Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism

Abstract

Three distinct classes of S-adenosyl-l-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-Å crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti–Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-l-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

“…The CFI m 25-RNA structures provide the second example of an intramolecular base pair playing a crucial role in the recognition of single-stranded RNA, first identified in the complex of the RRM domain of human alternative splicing factor Fox-1 with RNA, in which the same G-A base pair is observed (34). Interestingly, an identical G-A base pair provides the key recognition between G26 of the SAM-III riboswitch and A of S-adenosylmethionine (35,36). We speculate that the array of recognition mechanisms that we observe provides strong selective pressure to maintain not only the integrity of the protein fold and the identity of key amino acids but also the specific RNA sequence required for binding.…”

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

“…SAM II adopts a related strategy, using O2 and O4 of two U's from an AUU triple (Gilbert et al 2008) near the sulfur. The SAM III strategy is parallel to these (Lu et al 2008), but produces a [100-fold preference for SAM by directing a U O4 and a 2 0 O atom from an adjacent nucleotide at the charged sulfur. This description should not be thought of as exhaustive; for example, SAM I and SAM III use a syn Fig.…”

“…SAM I has the methyl group pointing along the broad minor groove of a helix (Montange and Batey 2006), added bulk at this position makes little difference as long as the charge is maintained (Lim et al 2006). SAM III points the methyl away from the site, into solvent, and makes little distinction between methyl-and ethyl-sulfonium ion (Lu et al 2008). In fact, SAM III does not detectably interact with methionine beyond the sulfur in any sense, because no electron density is detected there.…”

“…(Woese 1967) Nonetheless, it is clear that at some early stage in the evolution of life the direct association of amino acids with polynucleotides, which was later to evolve into the genetic code, must have begun. (Orgel 1968) methionines in three different riboswitches specific for Sadenosyl methionine (Gilbert et al 2008;Lu et al 2008;Montange and Batey 2006). Moreover, structures for the aptamer domain for the lysine riboswitch (Garst et al 2008;Serganov et al 2008) and an aptamer for citrulline and arginine (Yang et al 1996), and a natural arginine binding site (Pugilisi et al 1993) can also be consulted.…”

Downward causation by information control in micro-organisms

“…(e) Functional convergence of class II and class III of S-adenosyl-methionine (SAM) riboswitches [44]. These two distinct structural classes have different modalities of recognizing SAM [45,46]. Figure adapted from Serganov [47].…”