The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

Abstract

A novel family of riboswitches, called SAM-IV, is the fourth distinct set of mRNA elements to be reported that regulate gene expression via direct sensing of S-adenosylmethionine (SAM or AdoMet). SAM-IV riboswitches share conserved nucleotide positions with the previously described SAM-I riboswitches, despite rearranged structures and nucleotide positions with familyspecific nucleotide identities. Sequence analysis and molecular recognition experiments suggest that SAM-I and SAM-IV riboswitches share similar ligand binding sites, but have different scaffolds. Our findings support the view that RNA has considerable structural versatility and reveal that riboswitches exploit this potential to expand the scope of RNA in genetic regulation.

Structural basis for diversity in the SAM clan of riboswitches

“…The crystal structure of the env87 SAM-I/IV RNA has revealed the organization of the PK-2 subdomain and its relationship to the SAM-binding pocket. These data validate the hypothesis that the ligand-binding core of all members of the SAM clan are essentially identical but use differing combinations of peripheral subdomains to enhance ligand-binding affinity and/or communicate with the downstream regulatory switch (7). Notably, these two subdomains are found at opposite sides of the SAM-binding core and, from a ligandbinding perspective, are mutually compatible.…”

“…(C) 90°clockwise rotation perspective of the structure. predicted from covariance models of both the SAM-IV and SAM-I/IV families to form a base pair with U92 that is deleted, which would enable P3 and PK-2 to coaxially stack (7,8). Although this deletion likely slightly locally disrupts the PK-2 subdomain by disallowing perfect coaxial stacking of P3 and PK-2, it should be reiterated that the structure reflects a significant portion of the population of the SAM-I/IV riboswitch that has a similar unpaired nucleotide on the 3′-side of L3 (Table S3).…”

“…Intermediate between these two extreme cases are the three families of riboswitches making up the "SAM clan" [SAM-I (RF00162), SAM-IV (RF00642), and SAM-I/IV (RF01725)], whose members share a common binding core but have widely divergent peripheral architectures (6)(7)(8)(9). Structures of the SAM-I family revealed that S-adenosylmethionine is recognized by features within and surrounding a central four-way junction (yellow, Fig.…”

“…Nucleotides crucial for effector binding, along with the secondary structural features in which they are embedded, are nearly invariant within the clan (7). However, the three families of the SAM clan significantly differ in the peripheral architectural features surrounding the ligand-binding core (7). Within the SAM-I family, the central ligand-binding core is organized by the "PK-1" peripheral subdomain, defined by a pseudoknot (PK-1) between L2 and J3/4 (green, Fig.…”

“…These peripheral tertiary interactions serve to preorganize the core for SAM recognition (12). In the SAM-IV family, this subdomain differs by a non-kink-turn motif in P2 that presumably introduces a similar bend in the helix, along with the absence of the P4 helix (7). Because loss of P4 destabilizes the core (13), a second peripheral subdomain is observed, called "PK-2," comprising a new hairpin following P1 (P5) and a 3′-tail that base pairs with L3 to form a second pseudoknot (PK-2; Fig.…”