Determination of single nucleotide variants in Escherichia coli DH5α by using short-read sequencing.
Escherichia coli DH5α is a common laboratory strain that provides an important platform for routine use in cloning and synthetic biology applications. Many synthetic circuits have been constructed and successfully expressed in E. coli DH5α; however, its genome sequence has not been determined yet. Here, we determined E. coli DH5α genome sequence and identified genetic mutations that affect its phenotypic functions by using short-read sequencing. The sequencing results clearly described the genotypes of E. coli DH5α, which aid in further studies using the strain. Additionally, we observed 105 single nucleotide variants (SNVs), 83% of which were detected in protein-coding regions compared to the parental strain E. coli DH1. Interestingly, 23% of the protein-coding regions have mutations in their amino acid residues, whose biological functions were categorized into two-component systems, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis. These results underscore the advantages of E. coli DH5α, which tolerates the components of transformation buffer and expresses foreign plasmids efficiently. Moreover, these SNVs were also observed in the commercially available strain. These data provide the genetic information of E. coli DH5α for its future application in metabolic engineering and synthetic biology.
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
Yoseb
Y
Song
Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea.
Bo-Rahm
BR
Lee
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
Suhyung
S
Cho
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
Yoo-Bok
YB
Cho
Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea.
Seon-Won
SW
Kim
Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul 100-715, Republic of Korea.
Taek Jin
TJ
Kang
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea.
Sun Chang
SC
Kim
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea bcho@kaist.ac.kr.
Byung-Kwan
BK
Cho
D000596:Amino Acids; D004926:Escherichia coli / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D008070:Lipopolysaccharides / Q000235:genetics; D009154:Mutation; D009711:Nucleotides / Q000032:analysis*; D010457:Peptidoglycan / Q000235:genetics; D010641:Phenotype; D010957:Plasmids; D017422:Sequence Analysis, DNA / Q000379:methods*
D000596:Amino Acids; D008070:Lipopolysaccharides; D009711:Nucleotides; D010457:Peptidoglycan
Escherichia coli DH5α; genome sequencing; single nucleotide variants