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Breaker's biologist side was taking over. "As a biologist, I want to study something that is actually in a cell," Breaker says. "Evolution isn't kind to inefficient molecules, and the biologist in me argued that if RNA was so good at sensing metabolites, there were probably still riboswitches in modern cells." His group was studying a gene whose product helps transport vitamin B12 into the cell. By identifying parts of the mRNA that formed new structures in the presence of B12, Breaker's group discovered a structure that bound a B12 derivative and prevented ribosomes from reading the mRNA.
Nature hadn't forgotten the RNA sensor technology at all, as Breaker and his team detailed in the September 2002 issue of Chemistry & Biology. Soon thereafter, Breaker's team documented riboswitches at work in the biosynthesis of riboflavin and another B vitamin, thiamine.
Since their discovery in 2002, dozens of natural riboswitches, which bind vitamin derivatives, amino acids, nucleic acids, and other metabolites, have been discovered. The constant among them is that they consist of an aptamer sequence that senses metabolites and a sequence that turns gene expression on or off in response to that environmental monitoring. It's an elegant model that allows the riboswitch to control its gene expression by binding a metabolite and either preventing or inducing termination of mRNA synthesis, protein synthesis, or RNA self-destruction through self-cleavage.
Riboswitches demonstrate striking complexity. For example, the glycine riboswitch in Bacillus subtilis employs two glycine-binding domains to control a set of genes whose products allow the bacteria to live off of glycine, an essential amino acid. The two-aptamer regions cooperate with each other to allow the bacteria to sense small changes in available glycine, says Breaker.
Another riboswitch has proven itself as sophisticated as certain proteins, findings that Breaker's team reported in the October 13, 2006, issue of Science. The bacteria Escherichia coli and Bacillus clausii both have two different enzymatic proteins that turn the amino acid homocysteine into methionine. One pathway is more efficient but needs vitamin B12 to help. The other is less efficient, and bacteria use it only when B12 and another nutrient, S-adenosylmethionine (SAM), are in short supply. E. coli uses proteins to monitor the concentrations of these nutrients and regulate the expression of these enzymes. B. clausii, on the other hand, uses a riboswitch to control expression of the less efficient enzyme. What's interesting is that the riboswitch harbors two different aptamer binding sites—one for SAM and one for B12. If either nutrient binds the riboswitch, the gene for the less efficient enzyme is switched off.
Although metabolite-binding riboswitches are relatively common among bacteria, only one riboswitch has been found in a higher organism: the TPP riboswitch, which exists in bacteria, is also found in fungi and the flowering plant Arabidopsis. In bacteria, this riboswitch regulates thiamine production and transport by binding thiamine pyrophosphate. In fungi, it's involved in a process called RNA splicing, which removes nonsensical bits from mRNA transcripts.
"As bioinformatics search strategies improve, we might still find some riboswitches in common between bacteria and humans," Breaker suggests. "If humans do have riboswitches, they likely form different shapes and sense different compounds than those found in bacteria."