Riboswitch

In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.Cobalamin riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00174.Cyclic di-GMP-I riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF01051.Cyclic di-GMP-II riboswitch: Secondary structure for the riboswitch marked up by sequence conservation.FMN riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00050.GlmS ribozyme: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00234.Glycine riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00504.Lysine riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00168.PreQ1 riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00522.PreQ1-II riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF01054.Purine riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00167.SAM riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00162.SAM-II riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00521.SAM-III riboswitch (SMK): Secondary structure for the riboswitch marked up by sequence conservation.SAM-IV riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00634.SAM-V riboswitch: Secondary structure for the riboswitch marked up by sequence conservation.SAM-SAH riboswitch: Secondary structure for the riboswitch marked up by sequence conservation.SAH riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF01057.TPP riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00059.Tetrahydrofolate riboswitch: Secondary structure for the riboswitch marked up by sequence conservation.YkoK leader: Secondary structure for the riboswitch marked up by sequence conservation. Family RF00380.Moco riboswitch: Secondary structure for the riboswitch marked up by sequence conservation. Family RF01055. In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules. The original definition of the term 'riboswitch' specified that they directly sense small-molecule metabolite concentrations. Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches. Most known riboswitches occur in bacteria, but functional riboswitches of one type (the TPP riboswitch) have been discovered in archaea, plants and certain fungi. TPP riboswitches have also been predicted in archaea, but have not been experimentally tested. Prior to the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. Accumulating evidence increasingly suggested the then-unprecedented idea that the mRNAs involved might bind metabolites directly, to affect their own regulation. These data included conserved RNA secondary structures often found in the untranslated regions (UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation. Many of the earliest riboswitches to be discovered corresponded to conserved sequence 'motifs' (patterns) in 5' UTRs that appeared to correspond to a structured RNA. For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box (now the SAM-I riboswitch), the THI-box (a region within the TPP riboswitch), the RFN element (now the FMN riboswitch) and the B12-box (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. Bioinformatics has played a role in more recent discoveries, with increasing automation of the basic comparative genomics strategy. Barrick et al. (2004) used BLAST to find UTRs homologous to all UTRs in Bacillus subtilis. Some of these homologous sets were inspected for conserved structure, resulting in 10 RNA-like motifs. Three of these were later experimentally confirmed as the glmS, glycine and PreQ1-I riboswitches (see below). Subsequent comparative genomics efforts using additional taxa of bacteria and improved computer algorithms have identified further riboswitches that are experimentally confirmed, as well as conserved RNA structures that are hypothesized to function as riboswitches. Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. The expression platform is what regulates gene expression.