Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39

Nucleic Acids Res. 2000 Mar 15;28(6):1397-406. doi: 10.1093/nar/28.6.1397.


The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Bacterial Proteins / genetics
  • Bacteriophages / genetics
  • Base Sequence
  • Chlamydia Infections / microbiology
  • Chlamydia trachomatis / enzymology
  • Chlamydia trachomatis / genetics*
  • Chlamydia trachomatis / metabolism
  • Chlamydia trachomatis / pathogenicity
  • Chlamydophila pneumoniae / enzymology
  • Chlamydophila pneumoniae / genetics*
  • Chlamydophila pneumoniae / pathogenicity
  • Chlamydophila pneumoniae / virology
  • Chromosome Inversion
  • Conserved Sequence / genetics
  • Evolution, Molecular
  • Genes, Bacterial / genetics
  • Genes, Duplicate / genetics
  • Genome, Bacterial*
  • Humans
  • Mice / microbiology
  • Molecular Sequence Data
  • Nucleotides / metabolism
  • Physical Chromosome Mapping
  • Recombination, Genetic / genetics
  • Replication Origin / genetics


  • Bacterial Proteins
  • Nucleotides

Associated data

  • GENBANK/AE002160
  • GENBANK/AE002161