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The transcriptional landscape of Chlamydia pneumoniae

Marco Albrecht1, Cynthia M Sharma2, Marcus T Dittrich3, Tobias Müller3, Richard Reinhardt4, Jörg Vogel5 and Thomas Rudel1*

Author Affiliations

1 Department of Microbiology, Biocenter, University of Würzburg, Am Hubland, Würzburg, 97074, Germany

2 Research Center for Infectious Diseases, University of Würzburg, Joseph Schneider Str. 2, Würzburg, 97080, Germany

3 Department of Bioinformatics, Biocenter, University of Würzburg, 97074, Würzburg, Germany

4 Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany

5 Institute for Molecular Infection Biology, University of Würzburg, Würzburg, 97080, Germany

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Genome Biology 2011, 12:R98  doi:10.1186/gb-2011-12-10-r98

Published: 11 October 2011

Abstract

Background

Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae.

Results

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.

Conclusions

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.