Consecutive Elongation of D-Amino Acids in Translation Takayuki Katoh, Kenya Tajima, Hiroaki Suga  Cell Chemical Biology  Volume 24, Issue 1, Pages 46-54 (January 2017) DOI: 10.1016/j.chembiol.2016.11.012 Copyright © 2017 Elsevier Ltd Terms and Conditions

Cell Chemical Biology 2017 24, 46-54DOI: (10. 1016/j. chembiol. 2016 Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Incorporation of Two Consecutive D-Ala Residues into a Model Peptide using tRNAGluE2 (A) mRNA sequence (mR1) and the corresponding peptide sequences (wP1 and rP1) used in this experiment. The sequence of rP1 is reprogrammed based on the codon table shown in Figure S1B. Bold letters indicate the reprogrammed codons and the corresponding amino acids. (B–D) Sequences of transcribed tRNAAsnE2GGA (B), tRNAGluUUC (C), and tRNAGluE2GGA (D). Alteration of nucleotides from the wild-type E. coli tRNAAsn (B) and tRNAGlu (D) are indicated in red. (E) Tricine SDS-PAGE analysis of the rP1 peptide synthesized by the FIT system. tRNAAsnE2GGA or tRNAGluE2GGA was used for incorporation of D- or L-Ala at the UCC codons of mR1. Arrows indicate the bands corresponding to the desired products. (F) MALDI-TOF MS analysis of peptide rP1 synthesized by the FIT system using tRNAGluE2GGA for introduction of D- or L-Ala. Arrows indicate the peaks corresponding to the desired products. Calc. and Obs. indicate calculated and observed m/z values, respectively. Cell Chemical Biology 2017 24, 46-54DOI: (10.1016/j.chembiol.2016.11.012) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Titration of Translation Factors in Translation of rP1-DA2 Peptide (A) Titration of IF2 concentration. Translation was carried out for 30 min with 0.1 μM EF-G and 10 μM EF-Tu/Ts using tRNAGluE2GGA for introduction of D-Ala. Error bars, SD (n = 3). (B) Titration of EF-Tu/Ts concentration. Translation was carried out for 30 min with 0.1 μM EF-G and 3 μM IF2 using tRNAGluE2GGA for introduction of D-Ala. Error bars, SD (n = 3). (C) Titration of EF-G concentration. Translation was carried out for 30 min with 0.4 μM IF2 and 10 μM EF-Tu/Ts using tRNAGluE2GGA for introduction of D-Ala. Error bars, SD (n = 3). Cell Chemical Biology 2017 24, 46-54DOI: (10.1016/j.chembiol.2016.11.012) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 Incorporation of Ten Consecutive D-Ser Residues into a Model Peptide (A) mRNA sequence (mR3) and the corresponding peptide sequence (rP3). n indicates the number of consecutive ACU codons in mR3 and L- or D-Ser in rP3. Sequence of flag is the same as mR1 and rP1. The sequence of rP3 is reprogrammed by using the codon table shown in Figure S1C. Bold letters indicate the reprogrammed codons and the corresponding amino acids. (B) Tricine SDS-PAGE analysis of rP3 synthesized by the FIT system. n indicates the number of consecutive L- or D-Ser. (C) MALDI-TOF MS analysis of peptide rP3 containing consecutive D-Ser. Arrows indicate the peaks corresponding to desired products. Calc. and Obs. indicate calculated and observed m/z values, respectively. See also Figure S3 for the result of peptide rP3 containing consecutive L-Ser. Cell Chemical Biology 2017 24, 46-54DOI: (10.1016/j.chembiol.2016.11.012) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 Ribosomal Synthesis of D-Form Macrocyclic Peptide Closed by a Disulfide Bond (A) mRNA sequence (mR4) and the corresponding peptide sequences (wP4 and rP4). Sequence of flag is the same as mR1 and rP1. The sequence of rP4 is reprogrammed based on the codon table shown in Figure S1D. Bold letters indicate the reprogrammed codons and the corresponding amino acids. Two cysteine residues included in the rP4 form a disulfide bond to give a macrocyclic structure. (B) Tricine SDS-PAGE analysis of rP4 synthesized by the FIT system. Combinations of stereochemistry in Cys, Ser, and Ala are indicated. (C) MALDI-TOF MS analysis of peptide rP4 with D-Cys/D-Ser/D-Ala and L-Cys/L-Ser/L-Ala. Arrows indicate the peaks of desired products. Calc. and Obs. indicate calculated and observed m/z values, respectively. See also Figure S4 for the result of peptide rP4 with other combinations of D/L-Cys, D/L-Ser, and D/L-Ala. Cell Chemical Biology 2017 24, 46-54DOI: (10.1016/j.chembiol.2016.11.012) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 5 Ribosomal Synthesis of D-Form Macrocyclic Peptide Closed by a Thioether Bond (A) mRNA sequence (mR5) and the corresponding peptide sequences (wP5 and rP5). Sequence of flag is the same as mR1 and rP1. The sequence of rP5 is reprogrammed by using the codon table shown in Figure S1E. Bold letters indicate the reprogrammed codons and the corresponding amino acids. ClAcF indicates N-chloroacetyl phenylalanine. (B) Structure of macrocyclic peptide rP5. The sulfhydryl group of the Cys in rP5 attacks the α carbon of the N-terminal chloroacetyl group to form a thioether bond and give a macrocyclic structure. (C) Tricine SDS-PAGE analysis of rP5 synthesized by the FIT system. Combinations of stereochemistry in ClAcPhe, Ser, and Cys are indicated. (D) MALDI-TOF MS analysis of peptide rP5 with D-ClAcPhe/D-Ser/D-Cys, and L-ClAcPhe/L-Ser/L-Cys. Arrows indicate the peaks corresponding to desired products. Calc. and Obs. indicate calculated and observed m/z values, respectively. See also Figure S5 for the result of peptide rP5 with other combinations of D/L-ClAcPhe, D/L-Ser, and D/L-Cys. Cell Chemical Biology 2017 24, 46-54DOI: (10.1016/j.chembiol.2016.11.012) Copyright © 2017 Elsevier Ltd Terms and Conditions