Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Qld 4072, Australia.
BMC Genomics. 2013 Jan 16;14:15. doi: 10.1186/1471-2164-14-15.
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.
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.
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.
放线菌形成了一个主要的细菌门，其中包括许多人类病原体。放线菌是碳循环的主要贡献者，也是抗生素和生物农药等工业高价值产品的主要来源。与放线菌门的其他成员一致，红色糖多孢菌经历了一个过渡开关。这个开关的特点是许多代谢和形态上的变化。
我们进行了 RNA 测序，以分析红色糖多孢菌在分批培养中生长时发生的转录变化。通过在发酵过程中对 RNA 进行测序，平均覆盖率为 4000X，我们发现绝大多数基因都有明显的表达，这表明我们接近饱和地测序了转录组。在代谢开关过程中，基因表达的全局变化影响了红色糖多孢菌的代谢机制，重置了一个全新的基因表达程序。开关后，全局变化包括复杂转录机制调节的一半基因的广泛抑制。旁系转座子簇划定了这些转录程序。新的转录程序由一个瓶颈事件协调，在这个事件中，mRNA 水平受到靶向 mRNA 降解的严重限制。
我们的结果几乎达到了转录组测序的饱和覆盖，揭示了意想不到的转录复杂性，近三分之一的转录内容来自未注释的序列。我们表明，代谢开关是一种复杂的转录调控机制，能够以非凡的速度和规模重置和重新同步基因表达程序。
