General Features and Organization of the L pneumophila Genomes

The complete genome sequences of three strains of L. pneumophila (Paris, Lens and Philadelphia 1) are available at the time of writing (Cazalet et al. 2004; Chien et al. 2004). Legionella pneumophila has a single, circular chromosome, 3,503 610 base pairs (bp) (Paris), 3,345 687 bp (Lens) and 3,397 754 bp (Philadelphia 1) in size, with an average G + C content of 38% (Table 1.1; Figure 1.1. Strains Paris and Lens each contain a plasmid, 131.9 kb and 59.8 kb in size, respectively. In strain Philadelphia 1 no plasmid was identified. The genomes contain each ~3000 genes distributed fairly evenly between the two strands (~57% on the leading strand) and accounting for ~88% of the potential coding capacity. No function

Table 1.1. General features of the three sequenced Legionella pneumophila genomes.

L. pneumophila

L. pneumophila

L. pneumophila

Paris

Lens

Philadelphia

Size of the

3,503,610

3,345,687

3,397,754

chromosome (bp)

G + C content

38.3% (37.4%)

38.4% (38.4%)

38%

Total number of

3077 (141)

2931 (57)

2953

protein-coding genes

Average length of

331*

333*

338*

protein-coding genes

Number of rRNA operons

3

3

3

(16S-23S-5S)

Number of tRNA genes

43

43

43

Percentage coding

87.9% (92%)

88% (83.7%)

89.8

Plasmid1

1 (131.9 kb)

1 (59.8 kb)

-

Number of strain

313 (125)

259 (44)

335

specific genes

Number of orthologous

2500

2500

'codons 1kilobase-pairs () plasmid related genes

'codons 1kilobase-pairs () plasmid related could be predicted for 42.1% of the L. pneumophila Paris, 44.1% of the L. pneumophila Lens and for 28% of the L. pneumophila Philadelphia 1 genes. A high proportion of the predicted genes (21% for strain Paris, 20.4% for strain Lens, 17% for strain Philadelphia 1) are unique to the genus Legionella. Comparative analysis of the genome structure of the three L. pneumophila genomes showed high colinearity, with only few translocations, duplications, deletions or inversions (Figure 1.2). Principally, the genomes contain three large plasticity zones, where the synteny is disrupted: a 260kb inversion in strain Lens with respect to strains Paris and Philadelphia 1, a 130kb fragment which is partly similar partly different and which is inserted in a different genomic location in strains Paris and Philadelphia 1 but which is truncated in strain Lens and the chromosomal region carrying the Lvh type IV secretion system (Figure 1.2). The Lvh type IV secretion system, previously described in strain Philadelphia (Segal et al. 1999) is encoded by a 36 kb region (strain Paris) or a 45 kb region (strain Philadelphia 1) that can be either carried on a multi-copy plasmid or be integrated into the chromosome. Further diversity on the genome level is present as deletions and insertions of several smaller regions were identified in each strain, as well as regions where the gene content is variable. Finally, also variations at the gene level are present as discussed later. The sequences and their analysis are accessible at http://genolist.pasteur.fr/LegioList; http://genome3.cpmc.columbia.edu/~legion/project/.

Pneumophila

Figure 1.1. Circular genome map of L. pneumophila strain Paris and the specific genes with respect to strain Lens and Philadelphia. From the outside—circle 1: Strain Paris genes on the + and - strands, respectively. Red line, inversion in strain Lens. Numbers indicate their position: 1 lvh-lvr type IV secretion system (lvrABC, lvhB2B3B4B5, lvrD, lvhB6B8B9B10B11D4, lvrE); 2 dot/icm type IV secretion system (icmTSRQOMLKEGCDJBF); 3 mip, 4 lspA, 5 lspDE, 6 htrA, 7 lspFGHIJK, 8 enhABC, 9 dot/icm type IV secretion system (icmVWX and dotABCD), 10 momp; circle 2: specific genes of strain Paris with respect to strain Lens; circle 3: specific genes of strain Paris with respect to strain Philadelphia; circle 4: G/C bias (G + C/G-C) of strain Paris; circle 5: G + C content of strain Paris with <32.5% G + C short length, between 32.5% and 44.1% medium length and with >44.1% G + C long lines. The scale (Mb) is indicated on the outside, origin of replication at position 0.

Figure 1.1. Circular genome map of L. pneumophila strain Paris and the specific genes with respect to strain Lens and Philadelphia. From the outside—circle 1: Strain Paris genes on the + and - strands, respectively. Red line, inversion in strain Lens. Numbers indicate their position: 1 lvh-lvr type IV secretion system (lvrABC, lvhB2B3B4B5, lvrD, lvhB6B8B9B10B11D4, lvrE); 2 dot/icm type IV secretion system (icmTSRQOMLKEGCDJBF); 3 mip, 4 lspA, 5 lspDE, 6 htrA, 7 lspFGHIJK, 8 enhABC, 9 dot/icm type IV secretion system (icmVWX and dotABCD), 10 momp; circle 2: specific genes of strain Paris with respect to strain Lens; circle 3: specific genes of strain Paris with respect to strain Philadelphia; circle 4: G/C bias (G + C/G-C) of strain Paris; circle 5: G + C content of strain Paris with <32.5% G + C short length, between 32.5% and 44.1% medium length and with >44.1% G + C long lines. The scale (Mb) is indicated on the outside, origin of replication at position 0.

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  • Jeanett
    Is genome of legionella pneumophila circular?
    8 months ago

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