Conversion of Exposed Cytidine Residues to Uridine Residues in Escherichia coli Formylmethionine Transfer Ribonucleic Acid

Abstract

Abstract Treatment of Escherichia coli formylmethionine tRNA with sodium bisulfite results in conversion of 6 cytidine residues to uridine residues under conditions where other cytidine residues in the tRNA are unreactive. Comparison of double and single stranded polymers shows that the bisulfitemediated deamination reaction is strongly inhibited by ordered structure. Under conditions where over 90% of the cytidine residues in poly(C) are deaminated, there is no detectable reaction of poly(I) poly(C). The 6 reactive cytidine residues in formylemethionine tRNA are modified at the same rate as cytidine residues in poly(C) and all are located in single stranded regions of the clover-leaf model. The modified residues include the cytidine at the 5'-phosphate terminus, the cytidine in the anticodon, the two cytidines in the dihydrouridine loop, and the two cytidines in the 3'-terminal CpCpA sequence. The O-methylcytidine in the anticodon loop shows only about 20% reaction under conditions where reactive cytidines are completely modified. No reaction of the cytidine in the small loop or of the cytidine in the TψC loop is observed. Aside from the unusual unpaired base at the 5' terminus, the initiator tRNA resembles several other tRNAs with respect to the locations of exposed and protected cytidine residues in the ordered structure of the molecule.