Topology. 1 Introduction. 2 Chromosomes Topology & Counts. 3 Genome size. 4 Replichores and gene orientation. 5 Chirochores.
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1 Topology 1 Introduction 2 3 Genome size 4 Replichores and gene orientation 5 Chirochores 6 G+C content 7 Codon usage 27 marc.bailly-bechet@univ-lyon1.fr
2 The big picture Eukaryota Bacteria Many linear chromosomes A single circular chromosome + plasmids 28 marc.bailly-bechet@univ-lyon1.fr
3 V. cholerae : 2 circular chromosomes 1,000, , , , , , , , , ,000 2,400,000 2,300,000 2,200,000 2,100,000 2,000,000 2,600,000 2,500,000 1,900,000 2,700,000 1,800,000 2,900,000 2,800,000 1,700, ,600,000 1,500, , ,000 1,300,000 1,400, , , , , , , ,000 1,000,000 1,100,000 1,200, marc.bailly-bechet@univ-lyon1.fr
4 350, , , , , , , , , , ,000 30, , , ,000 40, ,000 50, ,000 60, , ,000 30,000 40, , ,000 strangelove 150, , , , , ,000 Amino acid biosynthesis Cofactors, prosthetic groups, and carriers Cell envelope Cellular processes Central intermediary metabolism DNA metabolism Energy metabolism Fatty acid and phospholipid metabolism Protein fate/protein synthesis Nucleosides, and nucleotides Regulatory functions Transcription Transport and binding proteins Conserved hypothetical Other categories No database match Unknown 20,000 90, ,000 10,000 80,000 20,000 70,000 D. radiodurans : 2 circular chromosomes + 2 circular plasmids 2,600,000 2,500,000 2,400,000 2,300, , , , ,000 Annotation Key * Layer Element 1 Genes, plus strand 2 Genes, minus strand 3 Repeats 4 IS Elements 5 Transporters 6 trnas (black) rrnas (green) srna (red) Chromosome I 2,648,638 bp 1,700,000 1,600,000 1,500,000 1,400, , ,000410, ,000 20,000 1,200,000 1,300,000 1,000,000 1,100,000 Color ** Gene Classification *Layers correspond to concentric circles enumerated from outermost circle inward. ** Color assignments of genes in layers 1 and 2 only. What is the peculiarity of D. radiodurans? Plasmid 45,704 bp Chromosome II 412,348 bp Megaplasmid 177,466 bp 30 marc.bailly-bechet@univ-lyon1.fr
5 S. coelicolor : 1 linear chromosome 31 marc.bailly-bechet@univ-lyon1.fr
6 C. acetobutyliticum : 1 circular chromosome + 1 circular megaplasmid 32 marc.bailly-bechet@univ-lyon1.fr
7 S. enterica serovar Typhimurium LT2 : 1 circular chromosome + 1 circular plasmid a 4,500, ,000 b 90, ,000 80,000 4,000,000 20,000 ORI 1,000,000 70,000 30,000 60,000 3,500,000 TER 50,000 40,000 1,500,000 Gene distribution 3,000,000 2,500,000 2,000,000 Typhimuriumspecific Salmonellaspecific All genomes Others 33 marc.bailly-bechet@univ-lyon1.fr
8 A. tumefaciens : 1 circular chromosome + 1 linear chromosome + 2 circular plasmid 34 marc.bailly-bechet@univ-lyon1.fr
9 B. burgdorferi : many things! Replicon Geometry Size (bp) Chromosome h Linear cp9 Circular 9386 cp26 Circular cp32-1 Circular cp32-3 Circular cp32-4 Circular cp32-6 Circular cp32-7 Circular cp32-8 Circular cp32-9 Circular lp5 i Linear 5228 lp17 i Linear k lp21 i Linear lp25 i Linear lp28-1 i Linear k lp28-2 Linear lp28-3 i Linear lp28-4 i Linear lp36 j Linear lp38 i Linear lp54 Linear lp56 (cp32) j Linear lp56 (other) i,j Linear k What is the difference between a plasmid, a megaplasmid, and a chromosome? Pseudogene plasmid i total Other plasmid total All plasmid total marc.bailly-bechet@univ-lyon1.fr
10 What is the distribution of chromosomes and plasmids among bacteria? Study this yourself: Get the file ( AMIG, file goldtable.txt) Pass it to (there s a few tricks...) Study the distribution of the number of chromosomes and plasmids among Bacteria and Archaea 36 marc.bailly-bechet@univ-lyon1.fr
11 Distribution of the number of chromosomes and plasmids 37
12 Evolution goes circular linear 144 J.-N. Vol, J. Altenbuchner / FEMS Microbiology Letters 186 (2000) 143^ marc.bailly-bechet@univ-lyon1.fr
13 Problem with linear chromosomes 5 -CCCCAACCCCAACCCCAACCCCAACCCCAA GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT... After replication, strands have separated, complements are synthesized 5 -CCCCAACCCCAACCCCAACCCCAACCCCAA GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT xxxxxxxxxxxxxxxxxaccccaaccccaa GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT... If nothing happens to fix things, a second round of replication will yield the following: 5 -CCCCAACCCCAACCCCAACCCCAACCCCAA GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT xxxxxxxxxxxxxxxxxaccccaaccccaa GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT ACCCCAACCCCAA... bases 3 - TGGGGTTGGGGTT... lost 5 -xxxxxxxxxxxxxxxxxxxxxcaaccccaa GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT marc.bailly-bechet@univ-lyon1.fr
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