Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

Marcellin, Esteban, Mercer, Tim R., Licona-Cassani, Cuauhtemoc, Palfreyman, Robin W., Dinger, Marcel E., Steen, Jennifer A., Mattick, John S. and Nielsen, Lars K. (2013) Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics, 14 1: 15.1-15.9. doi:10.1186/1471-2164-14-15


Author Marcellin, Esteban
Mercer, Tim R.
Licona-Cassani, Cuauhtemoc
Palfreyman, Robin W.
Dinger, Marcel E.
Steen, Jennifer A.
Mattick, John S.
Nielsen, Lars K.
Title Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-01
Year available 2013
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-15
Open Access Status DOI
Volume 14
Issue 1
Start page 15.1
End page 15.9
Total pages 9
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2014
Language eng
Formatted 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.
Keyword Rna Sequencing
Actinobacteria
Saccharopolyspora erythraea
Erythromycin
Metabolic switch
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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Created: Sun, 28 Apr 2013, 00:50:20 EST by System User on behalf of Aust Institute for Bioengineering & Nanotechnology