The transcriptional landscape of Chlamydia pneumoniae

Using a differential RNA-sequencing approach with specific enrichment of primary transcripts, we defined the transcriptome of purified elementary bodies and reticulate bodies of C. pneumoniae strain CWL-029; 565 transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for co-transcription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes. Semi-quantitative analysis of mapped cDNA reads revealed significant differences for 288 genes in the RNA levels of genes isolated from elementary bodies and reticulate bodies. We have identified and in part confirmed 75 novel putative non-coding RNAs. The detailed map of transcription start sites at single nucleotide resolution allowed for the first time a comprehensive and saturating analysis of promoter consensus sequences in Chlamydia.The precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes. Novel non-coding RNAs and identified common promoter motifs will help to understand gene regulation of this important human pathogen.The human pathogen Chlamydia pneumoniae (Cpn; also referred to as Chlamydophila pneumoniae [1]) is a major cause of pneumonia and chronic infection has also been associated with atherosclerosis [2] and Alzheimer's disease [3]. Cpn can cause a spectrum of infections that usually take a mild or sub-clinical course. It causes acute respiratory disease [4] and accounts for 6 to 20% of community-acquired pneumonia cases in adults [5]. Almost all humans can expect to be infected with Cpn at least once during their lifetime and infections can become chronic. Re-infections during the lifetime are common, leading to a seroprevalence of 80% in adults [6]. Cpn is an obligate intracellular Gram-negative bacteria with a unique biphasic devel