Difference between revisions of "Team:Austin UTexas/Experiments"

Experiments

Although bacteria can naturally synthesize GABA, we wanted to increase expression of the gadB gene and subsequently GABA production in order to imbue a more potent medicinal quality to our probiotic, with the idea that this GABA-overproducing probiotic can then be consumed by patients with bowel disorders or anxiety. To make our GABA-producing probiotic we first needed to assemble a GABA overexpression cassette plasmid using the Golden Gate assembly method. The intention here is that bacteria containing this GABA overexpression cassette plasmid should produce high levels of GABA. In short, Golden Gate Assembly is a new cloning method that allows for the creation of a multi-part DNA assembly (i.e. cassette plasmid) in a single reaction through the use of DNA parts containing specific, predefined suffixes and prefixes with recognition sites for Type IIs restriction enzymes (e.g. BsmBI and BsaI). The specificity of these suffixes and prefixes provides directionality of the desired DNA parts during the assembly process. For our purposes, we used the MoClo Yeast Tool Kit by John Dueber (Lee et al., 2015). The first part of our Golden Gate assembly workflow was part assembly, in which the gadB gene and the P8/P32 promoters were individually cloned into the entry vector pYTK001 (Fig. 1). The gadB gene and P8/P32 promoter sequences contain flanking BsmBI sites that produce overhangs compatible with those cut by BsmBI in the entry vector pYTK001. Thus, BsmBI cloning should result in part plasmids containing the gadB gene and P8/P32 promoters set within the pYTK001 backbone.

Figure 1. gadB gene and P8/P32 promoter part assembly process. Golden Gate compatible gadB and P8/P32 promoter sequences are cloned into the pYTK001 entry vector via BsmBI assembly.

Additionally, the BsmBI sites and overhangs in pYTK001 are flanking a gfp reporter gene. During the part assembly process, our DNA sequences of interest should replace this gfp reporter gene. This provides a phenotypic screen that allows us to visually see which transformant colonies are negative and potentially positive. Under UV illumination, positive colonies containing our intended part plasmid assembly did not exhibit fluorescence under the UV illumination, while negative colonies did (Fig. 2.). The non-fluorescent colonies on the part plasmid transformation plates were miniprepped and subsequently sequence verified.

Figure 2. gadB gene and P8/P32 promoter part plasmid E. coli transformations, compared to control transformations with pYTK001. Under UV illumination, transformants containing the correctly assembled part plasmids were non-fluorescent while negative transformants appeared fluorescent like colonies on the control plates.

After successfully creating the gadB gene and P8/P32 promoter part plasmids, the functionality of these part plasmids were then assessed by assembling them into cassette plasmids. To test if our Lactococcus lactis constitutive promoters function well within E. coli, we created test cassette plasmids containing the E2-Crimson reporter gene (which encodes a red fluorescent protein) inserted downstream of either the P8 or P32 promoters using BsaI Golden Gate assembly. To create these test cassette, we used the P8/P32 promoter part plasmids, E2-Crimson part plasmid, an M13 terminator part plasmid, connector part plasmids, and pYTK095 vector as the backbone (Fig. 3). If the P8 and P32 promoters are functional in E. coli, we should observe red fluorescence In colonies transformed with our test cassette plasmids.

Figure 3. Golden Gate assembly process of the P8 and P32 test cassette plasmids.

Upon first look, E. coli colonies transformed with these assemblies appeared purple-blue in color. This phenotype was due to the expression of the red fluorescent protein. Further, we noticed that E. coli colonies transformed with these assemblies fluoresced red under UV light, indicating that the P8 and P32 promoters are indeed expressing the E2-Crimson reporter gene and thus are functional in E. coli (Fig. 4).

Figure 4. P8/P32 test cassette plasmid transformation plates, under normal and UV lights. Under normal lights, the colonies appeared purple-blue in color. Under UV, the colonies fluoresced red.

Using Golden Gate Assembly, we created cassette plasmids to test if the gadB gene could be overexpressed in E. coli via the P8 and P32 promoters. These cassette plasmids contained the gadB gene inserted downstream of either the P8 or P32 promoters. Part plasmids used for this cassette assembly included:

Figure 5. Golden Gate assembly process of P8/gadB and P32/gadB test cassette plasmids.

Similar to the pYTK001 entry vector in part assembly, the pYTK095 backbone used for cassette assembly contained a gfp reporter gene that is replaced by sequences of interest. This allowed us to easily perform a phenotypic screen for positive colonies. Non-fluorescent colonies may potentially have had the correct cassette assembly, while fluorescent colonies did not (Fig. 6). The non-fluorescent colonies were then screened using colony PCR (Fig. 7). The positive colonies were then miniprepped and sequenced. The sequencing results indicated that in all of the samples there were several point mutations within the gadB gene. We hypothesized that overexpression of the gadB gene via the P8 and P32 constitutive promoters and the high-copy number ColE1 origin induced a high metabolic load on the cells, resulting in mutational degradation of gadB. To troubleshoot this problem, we decided to use a backbone containing the low-copy number p15A origin for the cassette assembly (Fig. 8)

Figure 6. P8/gadB and P32/gadB cassette E. coli transformations alongside a pYTK095 control transformation under UV illumination. Potentially positive colonies containing the correct assemblies appeared non-fluorescent, while negative colonies appeared fluorescent.

Figure 7. Gel results for colony PCR of P8/gadB and P32/gadB non-fluorescent transformants. The primer pair used for this PCR experiment targeted the region of the cassette plasmid containing the DNA inserts (i.e. connectors, P8/P32 promoters, gadB gene, and M13 terminator). The expected band length was 2 kb. Lane 1 contains a negative PCR control. Lane 2 contains a positive PCR control. Lanes 3-5 contain the PCR products from three p8/gadB colonies. Lanes 6-8 contain the PCR products from three p8/gadB colonies. Evidently, all of the picked colonies were positive for the desired amplified region.

Figure 8. Modified Golden Gate assembly process of P8/gadB and P32/gadB test cassette plasmids using a backbone containing the low-copy number p15A origin.

MIC Figure