Hwang Soonkyu, Lee Namil, Choe Donghui, Lee Yongjae, Kim Woori, Jeong Yujin, Cho Suhyung, Palsson Bernhard O, Cho Byung-Kwan
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
mSystems. 2021 May 4;6(3):e01013-20. doi: 10.1128/mSystems.01013-20.
Identification of transcriptional regulatory elements in the GC-rich genome is essential for the production of novel biochemicals from secondary metabolite biosynthetic gene clusters (smBGCs). Despite many efforts to understand the regulation of transcription initiation in smBGCs, information on the regulation of transcription termination and posttranscriptional processing remains scarce. In this study, we identified the transcriptional regulatory elements in β-lactam antibiotic-producing ATCC 27064 by determining a total of 1,427 transcript 3'-end positions (TEPs) using the term-seq method. Termination of transcription was governed by three classes of TEPs, of which each displayed unique sequence features. The data integration with transcription start sites and transcriptome data generated 1,648 transcription units (TUs) and 610 transcription unit clusters (TUCs). TU architecture showed that the transcript abundance in TU isoforms of a TUC was potentially affected by the sequence context of their TEPs, suggesting that the regulatory elements of TEPs could control the transcription level in additional layers. We also identified TU features of a xenobiotic response element (XRE) family regulator and DUF397 domain-containing protein, particularly showing the abundance of bidirectional TEPs. Finally, we found that 189 noncoding TUs contained potential - and -regulatory elements that played a major role in regulating the 5' and 3' UTR. These findings highlight the role of transcriptional regulatory elements in transcription termination and posttranscriptional processing in sp. sp. is a great source of bioactive secondary metabolites, including antibiotics, antifungal agents, antiparasitic agents, immunosuppressant compounds, and other drugs. Secondary metabolites are synthesized via multistep conversions of the precursor molecules from primary metabolism, governed by multicomplex enzymes from secondary metabolite biosynthetic gene clusters. As their production is closely related with the growth phase and dynamic cellular status in response to various intra- and extracellular signals, complex regulatory systems tightly control the gene expressions related to secondary metabolism. In this study, we determined genome-wide transcript 3'-end positions and transcription units in the β-lactam antibiotic producer ATCC 27064 to elucidate the transcriptional regulatory elements in transcription termination and posttranscriptional processing by integration of multiomics data. These unique features, such as transcript 3'-end sequence, potential riboregulators, and potential 3'-untranslated region (UTR) -regulatory elements, can be potentially used to design engineering tools that can regulate the transcript abundance of genes for enhancing secondary metabolite production.
在富含GC的基因组中鉴定转录调控元件对于从次级代谢物生物合成基因簇（smBGCs）生产新型生化物质至关重要。尽管人们为了解smBGCs中转录起始的调控付出了诸多努力，但关于转录终止和转录后加工调控的信息仍然匮乏。在本研究中，我们通过使用term-seq方法确定了总共1427个转录本3'末端位置（TEP），从而鉴定了产β-内酰胺抗生素的ATCC 27064中的转录调控元件。转录终止由三类TEP控制，每类TEP都显示出独特的序列特征。将这些数据与转录起始位点和转录组数据整合，生成了1648个转录单元（TU）和610个转录单元簇（TUC）。TU结构表明，TUC的TU异构体中的转录本丰度可能受其TEP的序列背景影响，这表明TEP的调控元件可以在其他层面控制转录水平。我们还鉴定了异源生物响应元件（XRE）家族调节因子和含DUF397结构域蛋白的TU特征，特别显示出双向TEP的丰度。最后，我们发现189个非编码TU包含在调节5'和3'非翻译区（UTR）中起主要作用的潜在σ-和ρ-调控元件。这些发现突出了转录调控元件在sp. sp.转录终止和转录后加工中的作用。sp. sp.是生物活性次级代谢物的重要来源，包括抗生素、抗真菌剂、抗寄生虫剂、免疫抑制化合物和其他药物。次级代谢物通过初级代谢中前体分子的多步转化合成，由次级代谢物生物合成基因簇中的多复合体酶控制。由于它们的产生与生长阶段以及响应各种细胞内和细胞外信号的动态细胞状态密切相关，复杂的调控系统严格控制与次级代谢相关的基因表达。在本研究中，我们确定了β-内酰胺抗生素生产者ATCC 27064全基因组的转录本3'末端位置和转录单元，通过整合多组学数据来阐明转录终止和转录后加工中的转录调控元件。这些独特特征，如转录本3'末端序列、潜在的核糖调节因子和潜在的3'非翻译区（UTR）调控元件，可潜在地用于设计工程工具，以调节基因的转录本丰度，从而提高次级代谢物的产量。
