- Genome sequence:

  The sequenced chlamydial genome consists of a 1,042,519 - base pair chromosome (58.7%  A+ T) and a 7493- base pair plasmid.  Analysis of the chlamydial genome resulted in the identification of 894 likely protein-coding genes. Similarity searching permitted the inferred functional assignment of 604 (68%) encoded proteins, and 35 (4%) were similar to hypothetical proteins deposited for other  bacteria. The remaining 255 (28%) predicted proteins were not similar to other sequences deposited in Gen-Bank.  Clustering by sequence similarity showed that 256 chlamydial proteins (29%)  belong to 58 families of similar genes within the genome (paralogs), a fraction similar to other bacteria with relatively small genomes  such as the mycoplasmas and Haemophilus influenzae.
  For years Chlamydiae were thought to lack key enzymes and cellular machinery for generating ATP,  instead sequestering host nucleoside triphosphates by translocation mechanisms. The new sequence does reveal two potential ATP/ADP translocases, but it also identifies genes that may allow Chlamydiae to generate at least minimal amounts of ATP on its own.
  The peptidoglycan deficiency is thought to be compensated by a unique disulfide-cross linked, supramolecular protein complex in the cell wall, which provides the structural stability normally afforded by peptidoglycan. The sequence has revealed the surprising result that Chlamydiae actually have a full complement of peptidoglycan synthesis genes. But how much is made and for what purpose?
   The genes encoding a potential surface structure, a type III secretion apparatus, were also found. Type III secretory systems not only permit export  of proteins out of Gram-negative bacteria but also facilitate entry of the exported proteins into host cells with which the bacteria make contact. Type III secretion is common to many Gram-negative pathogens of plants an animals, and allows the bacteria to invade host cells or to subvert host defense mechanisms. Structural genes and those for assembly of the apparatus are conserved, but the substrates, which are secreted directly into host eukaryotic cells, tend to be unique to the species.
  Several genes thought to be present in all bacteria were not found. Maybe the most intriguing finding for evolucionary microbiologists is that Chlamydiae appear to have acquired and unusual number of eukaryotic genes, 20 or more, as compared to 3 or 4 in other bacteria whose genomes have been sequenced. Many of these genes more closely resemble those of plants than those of animals.