title: Genomic and transcriptomic landscape of Escherichia coli BL21(DE3).
abstract: 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.
authors.affiliation: Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
authors.forename: Sinyeon
authors.initials: S
authors.lastname: Kim
authors.affiliation: Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
authors.forename: Haeyoung
authors.initials: H
authors.lastname: Jeong
authors.affiliation: School of Basic Sciences, Hanbat National University, Daejeon 34158, Republic of Korea.
authors.forename: Eun-Youn
authors.initials: EY
authors.lastname: Kim
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, Republic of Korea.
authors.forename: Jihyun F
authors.initials: JF
authors.lastname: Kim
authors.affiliation: Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, Daejeon 34141, Republic of Korea.
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.affiliation: Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
authors.forename: Sung Ho
authors.initials: SH
authors.lastname: Yoon
mesh_terms: D003470:Culture Media / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D016680:Genome, Bacterial; D023281:Genomics; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D003470:Culture Media; D022661:RNA, Untranslated