Project Overview
FRAMEchanger – A new tool for regulating gene expression
Goal – To develop a new tool for regulation of gene expression for the parts registry
As the Registry of Standard Biological Parts expands, there are more and more options becoming available for tight regulation of gene expression. For example, there are a number of well characterized promoters and ribosomal binding sites, each with a distinctive induction pattern or strength. However, biological systems use more than just these two types of elements to control gene expression. The goal of the 2013 Lethbridge iGEM team was to create a new type of regulatory part for the iGEM community. This new class of part could allow synthetic biologists to:
- Encode twice the amount of protein sequence in DNA
- Tag the same protein in multiple different ways at a predetermined frequency
- Express operons at their appropriate ratios in non-native organisms
- And more!
You may be wondering, “What kind of part can do all of these things, and how does it work?” Let us introduce you to the RNA secondary structural element called a pseudoknot (Fig). This small but highly structured RNA element is capable of inducing ribosomal frameshifts during translation that change the reading frame co-translationally. We have constructed and characterized the first BioBrick part (BBa_K1210000, link to parts page) that uses an RNA pseudoknot to cause a programmed –1 ribosomal frameshift. While this part has been optimized for use in prokaryotic systems, a small adjustment can be made (see below, The Spacer link) to allow for this element to be used in eukaryotic systems as well. In this way, we have created a new tool for gene regulation in essentially any cell chassis of your choice.
Pseudoknots
Pseudoknots are one of the most common RNA secondary structural elements and are sometimes used in nature to induce ribosomal frameshifts. These elements are generally comprised of two helical regions connected by and interacting with adjacent single-stranded regions or loops. Besides the knot itself, frameshifting also requires a slippery sequence of repeating A’s or U’s and a spacer sequence between the slippery sequence and the pseudoknot (Fig. 1).
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