title: Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch.
abstract: BACKGROUND
  Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value products such as antibiotics and biopesticides. Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes.
  
  
  RESULTS
  We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. By sequencing RNA across the fermentation time course, at a mean coverage of 4000X, we found the vast majority of genes to be prominently expressed, showing that we attained close to saturating sequencing coverage of the transcriptome. During the metabolic switch, global changes in gene expression influence the metabolic machinery of Saccharopolyspora erythraea, resetting an entirely novel gene expression program. After the switch, global changes include the broad repression of half the genes regulated by complex transcriptional mechanisms. Paralogous transposon clusters, delineate these transcriptional programs. The new transcriptional program is orchestrated by a bottleneck event during which mRNA levels are severely restricted by targeted mRNA degradation.
  
  
  CONCLUSIONS
  Our results, which attained close to saturating sequencing coverage of the transcriptome, revealed unanticipated transcriptional complexity with almost one third of transcriptional content originating from un-annotated sequences. We showed that the metabolic switch is a sophisticated mechanism of transcriptional regulation capable of resetting and re-synchronizing gene expression programs at extraordinary speed and scale.
authors: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld 4072, Australia.
authors: Esteban
authors: E
authors: Marcellin
authors: Tim R
authors: TR
authors: Mercer
authors: Cuauhtemoc
authors: C
authors: Licona-Cassani
authors: Robin W
authors: RW
authors: Palfreyman
authors: Marcel E
authors: ME
authors: Dinger
authors: Jennifer A
authors: JA
authors: Steen
authors: John S
authors: JS
authors: Mattick
authors: Lars K
authors: LK
authors: Nielsen
mesh_terms: D004917:Erythromycin / Q000096:biosynthesis / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005812:Genes, Switch; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics; D020871:RNA Stability / Q000235:genetics*; D016930:Saccharopolyspora / Q000235:genetics* / Q000472:pathogenicity; D014158:Transcription, Genetic
chemical_list: D004917:Erythromycin