Transcriptome complexity in a genome-reduced bacterium.
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.
Güell
Marc
M
Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.
van Noort
Vera
V
Yus
Eva
E
Chen
Wei-Hua
WH
Leigh-Bell
Justine
J
Michalodimitrakis
Konstantinos
K
Yamada
Takuji
T
Arumugam
Manimozhiyan
M
Doerks
Tobias
T
Kühner
Sebastian
S
Rode
Michaela
M
Suyama
Mikita
M
Schmidt
Sabine
S
Gavin
Anne-Claude
AC
Bork
Peer
P
Serrano
Luis
L
D001483:Base Sequence; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009177:Mycoplasma pneumoniae / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000032:analysis / Q000235:genetics*; D014158:Transcription, Genetic
D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated