This pathogenic bacterium is an obligate pathogen that has evolved mechanisms to avoid the immune system and persist within the epithelial cells of its only natural host: humans. All chlamydiae have small genomes, limited biosynthetic capability, and a unique, unsynchronized, developmental cycle that is tied to its intracellular survival. The cycle begins with small, metabolically reduced 'elementary bodies' (EB) with electron-dense, compacted DNA and rigid trilaminar cell walls that infect host cells through endocytosis. The EB within the chlamydial endocytic vesicle become non-infectious, larger, metabolically active 'reticulate bodies' (RB) with less condensed nucleoid structure and more flexible cell walls. These RB cells use nutrients and ATP from the host cytoplasm and divide by binary fission. The endocytic vesicles (also referred to as vacuoles) combine to form large inclusions within the cytoplasm of the host cells. The RBs reorganize their cellular structure and transition back into EB, which are released from the host cell ~48 - 72 hrs after infection, repeating the developmental cycle when another host cell is infected. It's been found that the immune response of epithelial host cells to Chlamydia infection is secretion of interferon-γ (IFN--γ), which leads to induction of indoleamine 2,3-dioxygenase (IDO) that degrades the essential amino acid tryptophan (Trp) causing Trp deprivation for C. trachomatis. This leads to development of a special chlamydial persistent form, the nonreplicating aberrant reticulate bodies (ARB), which are viable, but noncultivable [Omsland14, Elwell16, Ostergaard16, Witkin17].

Chlamydia trachomatis D/UW-3/CX presented here is the type strain of the serovar D group and was the first Chlamydia species to have its complete genome sequenced [Stephens98]. Its genome is small but within the range of other C. trachomatis genomes, being slightly greater than 1.04 kbp and containing a single 7,493 bp plasmid (which was not sequenced as part of the NCBI BioProject genome sequencing used for this PGDB). Comparative genomic analysis of 12 C. trachomatis strains revealed that a large proportion of their pan-genome consists of conserved core genes: 836 core genes out of 874-927 total genes found in each C. trachomatis genome [Joseph11]. Because of the obligate intracellular nature of chlamydiae, a number of genes related to biosynthesis capabilities are missing and a large portion of their genome is devoted to virulence factors, such as effectors that are secreted through specialized secretion systems [Stephens98, Byrne10, Elwell16, Witkin17].

This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Chlamydia trachomatis D/UW-3/CX, as obtained from RefSeq (annotation date: 03-AUG-2016) and pathways were created computationally by the PathoLogic component of the Pathway Tools software (version 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [Caspi20]. Many genes associated with virulence have also been manually curated and verified from publications.

Development of this PGDB was supported by BioCyc subscription revenues and by grant GM080746 from the National Institute of Health.