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

Abstract

We have identified the S(MK) 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 S(MK) 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 S(MK) box is functional in vivo. The S(MK) box therefore represents a new SAM-binding riboswitch distinct from the previously identified S box RNAs.

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

“…This mechanism of gene control has previously been observed for several other riboswitches (Rodionov et al 2002;Mandal and Breaker 2004b;Fuchs et al 2006;Wang et al 2008). Similarly, representatives of the preQ 1 -I riboswitch are predicted to down-regulate expression of homologous COG4708 genes in response to preQ 1 ).…”

“…This narrow distribution has precedent, as SAM-III also appears limited to the same group of bacteria (Fuchs et al 2006). However, the bioinformatics searches that identified the preQ 1 -II riboswitch candidate did not uncover SAM-III Weinberg et al 2007), suggesting that there may be other RNA elements unique to this family that have yet to be identified.…”

“…Four different aptamer classes recognizing Sadenosylmethionine (AdoMet or SAM) have been identified to date. SAM-I or S-box (Epshtein et al 2003;McDaniel et al 2003;Winkler et al 2003), SAM-II (Corbino et al 2005), SAM-III or SMKbox (Fuchs et al 2006), and SAM-IV ) often regulate the same genes in different organisms (e.g., SAM synthase, homoserine O-succinyltransferase). The discovery of a second natural preQ 1 aptamer class shows that SAM is not a special case and that additional metabolites may be bound by multiple distinct RNA architectures to control similar sets of genes in different organisms.…”

Folding of the SAM-I riboswitch

“…11,[30][31][32][33][34] These riboswitches are located upstream of genes involved in the metabolism, biosynthesis and transport of methionine or SAM. 11,35 The SAM riboswitch class is one of the most abundant, 36 especially in Gram-positive organisms, and is unique in that six distinct SAM riboswitch families have been reported to date that bind SAM in diverse ways.…”

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

“…Two of these, the lysine and glycine riboswitches, can directly detect amino acids. While the structure of several SAM and lysine riboswitches has been determined (Fuchs et al 2006;Montange and Batey 2006;Gilbert et al 2008;Serganov et al 2008), the structural basis of glycine riboswitch function is still not known. The glycine riboswitch was identified in a bioinformatic search for conserved sequences and secondary structural elements.…”