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Comparative Microbial Genomics Group. Center for Biological Sequence Analysis The Technical University of Denmark DTU. title. Part 2: Gene Expression and Chromatin Structure In Bacterial Genomes. Dave Ussery Advanced Bioinformatics course lecture 14 November, 2003. - PowerPoint PPT PresentationTRANSCRIPT
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Cen
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Part 2: Gene Expression and Chromatin Structure
In Bacterial Genomes
Comparative Microbial Genomics Group
Dave Ussery
Advanced Bioinformatics course lecture
14 November, 2003
Spombe zoom
Comparative Microbial Genomics Group
Cen
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E. coli Affy
Comparative Microbial Genomics Group
Cen
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Mol. Genet. Genomics, 267:721-729, (2001).
niceDogma
Comparative Microbial Genomics Group
Cen
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C. jejuni Genome
Comparative Microbial Genomics Group
Cen
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Campy Cold ShockExpress
Comparative Microbial Genomics Group
Cen
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Data kindly provided by Alain Stintzi, Genome Letters, 2:18-27, (2003).
Campy Heat shock
Comparative Microbial Genomics Group
Cen
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CHRO2003J. Bact., 185:2009-2016, (2003).
Campy Heat shock
Comparative Microbial Genomics Group
Cen
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Campy exp2
Comparative Microbial Genomics Group
Cen
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Campy exp. 1
Comparative Microbial Genomics Group
Cen
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Origin of replication figure
Comparative Microbial Genomics Group
Cen
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Campy Heat shock
Comparative Microbial Genomics Group
Cen
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CHRO2003J. Bact., 185:2009-2016, (2003).
E. coli chromatin
Chromatin proteins
Comparative Microbial Genomics Group
Cen
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E. coli chromatin IHF
Comparative Microbial Genomics Group
Cen
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Biochimie, 83:201-212, (2001).
E. Coli chromatin FIS
Comparative Microbial Genomics Group
Cen
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Biochimie, 83:201-212, (2001).
Fis unsmoothed
Comparative Microbial Genomics Group
Cen
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Fis smoohted
Comparative Microbial Genomics Group
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Smoothed Chromatin
Comparative Microbial Genomics Group
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Biochimie, 83:201-212, (2001).
E. coli hundred exps
Comparative Microbial Genomics Group
Cen
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Future of microarrays
Comparative Microbial Genomics Group
Cen
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
What is the future of microarrays?
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1997 1998 1999 2000 2001 2002
Publications on microarrays
Ecoli Genomic Landscape
Ecoli genomic landscape
Comparative Microbial Genomics Group
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CHRO2003Data kindly provided by Alain Stintzi
protein synthesis
electron transport
DNA replication,flagella biosynthesis
anaerobic growth,alcohol metabolism,acid response
stress
membrane, secretion
aerobic growth, oxidation
cell cyclecontrol
Genomic landscape of E. coli kindly provided by Josh Stuart, Stanford; Science, 293:2087-2092 (2001).
Closer look
E.coli promoters map1
Comparative Microbial Genomics Group
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Mol. Genet. Genomics, 267:721-729, (2001).
E.coli promoters map2
Comparative Microbial Genomics Group
Cen
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Promoter cartoon
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Promoter cartoon
Promoter cartoon
’
-10-35
DNA curvature,flexibility importanthere
DNA melting important here
rigid
Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Comparative Microbial Genomics Group
More on sigmas
Comparative Microbial Genomics Group
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J. Mol. Biol., 299:907-930, (2000).
Number Sigmas/genome
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Comparative Microbial Genomics Group
Sigma Factors in 150 Bacterial Genomes
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Number of Sigma Factors per Mbp of Genome
Frequency
H.pylori
E. coli K-12
E. coli CFT073
Lactobacillus
Bacteriodes
Streptomyces coelicolor
P. putidaP. aeruginosa
B. cepacia
P. syringae
Sigma70s Blue
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Comparative Microbial Genomics Group
Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
FliA
Proteobacteria ’s
RpoH
RpoD
RpoS
RpoE
Sigma70s with colour
Comparative Microbial Genomics Group
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Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Proteobacteria ’s
RpoH
subdivision
subdivision
subdivision
subdivision
RpoD
RpoS
FliA
RpoE
RpoD vs. RpoS
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Comparative Microbial Genomics Group
Exploiting Genomes: Bases to Megabases in 50 years GSM 7-8 Sept. 2003
Summary
1. Chromatin structure is important in bacteria
summary
Comparative Microbial Genomics Group
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2. Where you are in the chromosome is important!
3. The number of sigma factors per genome can vary greatly between different bacteria.