Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Abstract

The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. The reduction of the genome size of M. pneumoniae during its reductive evolution from ancestral bacteria can be explained by the loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.

Functional and evolutionary roles of long repeats in prokaryotes

“…Bacteria present very diverse evolutionary strategies linked to pathogenesis, such as: pathogenicity islands in Salmonella and E. coli [17], and Vibrio cholerae [18], gene uptake systems in V. cholerae [19], tandem repeats for phase variation in Haemophilus influenzae [20], tandem repeats linked with contingency loci in H. pylori [10,21], and long repeats for antigenic variation in Mycoplasma [9,22], B. burgdorferi [23], and M. tuberculosis [12].…”

“…The genome of M. pneumoniae is also composed of repetitive DNA elements that constitute up to 8% of the genome. These repeats code for polypeptides that have high similarity to the adhesins of the tip structure that adheres to the host cell [9,25]. In particular, a large number of open reading frames (ORFs) are similar to those of the P1 operon, including the P1 and ORF6 proteins that are essential for adherence to the host cell.…”

“…In particular, a large number of open reading frames (ORFs) are similar to those of the P1 operon, including the P1 and ORF6 proteins that are essential for adherence to the host cell. In spite of the existence of multiple, but not exactly similar, copies of this operon, preliminary experiments have shown that none of these ORFs is expressed under standard laboratory conditions, though presumably they exchange genetic material by partial gene conversion [9]. Therefore both Mycoplasma use similar strategies for antigenic variation, though M. pneumoniae seems to possess a larger group of repeats [14,26].…”

“…In recent years, the analysis of completely sequenced genomes revealed that long repeats are ubiquitous in archaea and eubacteria [8][9][10][11][12]. Although many of these repeats still have unknown roles, our knowledge of their functions has increased significantly with the recent genomic exploratory analysis.…”

Building the blueprint of life

“…Because M. genitalium meets most of the definition of a minimal organism (except for a defined growth media), its 482 genes establish an upper bound on the number of genes in the minimal set. Unfortunately, func- 22 20 17 17 4 DNA recombination and repair 8 0 5 3 0 RNA processing and modification 3 3 2 3 2 tRNA synthesis and modification 34 35 26 27 25 Transcription machinery 12 5 7 7 4 Protein biosynthesis 82 71 76 67 71 Protein turnover 2 0 1 2 0 Protein folding 9 4 9 5 2 Cell division and cell cycle 10 8 7 9 0 Nucleosides and nucleotides 25 16 21 15 0 Carbohydrate metabolism 25 17 21 14 0 Cofactors, [21].The comparison of these two "minimal" genomes revealed that all 482 open reading frames found in the M. genitalium genome are also included in the M. pneumonia genome [22]. While the comparison with M. pneumonia did not help identify expendable genes in M. genitalium, the 110 genes found to be unique to M. pneumonia did help explain why M. genitalium is much more fastidious than M. pneumonia [22].…”