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Home , Circular chromosome

Bacterial structures Topology & Counts

Topology

1 Introduction

2 Chromosomes Topology & Counts

3 Genome size

4 Replichores and orientation

5 Chirochores

6 G+C content

7 Codon usage

27 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts

The big picture

Eukaryota

Many linear A single circular chromosomes +

28 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts

V. cholerae : 2 circular chromosomes

1 1,000,000 100,000 900,000 200,000 800,000 300,000

700,000 400,000 600,000 500,000

2,900,000 1 100,000 2,800,000 200,000 2,700,000 300,000 2,600,000 400,000 2,500,000 500,000 2,400,000 600,000 2,300,000 700,000 2,200,000 800,000 2,100,000 900,000 2,000,000 1,000,000 1,900,000 1,100,000 1,800,000 1,200,000 1,700,000 1,300,000 1,600,0001,500,000 1,400,000

29 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts D. radiodurans : 2 circular chromosomes + 2 circular plasmids

1 2,600,000 100,000 2,500,000 200,000 2,400,000 Annotation Key 300,000 Layer * Element 2,300,000 1 , plus strand 400,000 2 Genes, minus strand 3 Repeats 4 IS Elements 5 Transporters 6 tRNAs (black) rRNAs (green) sRNA (red)

Color** Gene Classification

Chromosome I Amino acid biosynthesis Cofactors, prosthetic groups, and carriers 2,648,638 bp envelope Cellular processes Central intermediary metabolism DNA metabolism

s Energy metabolism trang elove Fatty acid and phospholipid metabolism fate/protein synthesis , and nucleotides Regulatory functions Transport and binding Conserved hypothetical 1,700,000 Other categories No database match 1,000,000 Unknown D. 1,600,000 * Layers correspond to concentric circles What is the peculiarity of 1,100,000 enumerated from outermost circle inward. 1,500,000 ** 1,200,000 Color assignments of genes in layers 1,400,000 1,300,000 1 and 2 only. 400,000410,000 1 10,000 390,000 20,000 radiodurans 1 380,000 30,000 ? 40,000 370,000 40,000 50,000 360,000 60,000 350,000 10,000 45,704 bp

30,000

Chromosome II 20,000 1 412,348 bp 170,000 10,000 160,000 20,000

150,000

140,000

140,000 Megaplasmid 270,000 130,000 177,466 bp 150,000 260,000

120,000 250,000 160,000 240,000 170,000 230,000 180,000 110,000 190,000 70,000 220,000210,000 200,000 100,000 80,000 90,000

30 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts

S. coelicolor : 1

31 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts C. acetobutyliticum : 1 circular chromosome + 1 circular megaplasmid

32 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts S. enterica serovar Typhimurium LT2 : 1 circular chromosome + 1 circular plasmid

0 a 4,500,000 b 0 500,000 90,000 10,000 80,000

4,000,000 20,000

70,000 1,000,000 ORI 30,000 60,000

40,000 TER 50,000 3,500,000

1,500,000

Gene distribution Typhimurium- All 3,000,000 specific 2,000,000 Salmonella- Others specific 2,500,000

33 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts A. tumefaciens : 1 circular chromosome + 1 linear chromosome + 2 circular plasmid

34 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts

B. burgdorferi : many things !

Replicon Geometry Size (bp)

Chromosomeh Linear 910 725 cp9 Circular 9386 cp26 Circular 26 498 cp32-1 Circular 30 750 cp32-3 Circular 30 223 cp32-4 Circular 30 299 cp32-6 Circular 29 838 cp32-7 Circular 30 800 cp32-8 Circular 30 885 cp32-9 Circular 30 651 lp5i Linear 5228 lp17i Linear 16 928k What is the difference between a lp21i Linear 18 901 lp25i Linear 24 177 plasmid, a megaplasmid, and a lp28-1i Linear 28 250k lp28-2 Linear 29 766 chromosome? lp28-3i Linear 28 601 lp28-4i Linear 27 323 lp36j Linear 36 849 lp38i Linear 38 829 lp54 Linear 53 541 lp56 (cp32)j Linear 30 349 lp56 (other)i,j Linear 22 622k

Pseudogene plasmid i total 247 708 Other plasmid total 362 986 All plasmid total 610 694

35 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts What is the distribution of chromosomes and plasmids among bacteria?

Study this yourself: Get the file (http://pbil.univ-lyon1.fr/members/mbailly, 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

36 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts Distribution of the number of chromosomes and plasmids

37 [email protected] Bacterial genome structures Bacterial genome structures Chromosomes Topology & Counts

Evolution goes circular → linear

144 J.-N. Vol¡, J. Altenbuchner / FEMS Microbiology Letters 186 (2000) 143^150

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Bacterial genome structures Chromosomes Topology & Counts

Problem with linear chromosomes

5’-CCCCAACCCCAACCCCAACCCCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

After replication, strands have separated, complements are synthesized 5’-CCCCAACCCCAACCCCAACCCCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

5’-xxxxxxxxxxxxxxxxxACCCCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

If nothing happens to fix things, a second round of replication will yield the following: 5’-CCCCAACCCCAACCCCAACCCCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

5’-xxxxxxxxxxxxxxxxxACCCCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

5’- ACCCCAACCCCAA...... bases 3’- TGGGGTTGGGGTT...... lost 5’-xxxxxxxxxxxxxxxxxxxxxCAACCCCAA...... 3’-GGGGTTGGGGTTGGGGTTGGGGTTGGGGTT......

39 [email protected] Bacterial genome structures