The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis

Abstract

We present the complete genome sequence of Mycoplasma hyopneumoniae, an important member of the porcine respiratory disease complex. The genome is composed of 892,758 bp and has an average G+C content of 28.6 mol%. There are 692 predicted protein coding sequences, the average protein size is 388 amino acids, and the mean coding density is 91%. Functions have been assigned to 304 (44%) of the predicted protein coding sequences, while 261 (38%) of the proteins are conserved hypothetical proteins and 127 (18%) are unique hypothetical proteins. There is a single 16S-23S rRNA operon, and there are 30 tRNA coding sequences. The cilium adhesin gene has six paralogs in the genome, only one of which contains the cilium binding site. The companion gene, P102, also has six paralogs. Gene families constitute 26.3% of the total coding sequences, and the largest family is the 34-member ABC transporter family. Protein secretion occurs through a truncated pathway consisting of SecA, SecY, SecD, PrsA, DnaK, Tig, and LepA. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The DnaK-DnaJ-GrpR complex is intact, providing the only control over protein folding. There are several proteases that might serve as virulence factors, and there are 53 coding sequences with prokaryotic lipoprotein lipid attachment sites. Unlike other mycoplasmas, M. hyopneumoniae contains few genes with tandem repeat sequences that could be involved in phase switching or antigenic variation. Thus, it is not clear how M. hyopneumoniae evades the immune response and establishes a chronic infection.

FIG. 1.

Circular diagram of the M. hyopneumoniae genome structure. The dnaA gene is at position 1. Starting from the outside, the first circle shows replication arrows; the second circle shows the locations of the putative coding sequences on the positive strand; the third circle shows the locations of the putative coding sequences on the negative strand (the color codes for the functional assignments are shown at the bottom); the fourth circle shows the predicted lipoproteins; the fifth circle shows the positions and directions of transcription of the P97 (black) and P102 (orange) paralogs; the sixth circle shows the paralogous families consisting of three or more members (the colors indicate relationships and not functional assignments); the seventh circle shows rRNAs (blue) and tRNAs (red); the eighth circle shows the scale (in base pairs); the ninth circle shows the G+C content of each CDS (negative values are red, and positive values are violet); the tenth circle shows the GC skew ([G − C]/[G + C] averaged over a sliding window of arbitrary length) calculated for each 500 bp along the genome; and the eleventh circle shows the codon adaptation index (inverse; 1 − codon adaptation index is plotted) (53) (the magenta rays indicate values of <0.25, and the blue rays indicate values of ≥0.25). The figure was generated by using the GenVision (DNAStar) software.

FIG. 2.

REPuter analysis of the M. hyopneumoniae genome. Repeat sequences that are ≥25 bp long are connected by lines. The repeat lengths are color coded, as indicated on the right for each analysis. (A) Forward repeats. (B) Reverse repeats. (C) Complement repeats. (D) Reverse complement (palindromic) repeats.

FIG. 3.

Analysis of the cilium adhesin P97 and P102 paralogs in the M. hyopneumoniae genome: alignment of paralog protein sequences showing similarity (black), insertions (vertical lines), and deletions (white) relative to P97 (mhp183) or P102 (mhp182) sequences in the adhesin operon. The cross-hatched areas indicate P97 and P102 sequences. Gray indicates no homology. The open reading frame numbers are indicated on the left; the amino acid numbers are indicated.