Global stage-specific gene regulation during the developmental cycle of Chlamydia trachomatis

Abstract

Distinct morphological changes associated with the complex development cycle of the obligate intracellular bacterial pathogen Chlamydia trachomatis have been historically well characterized by microscopy. A number of temporally regulated genes have been characterized previously, suggesting that the chlamydial developmental cycle is regulated at the transcriptional level. This hypothesis was tested by microarray analysis in which the entire C. trachomatis genome was analyzed, providing a comprehensive assessment of global gene regulation throughout the chlamydial developmental cycle. Seven temporally cohesive gene clusters were identified, with 22% (189 genes) of the genome differentially expressed during the developmental cycle. The correlation of these gene clusters with hallmark morphological events of the chlamydial developmental cycle suggests three global stage-specific networks of gene regulation.

FIG. 1.

Temporally coordinated phenotypic changes during chlamydial development cycle in relation to transcriptional clusters and development stage. Clustered expression profiles for single gene representatives from each of the temporal clusters are illustrated. Expression profiles of genes are in rows, with temporal progression from left to right. Expression profiles were clustered with Cluster software and plotted with Treeview software. A complete list of all the genes in each temporal cluster is available (http://chlamydia-www.berkeley.edu:4231/).

FIG. 2.

Expression profiles of functionally related sets of genes. Transcription mediators (A), type III secretion apparatus proteins (B), gluconeogenesis/tricarboxylic acid cycle (C), and membrane proteins/DNA compaction proteins (D) are clustered together as functional groups, reflecting temporal hierarchy within each functional group. Functional groups are based on chlamydial genome project designations (27). Expression profiles of genes are in rows, with temporal progression from left to right. Expression profiles were clustered with Cluster software and plotted with Treeview software. Expression levels are color coded as in Fig. 1.

FIG. 3.

Temporal expression of C. trachomatis L2 genes representing constitutive, early, midlate I, midlate II, and very late cluster categories assessed by RT-PCR. Total RNA extracted from C. trachomatis L2-infected L929 cells was tested by RT-PCR, and each lane contains the DNA product for each time point postinfection. ORF numbers and names listed in the left column are based on those of Stephens et al. (27). The developmental stages to which each of the transcripts was categorized are listed in the right column.