SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch

[摘要] S-box (SAM-I) nboswitches are a widespread class of nboswitches involved in the regulation of sulfur metabolism in Gram-positive bacteria We report here the 3 0-angstrom crystal structure of the aptamer domain of the Bacillus subtilts yitJS-box (SAM-I) riboswitch bound to S-adenosyl-L-methionine (SAM) The RNA folds into two sets of helical stacks spatially arranged by tertiary interactions including a K-turn and a pseudoknot at a four-way junction The tertiary structure is further stabilized by metal coordination, extensive ribose zipper interactions, and SAM-mediated tertiary interactions Despite structural differences in the peripheral regions, the SAM-binding core of the B subtilis yitJ riboswitch is virtually superimposable with the previously determined Thermoanaerobacter tengcongensis yitJ riboswitch structure, suggesting that a highly conserved ligand-recognition mechanism is utilized by all S-box nboswitches SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing analysis further revealed that the alternative base-pairing element in the expression platform controls the conformational switching process In the absence of SAM, the apo yitJ aptamer domain folds predominantly into a pre-binding conformation that resembles, but is not identical with, the SAM-bound state We propose that SAM enters the hgand-binding site through the J1/2 J3/4 gate and locks down the SAM-bound conformation through an induced-fit mechanism Temperature-dependent SHAPE revealed that the tertiary interaction-stabilized SAM-binding core is extremely stable, likely due to the cooperative RNA folding behavior Mutational studies revealed that certain modifications in the SAM-binding region result in loss of SAM binding and constitutive termination, which suggests that these mutations lock the RNA into a form that resembles the SAM-bound form in the absence of SAM (C) 2010 Published by Elsevier Ltd

[发布日期] 2010-12-17

[关键词] riboswitch;S-box;SAM-I;SHAPE;SAM