Team:Hong Kong HKUST/riboregulator

Background

Regulatory RNAs are RNAs that regulate biological processes on genetic and metabolic levels, and their importance has been established through the discoveries including those of RNA interference (RNAi) and long noncoding RNAs (lncRNA). The elucidation of their mechanism has enabled their reverse engineering, transforming them into versatile tools in synthetic biology.

Riboregulators belong to a class of regulatory RNAs that controls translation by pairs of cis-repressing (CR) and trans-activating (TA) RNAs. They have received attention from at least 7 teams during the early years of iGEM. For example, Farren Isaacs in 2005, iGEM 2006 UC Berkeley team and iGEM 2007 Caltech team contributed many CR and TA devices to the Registry. Though there are more than > 100 riboregulator BioBrick records, comprehensive characterization information is missing. This hinders the iGEM community to compare and contrast different riboregulators pairs and evaluate their performances. For example, if we want to use the CR and TA devices that Berkeley 2006 made, we would not know which one to use and whether the device would work, because documentations then were not put down in the Registry or wiki page and were therefore no longer accessible.

Given this situation, iGEM 2014 HKUST team decided to embark on "Project Riboregulator" with the following goals:

1. To provide characterization information on riboregulator BioBricks so that teams and labs will be confident in using these devices.
2. To summarize available information of existing riboregulators into a Feature Page and promote their uses.
3. To create a Catalog Page for all identifiable regulatory RNAs;
   To update the choice of “Categories” when documenting “hard information” of a BioBrick, and;
   To write up a guideline for other teams to tag their new regulatory RNAs so they will show up on the catalog page under the relevant sub-category.

Figure 1. Riboregulator Overview Diagram

Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by Isaacs in 2005. The riboregulator system as a whole acts to regulate translation at the RNA level. One component of the system ,crRNA, which contains a cis-repressing sequence at the 5' of the RBS, RBS, and gene of interest.

The cis-repressing sequence can form a loop form complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly described as a "lock" because it "locks" the RBS and prevent translation. The "key" to this system is the taRNA. taRNA can interact (in trans) with the cis-repressing sequence to unlock the RBS and therefore activate translation (Figure 1.).

The benefits of this system, as described in Isaacs et al.'s paper, are leakage minimization, fast response time, tunability, independent regulation of multiple genes etc.