The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase

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Abstract
We have identified the SMK box as a conserved RNA motif in the 5′ untranslated leader region of metK (SAM synthetase) genes in lactic acid bacteria, including Enterococcus, Streptococcus and Lactococcus species. This RNA element bound SAM in vitro, and binding of SAM caused an RNA structural rearrangement that resulted in sequestration of the Shine-Dalgarno (SD) sequence. Mutations that disrupted pairing between the SD region and a sequence complementary to the SD blocked SAM binding, whereas compensatory mutations that restored pairing restored SAM binding. The Enterococcus faecalis SMK box conferred translational repression of a lacZ reporter when cells were grown under conditions where SAM pools are elevated, and mutations that blocked SAM binding resulted in loss of repression, demonstrating that the SMK box is functional in vivo. The SMK box therefore represents a new SAM-binding riboswitch distinct from the previously identified S box RNAs.