title: An Engineered Rare Codon Device for Optimization of Metabolic Pathways.
abstract: Rare codons generally arrest translation due to rarity of their cognate tRNAs. This property of rare codons can be utilized to regulate protein expression. In this study, a linear relationship was found between expression levels of genes and copy numbers of rare codons inserted within them. Based on this discovery, we constructed a molecular device in Escherichia coli using the rare codon AGG, its cognate tRNA (tRNA(Arg) (CCU)), modified tRNA(Asp) (GUC → CCU), and truncated aspartyl-tRNA synthetase (TDRS) to switch the expression of reporter genes on or off as well as to precisely regulate their expression to various intermediate levels. To underscore the applicability of our work, we used the rare codon device to alter the expression levels of four genes of the fatty acid synthesis II (FASII) pathway (i.e. fabZ, fabG, fabI, and tesA') in E. coli to optimize steady-state kinetics, which produced nearly two-fold increase in fatty acid yield. Thus, the proposed method has potential applications in regulating target protein expression at desired levels and optimizing metabolic pathways by precisely tuning in vivo molar ratio of relevant enzymes.
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: You
authors: Y
authors: Wang
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Chunying
authors: C
authors: Li
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.
authors: Md Rezaul Islam
authors: MR
authors: Khan
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.
authors: Yushu
authors: Y
authors: Wang
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Yunfeng
authors: Y
authors: Ruan
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Bin
authors: B
authors: Zhao
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Bo
authors: B
authors: Zhang
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Xiaopan
authors: X
authors: Ma
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Kaisi
authors: K
authors: Zhang
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Xiwen
authors: X
authors: Zhao
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Guanhao
authors: G
authors: Ye
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.
authors: Xizhi
authors: X
authors: Guo
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.
authors: Guoyin
authors: G
authors: Feng
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.|Shanghai genome Pilot Institutes for Genomics and Human Health, Shanghai, 200030, China.
authors: Lin
authors: L
authors: He
authors: Bio-X institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, PR China.|2011 SJTU-BioX-Shanghai Team for The International Genetically Engineered Machine Competition (iGEM), Shanghai Jiao Tong University, Shanghai, PR China.
authors: Gang
authors: G
authors: Ma
mesh_terms: D001226:Aspartate-tRNA Ligase / Q000235:genetics / Q000378:metabolism; D003062:Codon; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D054889:Fatty Acid Synthase, Type II / Q000235:genetics / Q000378:metabolism; D005227:Fatty Acids / Q000096:biosynthesis; D017930:Genes, Reporter; D047668:Inteins / Q000235:genetics; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways; D016296:Mutagenesis; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins; D005227:Fatty Acids; D012343:RNA, Transfer; D054889:Fatty Acid Synthase, Type II; D001226:Aspartate-tRNA Ligase