Possibility to direct all of the cellular resources towards the production of a single protein [23]; to control the level of an orthogonal aaRS/ tRNA pair and of the UAA employed in protein expression due to the absence of a cell wall. Another advantage of the in vitro approach is the possible use of aforementioned UAAs which can not be applied in vivo. Here, we describe a general strategy based on the use of commercially available cell-free expression systems, combined with orthogonal M. jannaschii synthetases and cognate MjtRNACUA or synthetic tRNACUAOpt [4,24], to obtain high yields of UAAlabeled proteins. This approach allowed us to incorporate tyrosine, as well as p-acetyl-L-phenylalanine (pAcPhe), p-benzoyl-L-phenylalanine (pBpa) and p-Iodo-L-phenylalanine (pIPhe; Fig. 1) into Green Fluorescent Protein (GFP), in response to the TAG stop codon with high fidelity and efficiency. The final yield of modified proteins varied widely and under optimal conditions reached roughly 50?20 of the wild type expression levels, depending on the type of suppressor tRNA, aaRS used and UAA used.Materials and Methods GFP MutantsThe X-ray crystallographic structure of template GFP (PDB accession number: 1EMA), encoded by the GFP control vector (RTS, 5 PRIME, Hamburg, Germany), was analyzed to choose sites for UAA incorporation. To examine the effect of the nucleotide following the stop codon on protein yields, we selected four amino acid residues on two external b-sheet of GFP and its adjacent loop. The selection of these residues for substitution by an UAA was chosen as not to obstruct proper GFP folding. The coding sequence of GFP was thus modified to replace the codons encoding tyrosine 39, lysine 41, 1315463 leucine 42 or lysine 45 to an amber stop codon (TAG), with the nucleotide following the stop codon being G, C, A or T, respectively. The codons of amino acids at another b-sheet, i.e. histidine 148, asparagine 149 andvaline 150, were substituted to TAG, such that A, G and T followed the stop codon, respectively. In order to generate mutation at permessive site of GFP the codon of tyrosine 151 was replaced to TAG, and the adjacent isoleucine 152 (ATC) was substituted by leucine (CTC), so that C has followed the amber stop codon. Mutagenesis was performed in the control vector containing the gene for GFP, by site-directed mutagenesis using QuikChange II Site-Directed Mutagenesis Kit (Stratagen, Agilent Technologies, Santa Clara, CA) and the following primers: QC-GFPY39 F (5′ CATGGCAGGGGTTCAAATCCCCTCCGCCGGA?’) and QC-GFPY39 R (5′?Rp loss in lipid-free apoA-I exposed to 0 (black bars) or 15 mM TCCGGCGGAGGGGATTTGAACCCCTGCCATGC?’); QC-GFPK41 F (5′ GGTGAAGGTGATGCAACATACGGATAGCTTACCCTTAAATTTATTTGC?’) and QC-GFPK41 R (5′ CAAATAAATTTAAGGGTAAGCTATCCGTATGTTGCATCACCTTCACCC?’); QC-GFPL42 F (5′?GATGCAACATACGGAAAATAGACCCTTAAATTTATTTGCAC?’) and QC-GFPL42 R (5′ TGCAAATAAATTTAAGGGTCTATTTTCCGTATGTTGCATC?’); QC-GFPK45 F (5′ ATACGGAAAACTTACCCTTTAGTTTATTTGCACTACTGG?’) and QC-GFPK45 R (5′ CAGTAGTGCAAATAAACTAAAGGGTAAGTTTTCCGTATG?3′); Title Loaded From File QC-GFPH148 F (5′ GAATACAACTATAACTCATAGAATGTATACATCATGGCAG?’) and QC-GFPH148 R (5′ TGCCATGATGTATACATTCTATGAGTTATAGTTGTATTCC?’); QC-GFPN149 F (5′ AACTATAACTCACACTAGGTATACATCATGGCAGAC?’) and QC-GFPN149 R (5′ TCTGCCATGATGTATACCTAGTGTGAGTTATAGTTG?’); QC-GFPV150 F (5′ GAATACAACTATAACTCACACAATTAGTACATCATGCAGAC?’) and QCGFPV150 R (5′ TCTGCCATGATGTACTAATTGTGTGAGTTATAGTTGTATTCC?’); QC-GFPY151 F (5′ TATAACTCACACAATGTATAGCTCATGGCAGACAAACAAAAGAATGG?’) and QC-GFPY151 R (5′?CCATTCTTTTGTTTGTCTGCCATGAGCTATACATTGTGTGAGTTATAG.Possibility to direct all of the cellular resources towards the production of a single protein [23]; to control the level of an orthogonal aaRS/ tRNA pair and of the UAA employed in protein expression due to the absence of a cell wall. Another advantage of the in vitro approach is the possible use of aforementioned UAAs which can not be applied in vivo. Here, we describe a general strategy based on the use of commercially available cell-free expression systems, combined with orthogonal M. jannaschii synthetases and cognate MjtRNACUA or synthetic tRNACUAOpt [4,24], to obtain high yields of UAAlabeled proteins. This approach allowed us to incorporate tyrosine, as well as p-acetyl-L-phenylalanine (pAcPhe), p-benzoyl-L-phenylalanine (pBpa) and p-Iodo-L-phenylalanine (pIPhe; Fig. 1) into Green Fluorescent Protein (GFP), in response to the TAG stop codon with high fidelity and efficiency. The final yield of modified proteins varied widely and under optimal conditions reached roughly 50?20 of the wild type expression levels, depending on the type of suppressor tRNA, aaRS used and UAA used.Materials and Methods GFP MutantsThe X-ray crystallographic structure of template GFP (PDB accession number: 1EMA), encoded by the GFP control vector (RTS, 5 PRIME, Hamburg, Germany), was analyzed to choose sites for UAA incorporation. To examine the effect of the nucleotide following the stop codon on protein yields, we selected four amino acid residues on two external b-sheet of GFP and its adjacent loop. The selection of these residues for substitution by an UAA was chosen as not to obstruct proper GFP folding. The coding sequence of GFP was thus modified to replace the codons encoding tyrosine 39, lysine 41, 1315463 leucine 42 or lysine 45 to an amber stop codon (TAG), with the nucleotide following the stop codon being G, C, A or T, respectively. The codons of amino acids at another b-sheet, i.e. histidine 148, asparagine 149 andvaline 150, were substituted to TAG, such that A, G and T followed the stop codon, respectively. In order to generate mutation at permessive site of GFP the codon of tyrosine 151 was replaced to TAG, and the adjacent isoleucine 152 (ATC) was substituted by leucine (CTC), so that C has followed the amber stop codon. Mutagenesis was performed in the control vector containing the gene for GFP, by site-directed mutagenesis using QuikChange II Site-Directed Mutagenesis Kit (Stratagen, Agilent Technologies, Santa Clara, CA) and the following primers: QC-GFPY39 F (5′ CATGGCAGGGGTTCAAATCCCCTCCGCCGGA?’) and QC-GFPY39 R (5′?TCCGGCGGAGGGGATTTGAACCCCTGCCATGC?’); QC-GFPK41 F (5′ GGTGAAGGTGATGCAACATACGGATAGCTTACCCTTAAATTTATTTGC?’) and QC-GFPK41 R (5′ CAAATAAATTTAAGGGTAAGCTATCCGTATGTTGCATCACCTTCACCC?’); QC-GFPL42 F (5′?GATGCAACATACGGAAAATAGACCCTTAAATTTATTTGCAC?’) and QC-GFPL42 R (5′ TGCAAATAAATTTAAGGGTCTATTTTCCGTATGTTGCATC?’); QC-GFPK45 F (5′ ATACGGAAAACTTACCCTTTAGTTTATTTGCACTACTGG?’) and QC-GFPK45 R (5′ CAGTAGTGCAAATAAACTAAAGGGTAAGTTTTCCGTATG?3′); QC-GFPH148 F (5′ GAATACAACTATAACTCATAGAATGTATACATCATGGCAG?’) and QC-GFPH148 R (5′ TGCCATGATGTATACATTCTATGAGTTATAGTTGTATTCC?’); QC-GFPN149 F (5′ AACTATAACTCACACTAGGTATACATCATGGCAGAC?’) and QC-GFPN149 R (5′ TCTGCCATGATGTATACCTAGTGTGAGTTATAGTTG?’); QC-GFPV150 F (5′ GAATACAACTATAACTCACACAATTAGTACATCATGCAGAC?’) and QCGFPV150 R (5′ TCTGCCATGATGTACTAATTGTGTGAGTTATAGTTGTATTCC?’); QC-GFPY151 F (5′ TATAACTCACACAATGTATAGCTCATGGCAGACAAACAAAAGAATGG?’) and QC-GFPY151 R (5′?CCATTCTTTTGTTTGTCTGCCATGAGCTATACATTGTGTGAGTTATAG.
