Regulation of Chlamydia Gene Expression by Tandem Promoters with Different Temporal Patterns

Abstract

Chlamydia is a genus of pathogenic bacteria with an unusual intracellular developmental cycle marked by temporal waves of gene expression. The three main temporal groups of chlamydial genes are proposed to be controlled by separate mechanisms of transcriptional regulation. However, we have noted genes with discrepancies, such as the early gene dnaK and the midcycle genes bioY and pgk, which have promoters controlled by the late transcriptional regulators EUO and 28 . To resolve this issue, we analyzed the promoters of these three genes in vitro and in Chlamydia trachomatis bacteria grown in cell culture. Transcripts from the 28 -dependent promoter of each gene were detected only at late times in the intracellular infection, bolstering the role of 28 RNA polymerase in late gene expression. In each case, however, expression prior to late times was due to a second promoter that was transcribed by 66 RNA polymerase, which is the major form of chlamydial polymerase. These results demonstrate that chlamydial genes can be transcribed from tandem promoters with different temporal profiles, leading to a composite expression pattern that differs from the expression profile of a single promoter. In addition, tandem promoters allow a gene to be regulated by multiple mechanisms of transcriptional regulation, such as DNA supercoiling or late regulation by EUO and 28 . We discuss how tandem promoters broaden the repertoire of temporal gene expression patterns in the chlamydial developmental cycle and can be used to fine-tune the expression of specific genes. IMPORTANCE Chlamydia is a pathogenic bacterium that is responsible for the majority of infectious disease cases reported to the CDC each year. It causes an intracellular infection that is characterized by coordinated expression of chlamydial genes in temporal waves.Chlamydial transcription has been shown to be regulated by DNA supercoiling, alternative forms of RNA polymerase, and transcription factors, but the number of transcription factors found in Chlamydia is far fewer than the number found in most bacteria. This report describes the use of tandem promoters that allow the temporal expression of a gene or operon to be controlled by more than one regulatory mechanism. This combinatorial strategy expands the range of expression patterns that are available to regulate chlamydial genes.A defining feature of the pathogenic bacterium Chlamydia is an unusual intracellular developmental cycle with three main stages (1). During the early stage, an extracellular form of chlamydiae, called the elementary body (EB), enters the host eukaryotic cell and differentiates into a reticulate body (RB), which is the metabolically active but noninfectious form. During the midstage, the RB replicates via multiple rounds of binary fission. Finally, in the late stage, RBs convert back into infectious EBs. This developmental cycle lasts 48 to 72 h and ends with the release of EBs to infect a new host cell. These fundamental steps of the developmental cycle are conserved among species of...

A combinatorial strategy of alternative promoter use during differentiation of a heterocystous cyanobacterium

“…promoter regions with several transcriptional start sites) are a common theme in bacteria with developmental alternatives (McGrath et al ., ). Combinatorial use of promoters is also a common strategy in pathogens, with examples that range from tandem promoters with different temporal profiles (Rosario and Tan, ) to transcripts with different susceptibility to regulatory sRNAs depending on the 5′UTR being transcribed in free‐living versus intracellular bacteria (Quereda et al ., ). In all those bacteria with complex lifestyles the contribution of individual promoters to the overall transcription of genes can only be assessed by methods, such as dRNASeq, able to dissect individual transcriptional starts perhaps being operative in different cell types (Sharma and Vogel, ).…”

GrgA controls Chlamydia trachomatis growth and development by regulating expression of transcription factors Euo and HrcA

“…We speculate that the GrgA protein prepacked into EBs plays a critical role in activation of euo transcription immediately following host cell entry. The Euo protein functions as a master repressor of late genes (11)(12)(13). By binding to the promoters of late genes and repressing their expression, EBs can utilize limited resources to express early genes required for converting themselves into proliferative RBs.…”

“…C. trachomatis encodes three σs. A super majority of C. trachomatis promoters are σ 66 -dependent, while some late genes possess σ 28 promoters or both σ 66 and σ 28 promoters (11)(12)(13). To date, only two late genes are thought to carry a σ 54 promoter (14).…”

“…Only two C. trachomatis transcription factors demonstrate ability to control the chlamydial developmental cycle, Euo and CtcC. Euo is produced immediately after EBs enter host cells (8,33,34) and binds late gene promoters to suppress transcription (11)(12)(13). CtcC is a part of a twocomponent system and is predicted to function as an activator of the σ 54 -RNAP holoenzyme on the basis of orthologs in other bacteria (25).…”

Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters

“…Recent advances in bacterial transcriptomics demonstrate a complex organization of the transcriptional apparatus (Nicolas et al, 2012; Junier et al, 2016). Genes and operons may have complex systems of transcription initiation including multiple promoters and TSSs (Maxson and Darwin, 2006; Rosario and Tan, 2016). Thus, the genome-scale identification of TSSs represents another layer of genome information that cannot be derived solely from its sequence but is crucial for its function.…”