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Synthetic biology, a field at the crossroads of engineering and biology, depends on input from both disciplines. A good example for a fruitful collaboration between these fields is Terry Hwa from the University of California, San Diego.

A physicist by training with a background in electrical engineering, he is interested in device characteristics, and the synergy between device study and synthetic biology. “By looking at a gadget's characteristics,” he explains, “you get some information on how a device might be used by the cell or, alternatively, by us.”

One such device that particularly captivated Hwa's attention was sRNAs that contribute to the regulation of protein expression in bacteria. Many of these noncoding RNAs bind specifically to the 5′ untranslated region (UTR) of mRNAs to prevent protein translation and essentially silence the target genes.

Developing tightly regulated gene circuits has been an important task in synthetic biology, and researchers have mainly looked to protein regulators that repress or activate promoters. Hwa was curious to investigate how different sRNAs might act as regulators. Specifically, he was curious to see how the noncatalytic nature of bacterial sRNA regulation, in other words, that sRNAs either co-degrade with or irreversibly bind to their target mRNAs, might affect their role as regulators.

True to their background, he and Erel Levine, a post-doctoral fellow, started by comparing the regulatory characteristics between sRNAs and proteins. They developed theoretical models based on the molecular biology of sRNA-mRNA interaction available in the literature, taking into account the rate constant for an sRNA to find its target, the degradation rate of the target mRNA with and without the sRNA, and the degradation rate of the sRNA with and without the target mRNA. This theoretical work suggested a list of properties inherent to sRNAs: their threshold linear response, that is, they are only active above a certain level of expression; their cross-talk, that is, expression of one sRNA target can relieve the repression of another; and their noise characteristics, that is, they are tightly regulated with very little background.

The next step took Hwa and Levine to the bench to show that these predicted regulations were not only biologically possible, but did actually happen in vivo. Hwa's team transformed bacteria with a reporter gene, its 5′ UTR fused to a natural sRNA target and the corresponding sRNA, each transcript under the control of its own inducible promoter so that the researchers could independently regulate the level of mRNA and sRNA. Measuring the reporter protein and mRNA levels at various degrees of sRNA expression, they confirmed the key properties of the sRNA-mediated regulation that they had predicted.

Hwa is optimistic that sRNA regulators will find use in developing gene circuits. He says: “Most people who work on bacterial gene circuits use the same small set of protein-based regulators. The feeling is that these tools are quite limited in terms of how you can induce them without causing other unintended changes to the cell. sRNA really gives us a whole new class of gadgets.” Hwa also points out that new sRNA-mRNA pairs can be designed based on known templates and they can be made very specific to avoid cross-talk.

Of course, important challenges remain. A number of mRNAs are very short-lived, which does not give the sRNA enough time to find its target and necessitates the stabilization of the mRNA. Another requirement for this regulation to work is the presence of a chaperone, thought to mediate RNA degradation. If an sRNA-based gene circuit were to be established in an 'artificial' cell, this chaperone would have to be supplied.

Despite these challenges, bacterial noncoding RNAs deserve a chance to prove their worth in regulating gene circuits.