The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Abstract

Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name, mycoplasmas) and responsible for murine respiratory diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome with a G + C content of 26.6 mol%, i.e. the lowest reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative coding sequences (CDSs) covering 91.4% of its length and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of hypothetical proteins, leaving 204 CDSs without significant database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The replication origin oriC was localized by sequence analysis and by using the G + C skew method. Sequence polymorphisms within stretches of repeated nucleotides generate phase-variable protein antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in major M.pulmonis surface antigens. Furthermore, a hemolysin, secreted nucleases and a glyco-protease are predicted virulence factors. Surprisingly, several of the genes previously reported to be essential for a self-replicating minimal cell are missing in the M.pulmonis genome although this one is larger than the other mycoplasma genomes fully sequenced until now.

Figure 1

A + T ratio and cumulated GC skew along the M.pulmonis chromosome. (A) The curve indicates the A + T ratio along the M.pulmonis chromosome. This ratio was calculated with a sliding window of 10 kb with a step of 1 kb. The yellow line indicates the average A + T ratio for the genome. The identity of regions showing unusual A + T ratio is indicated. (B) The curve indicates the cumulated GC skew along the M.pulmonis chromosome starting at position 1 as defined in the text. The transition in GC skew is easily identified around position 1, the putative origin of replication of the chomosome. In contrast, the other transition which would correspond to the termination of replication is more difficult to identify because there are distinct peaks in the region centered around 460 kb.

Figure 2

Density of coding sequences along the M.pulmonis chromosome. Yellow indicates the density of coding sequences in both strands of the sequence and red the density of the coding sequences in the clockwise strand (published sequence). This density was calculated with a sliding window of 50 kb. The first circle represents 100%, the second (inner circle) is 80%. The positions of rRNA genes and of other genes discussed in the text are indicated by black boxes.

Figure 3

General organization of the vsa locus and visualization of repeats within individual vsa genes Within this locus encoding seven vsa genes, the transcribed gene is vsaI as indicated by the location of the expression site which is fused to this gene. The vrs boxes which are the sites for DNA site-specific inversions are indicated by yellow triangles. We suggest that the recombinase responsible for the rearrangements within this locus is encoded by the gene located at the 3′-end. In addition to the vsa genes, three genes putatively encoding lipoproteins (LipA, LipB and LipD) and a gene encoding a conserved hypothetical protein (CHP) were identified. The repeats within each vsa gene were individually analyzed by dot-plot. Within each of the five boxes, the bracket below the colored gene indicates the region of the gene with repeated units.

Figure 4

Comparative organization of the three hsd loci encoding type I restriction modification systems in M.pulmonis. The organization of the three hsd is depicted on this figure. Within the hsdS genes the two types of recombination sequences are indicated by stars (hrs recombination sequences) and by triangles (vip recombination sequences). The position of the hsd loci on the genome is indicated and can also be found on a circular representation of the genome in Figure 2.