGACAATGATACTTTTAACAATACACAACAAACGAAAGGAGCGAAGTAATGAGAAAATATTCAAAAATAGCTTTTCTAGCTTTATTTGTAAATTTGACAGCTTTTGCTGACAACATACAAATTCAAGATGTTCCTAACCCTAATGCAAACACAGGCGAAAGCATTTTACAAACTAAGGAACAAGCTTTAAATAATTATACACAAACCAATATCAAAATAGATCCTTTAGGAAATCAAGGGCAAGGGCAAAGAATAGATAATTCAAGTTATGCTAATCCACAATATCAAGCCCAAGCTTTTGATACTTACTCTCAAAGCAATGGAGAACAGTTAAGCGAAGAGCAAATTGCTTTAATGAAAAGTGCGATTAGAAACCAAAATTTAAATGCTTTACAGCAAAGATTTTTTCAAAAAAAATATTCAGGATTTGAAAACACATTAAATCTTGATTATCAGCCCAATAAAACGCAAAAAATAAGAACACGCTTTGCAATGGCAACCACTCTTATTTTTGAAACGGATATTACAAATTATATCTTAGGAGATACGACAGGATTTAAGGTAGAAGAAATTCCAAGTATGCCTAATGCCATAGCTATTAAACCTATGCTAATCGGAATTGATACTTCTTTGACTATTTTTACCAAAGACAATAAACTTCACACCTTCTACATCTTTTCGACTGATTATAAAAATAGCAAAGATCCTTCTTTAGTAATTTATATACACGATCAAAATTCAAAAGAATTAATTAAAGAGAAACAAGAAAAATTGGCAAAAGATTACTTAATCATTAAAGAAGGTATTGCTGAAGTTCGTGTTAAAAAAAGTGAAATCTATAATCACTATAGCCAAAAAGCAAAAAAAGGCGACGAGTGGCTTATTAGCGAAGAAATTTTCAATGATAAAAAATTTACTTATTTCAAATACGACAAAGACAAAATGCCACAAGTCCCAGCAATATTTGCAGTAATTGATAAACAAGACAGTCCAGTAGAGACTAGGATCATCGGTAATTATGTAATTGCTGAAACCACTGCAAAAAAATTTACAATCAAAAGTGGAGATAGTTATGTATGTGTAGAGCGTTTGGATCAAAACAAAAAGGCTAAGAAATGAAAAAATCATTTTTAAGCCTAAGTCTTGCAACAATATTGTTAAGCAACAATCTTTTTGCAGAAGATATATTTGATCAAACAAGCGAAGAAAATGTATCTAAAAATATATCTAAAAAAGACAATCAAAGCCAAAATTTGCTTAACAAAGAAGATTTAGACTATCTTTTCAAAAATTCAGATACAAAATTTCCAGTCACCGATTATATTTATAAGGGCGGATTTAAAGAACCTAACGAAGATATTAAAATTCATAGTGAAGAAAAACCTAAAAAAGAAGAAGATAATAATATTACTAAGTTAGCAAAAATTGAAGAAAAAAAGCAAGAACTGATACAAAAAAATCAGCAAATTGCAAAAGAAATTCATCAAGATAATATTAGTTCTCAAGAAAGAAAAATCAAAAAACTTATCAGAGATAGTATTTTAGCTGATCGTGGCAACACGCAAATTTATTTTCAAGAAAATTCTTCAAAATACGGCGTTGATGGTTTTTCAAACCAAAAAAGCATAGATGTTTCAACAAACGAACACCGTCTTTATAGAATGATAAGAGCAGGAAGATTAATTCCTGCCCTTTTAACGAGTGCTATTTCTAGTGATTTGCAAGGTATAGTAACCGCTCAAATAGAGCAAGATATATATGCAAGTATGGGAAATGCAGTGTTAATTCCACGCGGAAGTAAGGCTATAGGATTTTACAAAAACGACAACAAAATAGGACAAAATCGCTTAGAAATACAATGGAGAGAAATTATTACACCACAAGGCGTTAATATACTTTTAACCAATGCTTTAGCTAGTGATAATATGGGTATGGCAGGAGCAGTTGGAAGCGTTAATAATAAATATCTTGAAAGATACGGAATGCCTTACGCACTCTCCACAATTTCAAATGTATTGCTTCTTAGCATAGCGTCAAAAGCAGGAAATAATAATTACGCTCAAGAAGTTTATTCTCAAAGTAAAAACGATGTATCTACGATAGTAGATGATATTATCCAACAACAAAGCCAGATTAAACCAACAATCGAAATTAAATCAGGAAGTAGAATTTTTATAGTTCCTACCAATCATATGTGGTTTGCAAAACCTAAAAACAACGAAGTATTGATCCAATATTTCCAAGATAATTAAAGGAGAAAAAATGCAAGAAATTAGTAATTATGAAAAAATCAAAAAAGACATTGAAGAAGGAATTCAAAAAAGAAAAGAAGAAGATAAAAAAAATAAGAAAATAATCAATCAGATAAAAATAATTAGTTCTTTAGAAAATAAAGTTCAAAAAGAGAAAGAAAAATTAGACAAGCTTGTAAAAAATGAAACAAAAGAGCTAGAGAATGAGTAATAATACTATTGTTTTAAATAATATTTTAAATGTTTTAAAACCTTACTTAGAAATGGAAGCAAACGAGCTTATTTTTAATAAACCTTGTGAAATCAAGGTAGATAAAGGCGATGTTTGGGAAACTATTTATGATGATAGGCTCAATTATAATTTTTTAGAAACCTTTTTAATTGAACTTGCTATTAAAAGAAATCAGAGATTTGATGAAAAACATTGTCATCTCTCTTGTGAGTTGCCTTACCCCTTTTTAAGATATAGGGTGCAAGCACAGCACAAGACAAGTCTTTTTAATTCTGAAATTTGTATTTGTATCAGAATACCTTCAAAAAGTCGTTTTGCACTTGAAAATTTTGTTTTAAACGATAAGTGTTTAGAAAAAGGTTGGACTTATGAAAAAATTAAAGATTTAATTAAAAATAAAAAGAATGTTTTAGTCTCAGGTGGAACAGGAAGTGGAAAAACTAGCTTTTTAAATTCTTTAATGGGTGAAATTGATCCAAATGAAAGAATTGTAACTATTGAAGACGCTCAAGAATTATATATCGAAAACGAGAACAAAACCCAATTAGCCGTGCCAAAAGAAGAAAGTGAAATCTATTCCTATCAAACGGCGATAAATAACGCTATGAGATTAAGACCTGATAGATTATTTTTAGGAGAAATTGATATCAGAAACACCTTTACATTTTTAAGGGTAAATAACACAGGACACGCAGGAAACTTAAGCACTCTGCACGCAAATAATCCAGAAGACGCGATCAAAGCTATTATCACAAATATTATTTTAGGTGGGGGCTTACAAAACCCTGATAATAAAATGCTTACTGAACTAATTATAACGGCTATAGATTTTATTATACAAATTTCGAGAAATAAAAAAACAGGGACTAGAGATATTACAGATATTTTAGATTTGAAAAATGATTACGCAAAATTATTAATCTAAGGAGTTAGTGTGGGAACAATCAGAGTTTATTTGAATGAGTATGAGCAAAGACAATTAAAAAAACTTTCAATAAAAAGAAATGAAAGTCAAAGTGCTGTTATTAGAAAGCTTATTGCTATAGAAAAATACGCAAAAACTCTTGAAATTTTAGAGAAAAATAATGAAATTAATGTGGAGTAT pVir sequence

