Genomic and transcriptomic landscape of Escherichia coli BL21(DE3)

Sinyeon Kim, Haeyoung Jeong, Eun Youn Kim, Jihyun F. Kim, Sang Yup Lee, Sung Ho Yoon

Research output: Contribution to journalArticlepeer-review

39 Citations (Scopus)


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. Highresolution 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 noncoding 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.

Original languageEnglish
Pages (from-to)5285-5293
Number of pages9
JournalNucleic acids research
Issue number9
Publication statusPublished - 2017 May 19

Bibliographical note

Publisher Copyright:
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

All Science Journal Classification (ASJC) codes

  • Genetics


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