Saccharopolyspora erythraea’sgenome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

BMC Genomics

Research Article

Robin W Palfreyman¹  Tim R Mercer¹  Lars K Nielsen¹  Jennifer A Steen¹  Esteban Marcellin¹  Cuauhtemoc Licona-Cassani¹  Marcel E Dinger²  John S Mattick² 

[1] Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072, Brisbane, Qld, Australia;Institute for Molecular Bioscience (IMB), The University of Queensland, 4067, Brisbane, QLD, Australia;

关键词: RNA-sequencing;    actinobacteria;    Saccharopolyspora erythraea;    Erythromycin;    Metabolic switch;   

DOI  :  10.1186/1471-2164-14-15

 received in 2012-10-04, accepted in 2012-12-20,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundActinobacteria 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.ResultsWe 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Marcellin et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.