  11. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group pVir Atlas CHRO2003

  12. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group pVir base2 Atlas CHRO2003

  13. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group pVir genome Atlas CHRO2003

  14. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group pVir zoom CHRO2003

  15. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Melting curve From Craig Benham, U.C. San Diego, 6 Sept. 2003 CHRO2003

  16. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Curvature 5 kbp CHRO2003

  17. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter cartoon Promoter cartoon DNA melting important here rigid DNA curvature, flexibility important here -35 -10 b / b’ s a Promoter cartoon CHRO2003

  18. 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). CHRO2003

  19. 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). CHRO2003

  20. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Table J. Mol. Biol., 299:907-930, (2000). CHRO2003

  21. Center for Biological Sequence Analysis The Technical University of Denmark DTU Sig70 + Sig38

  22. Center for Biological Sequence Analysis The Technical University of Denmark DTU RpoD tree

  23. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Know your Bacteria Know Your Bacteria Mette Jakob Lars Tine

  24. 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

  25. Center for Biological Sequence Analysis The Technical University of Denmark DTU Sig32 + Sig54

  26. Center for Biological Sequence Analysis The Technical University of Denmark DTU Sig32 + Sig54

  27. Chlamydia Firmicutes Proteobacteria Center for Biological Sequence Analysis The Technical University of Denmark DTU 54 family Sig54 tree

  28. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H.pylori OLD Atlas Res. Microbiol., 150:777- 773, (1999). CHRO2003

  29. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H.pylori NEW atlas CHRO2003

  30. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H.pylori 26695 CHRO2003

  31. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H. hepaticus CHRO2003

  32. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group C. jejuni Genome Genome Letters, 1:16-25, (2001). CHRO2003

  33. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group W. succinogenes Genome CHRO2003

  34. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group DNA Symmetry Elements Defined Repeats defined • What are symmetry elements? • REPEATS in DNA Sequences • Direct repeats • 5’ GGGAATNNGGGAAT 3’ • 3’ CCCTTANNCCCTTA 5’ • Inverted repeats • 5’ GGGAATNNATTCCC 3’ • 3’ CCCTTANNTAAGGG 5’ CHRO2003

  35. C. jejuni H. hepaticus Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Summary Global D CHRO2003

  36. H. pylori C. jejuni Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Summary Global I CHRO2003

  37. H. hepaticuus H. pylori C. jejuni Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Local Direct CHRO2003

  38. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Local Inverted H. hepaticuus H. pylori H. hepaticuus H. pylori C. jejuni C. jejuni CHRO2003

  39. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group blank

  40. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cjejuni BLAST atlas CHRO2003

  41. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cjejuni phylome atlas CHRO2003

  42. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group 26695 BLAST atlas CHRO2003

  43. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group H.hepaticus phylomeatlas CHRO2003

  44. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Wsuc CHRO2003

  45. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Hp26 CHRO2003

  46. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group HpJ99 CHRO2003

  47. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Hhep CHRO2003

  48. Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Cjej CHRO2003

  49. Wolinella succinogenes Helicobacter pylori Helicobacter hepaticus Arcobacter nitrofigilis Sulfurospirillum deleyianum Campylobacter curvus Campylobacter jejuni Campylobacter fetus subsp. fetus Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Phylogenetic tree (again) CHRO2003

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