Mycoplasma pneumoniae transcriptome analysis

Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. We have found 68 new non-annotated transcripts, of which the vast majority are potential regulatory RNAs, 53 of them in antisense to known genes. Integration of all data confirmed a dynamic and complex view of bacterial transcription: Under reference conditions in a rich medium, 138 polycistronic and 212 monocistronic transcripts could be identified, with almost half of the polycistronic operons showing a ‘staircase’-like expression pattern, i.e. the expression level within each gene is constant, but succeeding genes have lower expression. Furthermore, under different conditions, operons can divide into smaller transcriptional units, possibly by utilization of internal promoters resulting in many alternative transcripts. More complex bacteria show similar responses to external stresses, although M. pneumoniae lacks the respective transcription regulators, indicating the existence of yet uncharacterized common response mechanisms. This is supported by the concerted expression of genes, some of which with common upstream DNA motifs, form distinct operons under different conditions indicating additional factors regulating their expression. Frequent antisense transcripts, alternative transcripts and multiple regulators per gene thus cannot longer be seen as indicators of eukaryote-specific regulatory complexity. Keywords: stress response, time series Transcriptome of M.pneumoniae has been mapped at a 8 bases resolution using a tiling array. Three time series have been included in order to map the dynamic behavior of the transcriptome. Includes replicates from the reference condition.