title Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Genomics of five Clostridium species Comparative Microbial.

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Presentation transcript:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Promoter structures Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group Promoter Structural profile +1 CDS DNA curvature, flexibility important here melts rigid cruciform mRNA CDS  ’   Parma, 2003

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

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

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

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

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

Environmental influence Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group  ’   DNA curvature, flexibility important here mM salt 20  deg C  ’   mM salt 37  deg C Parma, 2003

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

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

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

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

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

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.

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

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

oligomers Center for Biological Sequence Analysis The Technical University of Denmark DTU Comparative Microbial Genomics Group LEADING STRAND, Oligomer bias (up to 8mers) Origin position: 0Strand difference(bits): Oligo bits G GA AG AGA GG GAG GAA A GGA AA AGG AAG AGAG AGAA AAGA GAAA GAGA ATG GAT GGG LAGGING STRAND, Oligomer bias Terminus position: Strand difference(bits): Oligo bits C TC CT TCT CC TTC CTC TCC T CCT TT TTCT CTCT CTT TCTT TTTC CCC CAT TCTC ATC 17657

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

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

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

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

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