Journal Article

Transcriptome Complexity in a Genome-Reduced Bacterium

Michalodimitrakis, Konstantinos, Kühner, Sebastian, Yamada, Takuji, Bork, Peer, Rode, Michaela, Serrano, Luis, Schmidt, Sabine, Gavin, Anne-Claude, Suyama, Mikita, Arumugam, Manimozhiyan, Leigh-Bell, Justine, Doerks, Tobias, Güell, Marc, Chen, Wei-Hua, van Noort, Vera, Yus, Eva

2009

Overview

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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Bacteria / Bacteriology / Base Sequence / Biological and medical sciences / Eukaryotic cells / Fundamental and applied biological sciences. Psychology / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Bacterial / Genes / Genes, Bacterial / Genetics / Genome, Bacterial / Genomes / Genomics / Microbiology / Molecular Sequence Data / Mycoplasma pneumoniae / Mycoplasma pneumoniae - genetics / Mycoplasma pneumoniae - metabolism / non-coding RNA / Oligonucleotide Array Sequence Analysis / Operon / Operons / RNA / RNA, Antisense - genetics / RNA, Antisense - metabolism / RNA, Bacterial - genetics / RNA, Bacterial - metabolism / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA, Untranslated - analysis / RNA, Untranslated - genetics / Steepest descent method / Tiling / transcription (genetics) / Transcription, Genetic / transcriptome / Transcriptomes / transcriptomics