Department of Microbiology, Biocenter, University of Würzburg, Am Hubland, Würzburg, 97074, Germany.
Genome Biol. 2011 Oct 11;12(10):R98. doi: 10.1186/gb-2011-12-10-r98.
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.
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.
由于严格细胞内寄生的肺炎衣原体无法进行遗传操作，且无法在宿主外培养，因此其基因功能分析受到阻碍。尽管已经对多个菌株的基因组进行了测序，但关于肺炎衣原体的基因结构和转录组的信息却非常有限。
我们采用了一种差异 RNA 测序方法，通过特异性富集初级转录本，定义了肺炎衣原体 CWL-029 株的原始小体和网状小体的转录组；共定位了 565 个注释基因和新转录本的转录起始位点。对相邻基因的共转录分析揭示了 246 个多顺反子转录本。总共，1074 个注释蛋白编码基因中有 862 个具有独特的转录起始位点或属于操纵子。对从小体和网状小体中分离的基因的 RNA 水平进行半定量分析，发现 288 个基因的 RNA 水平存在显著差异。我们已经鉴定并部分验证了 75 个新的潜在非编码 RNA。在单核苷酸分辨率下精确的转录起始位点图谱首次实现了对衣原体中启动子共有序列的全面和饱和分析。
作为基因组序列的补充，精确的转录景观将为理解基因的组织、调控和功能提供新的视角。新发现的非编码 RNA 和确定的常见启动子基序将有助于理解这种重要的人类病原体的基因调控。
