Modified constructs of the tRNA TΨC domain to probe substrate conformational requirements of m1A58 and m5U54 tRNA methyltransferases

The T Psi C stem and loop (TSL) of tRNA contains highly conserved nucleoside modifications, m(5)C(49), T-54, Psi(55) and m(1)A(58). U-54 is methylated to m(5)U (T) by m(5)U(54) methyltransferase (RUMT); A(58) is methylated to m(1)A by m(1)A(58) tRNA methyltransferase (RAMT), RUMT recognizes and methylates a minimal TSL heptadecamer and RAMT has previously been reported to recognize and methylate the 3'-half of the tRNA molecule. We report that RAMT can recognize and methylate a TSL heptadecamer. To better understand the sensitivity of RAMT and RUMT to TSL conformation, we have designed and synthesized variously modified TSL constructs with altered local conformations and stabilities. TSLs were synthesized with natural modifications (T-54 and Psi(55)), naturally occurring modifications at unnatural positions (m(5)C(60)), altered sugar puckers (dU(54) and/or dU(55)) or with disrupted U-turn interactions (m(1)Psi(55) or m(1)m(3)Psi(55)), The unmodified heptadecamer TSL was a substrate of both RAMT and RUMT. The presence of T-54 increased thermal stability of the TSL and dramatically reduced RAMT activity toward the substrate, Local conformation around U-54 was found to be an important determinant for the activities of both RAMT and RUMT.