Transcriptome Complexity in a Genome-Reduced Bacterium

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Science  27 Nov 2009:
Vol. 326, Issue 5957, pp. 1268-1271
DOI: 10.1126/science.1176951

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Simply Mycoplasma

The bacterium Mycoplasma pneumoniae, a human pathogen, has a genome of reduced size and is one of the simplest organisms that can reproduce outside of host cells. As such, it represents an excellent model organism in which to attempt a systems-level understanding of its biological organization. Now three papers provide a comprehensive and quantitative analysis of the proteome, the metabolic network, and the transcriptome of M. pneumoniae (see the Perspective by Ochman and Raghavan). Anticipating what might be possible in the future for more complex organisms, Kühner et al. (p. 1235) combine analysis of protein interactions by mass spectrometry with extensive structural information on M. pneumoniae proteins to reveal how proteins work together as molecular machines and map their organization within the cell by electron tomography. The manageable genome size of M. pneumoniae allowed Yus et al. (p. 1263) to map the metabolic network of the organism manually and validate it experimentally. Analysis of the network aided development of a minimal medium in which the bacterium could be cultured. Finally, G‡ell et al. (p. 1268) applied state-of-the-art sequencing techniques to reveal that this “simple” organism makes extensive use of noncoding RNAs and has exon- and intron-like structure within transcriptional operons that allows complex gene regulation resembling that of eukaryotes.


To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.

  • * Present address: Center for Genomic Medicine, Graduate School of Medicine, University of Kyoto, Kyoto, Japan.

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