Difference between revisions of "Part:BBa K5097001"

Revision as of 20:55, 30 September 2024

pH Response Element riboswitch mR34

In 1990, Bingham et al. identified a locus within E.coli whose activity was tied to pH changes, which they coined Alx. It exhibited increased expression at pH 8.5 (1). This activity was further characterized by Nechooshtan et. al., who determined that the Alx promoter and riboswitch are responsible for increased Alx expression in response to high pH (2). The Alx promoter and riboswitch have been previously entered into the parts repository by Team NAXI_GRAS under part number BBa_K2348000.

Pham et. al. reported that the putative RBS within the PRE riboswitch is of weak affinity. These researchers designed an improved version, PREmR34, which contains the strong RBS (Bba_B0034) (3). We utilized RNAfold (4) to model the structure of the PREm34, which is, expected, very similar to that of PRE. We also performed a Pairwise alignment on the sequences to visualize change.

Figure 1: Structure of PRE and PREmR34 riboswitches. The sequences of these two iterations of the PRE riboswitch were modeled in RNAFold, and the Forna structures were visualized (4,5). No significant differences in the structure of the riboswitch are apparent, save for a longer stem structure in PREmR34, created by the replacement of the native RBS with B0034, and the modification of the complementary region at the beginning of the riboswitch.

Figure 2: Pairwise alignment of the PRE riboswitch (Bba_K5097000) and PREmR34 (this part) illustrating the changes introduced to replace the native RBS.

Sequence and Features