Kim Sinyeon, Jeong Haeyoung, Kim Eun-Youn, Kim Jihyun F, Lee Sang Yup, Yoon Sung Ho
Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
Nucleic Acids Res. 2017 May 19;45(9):5285-5293. doi: 10.1093/nar/gkx228.
Escherichia coli BL21(DE3) has long served as a model organism for scientific research, as well as a workhorse for biotechnology. Here we present the most current genome annotation of E. coli BL21(DE3) based on the transcriptome structure of the strain that was determined for the first time. The genome was annotated using multiple automated pipelines and compared to the current genome annotation of the closely related strain, E. coli K-12. High-resolution tiling array data of E. coli BL21(DE3) from several different stages of cell growth in rich and minimal media were analyzed to characterize the transcriptome structure and to provide supporting evidence for open reading frames. This new integrated analysis of the genomic and transcriptomic structure of E. coli BL21(DE3) has led to the correction of translation initiation sites for 88 coding DNA sequences and provided updated information for most genes. Additionally, 37 putative genes and 66 putative non-coding RNAs were also identified. The panoramic landscape of the genome and transcriptome of E. coli BL21(DE3) revealed here will allow us to better understand the fundamental biology of the strain and also advance biotechnological applications in industry.
大肠杆菌BL21(DE3)长期以来一直是科学研究的模式生物，也是生物技术的主力军。在此，我们基于首次测定的该菌株转录组结构，展示了大肠杆菌BL21(DE3)的最新基因组注释。使用多个自动化流程对基因组进行注释，并与密切相关菌株大肠杆菌K-12的当前基因组注释进行比较。分析了来自丰富培养基和基本培养基中几个不同细胞生长阶段的大肠杆菌BL21(DE3)的高分辨率平铺阵列数据，以表征转录组结构并为开放阅读框提供支持证据。对大肠杆菌BL21(DE3)的基因组和转录组结构进行的这种新的综合分析，已导致对88个编码DNA序列的翻译起始位点进行了校正，并为大多数基因提供了更新信息。此外，还鉴定出37个推定基因和66个推定非编码RNA。此处揭示的大肠杆菌BL21(DE3)基因组和转录组的全景将使我们能够更好地理解该菌株 的基础生物学特性，并推动其在工业中的生物技术应用。
