Genome sequencing and our understanding of chlamydiae.

A driving force in the evolution of a microorganism is the ability to colonize a niche. A vertebrate organism represents a unique niche, but to an infecting microbe it is simply an environment to be exploited. Many pathogens explore yet another opportunity—the intracellular environment. The chlamydiae are obligate intracellular pathogens that have established a unique niche within the host cell. As a group their approach has been successful; chlamydiae cause a variety of diseases in animal species at virtually every phylogenetic level. Chlamydia trachomatis and C. pneumoniae are the most significant human pathogens. C. trachomatis is the leading cause of preventable blindness worldwide and the most common sexually transmitted bacterial species (43a, 45). C. pneumoniae causes 10% to 20% of community-acquired pneumonia worldwide and has recently been associated with coronary atherosclerosis (29) and possibly other conditions (18). The major determinants of chlamydial pathogenesis are complicated and unclear at present. Apparently, the chlamydiae are not acutely toxigenic, and in many cases infection is asymptomatic and persistent. Serious chlamydial disease is a function of several processes including the ability to attach and grow within target cells, mechanisms of dissemination and persistence, directed remodeling of the intracellular environment, and the nature of the immune response to infection (6). The chlamydiae undergo a developmental cycle unique among prokaryotes. Following uptake, chlamydiae develop and grow within an intracellular vacuole, called an inclusion, that is distinct from all identified parasitophorous vacuoles. The inclusion membrane is devoid of host cell markers, but lipid markers traffic to the inclusion and suggest a functional interaction with the Golgi apparatus (16). Within the inclusion, chlamydiae undergo a complex developmental cycle composed of functional and structurally distinct forms. The elementary body (EB) is infectious but is metabolically inactive and cannot replicate. This form differentiates upon infection into the noninfectious reticulate body (RB), a larger pleomorphic bacterium that is metabolically active and multiplies. Chlamydiae produce a group-specific lipopolysaccharide (LPS) determinant that is conserved within the genus (7). All chlamydiae encode an abundant protein termed the major outer membrane protein (MOMP, or OmpA) that is surface exposed in C. psittaci and C. trachomatis (9, 20) and is the major determinant for serologic classification of chlamydial isolates (47). Disulfide-mediated cross-linking of two major developmentally regulated cysteine-rich proteins results in a rigid lattice, which is apparently necessary for structural integrity (19), as the EB lacks detectable peptidoglycan (PG). Many of the genes involved in these processes were cloned and identified using conventional means: by homology, via expression libraries, and through functional complementation analysis. But in this system still lacking a generally available transformation technique, there are many aspects of the chlamydial infectious process and developmental cycle that remain unclear. Completion of the sequences of six chlamydial genomes (Table 1), with others soon to follow, has complemented and expanded much of the information acquired in the pregenomic era (46). The primary descriptions of these genome sequences (25, 46) provide thorough and valuable analyses of the different genomes, including much information not covered here. The purpose of this review is to examine the role of the solved genome sequences in our understanding of four model groups of chlamydial proteins. Two of the protein groups, inclusion membrane (Inc) proteins and the polymorphic membrane proteins (Pmp proteins), are, at present, unique to the chlamydiae. Two other groups, the proteins involved in PG synthesis and the chlamydial type III secretion apparatus, represent processes that are present in other organisms. While the four groups of proteins are distinct and unrelated, each represents one aspect of the unique nature of chlamydiae. We address how decoding the genome has expanded our early perspective of these organisms and also point out in each case what questions the genome sequences cannot directly answer.