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[iGEM 2018 UI_Indonesia] Experiment with BBa_K592024

We performed experiment to compare BBa_K2607002 with BBa_K592024. Figure 1 shows the plan on how we conduct the experiment.

Figure 1. Original plan workflow with newly-established (BBa_K2607002) and existing (BBa_K592024) parts of BFP.

Gel Electrophoresis Confirmation
Upon receiving our “Improved BFP” gBlock from IDT (with length of 1151 basepairs (bp), including BioBrick prefix and suffix and sequences for polymerase chain reaction (PCR), also SalI and NdeI restriction sites that are located at base 244-249 and 266-271, respectively), we performed PCR to amplify it until sufficient quantity (about 100 ng/uL). We then created two restriction digestion reactions, one with NdeI restriction enzyme and one with SalI restriction enzyme. Each reaction comprised of 100 uL PCR-amplified “Improved BFP” gBlock, 6 uL restriction enzyme, 15 uL CutSmart^® restriction buffer, and 29 uL nuclease-free water. The reaction was subsequently incubated for four hours at 37^oC incubator. The digestion products were then run for electrophoresis in 1% agarose gel with tris-acetic acid-EDTA (TAE) buffer 1x, power supply 50 volt for 70 minutes. Visualization was performed with Bio-Rad Gel DocTM XR+ Gel Documentation System. Figure 2 shows gel electrophoresis result of digested PCR-amplified "Improved BFP" gBlock.

Figure 2. Gel electrophoresis of restriction of “Improved BFP” gBlock with 1% agarose gel, TAE 1x, 50 V, and 70 minutes. Lane 1 = BioLabs, Inc. 100 bp DNA ladder (#N3231L) with size range 100-1517 bp. Lane 2 = uncut PCR-amplified “Improved BFP” gBlock (expected size 1151 bp). Lane 3 = “Improved BFP” gBlock cut with NdeI. Lane 4 = “Improved BFP” gBlock cut with SalI.

At lane 2 consisting of uncut “Improved BFP” gBlock (size 1151 bp), only single band is observed. The band is located between 1000-1200 bp marker at lane 1, which is consistent to the gBlock original size. Upon restriction with NdeI, the expected bands are 271 bp and 880 bp in size, while restriction with SalI will yield expected bands of 249 bp and 902 bp. At lane 3 and 4, there are three bands observed, indicating that the gBlocks were partially digested with respective enzymes, NdeI and SalI. The heaviest bands in lane 3 and 4 were parallel with the band in lane 2, indicating that the bands were uncut gBlocks. The middle bands in lane 3 and 4 were similar in size (around 900 bp in size), representing the larger fragments of digestion products with their respective enzymes. The lightest bands in lane 3 and 4 were also similar in size, located between 200-300 bp marker at lane 1. They represent the smaller fragments of digestion products. The smaller fragment upon NdeI digestion is 271 bp, while upon SalI digestion is 249 bp. The lightest band in lane 3 migrated slightly slower than lightest band in lane 4, denoting larger size of smaller fragment in lane 3 than lane 4, which is consistent to the expected restriction results.

Ultraviolet (UV) Check
First, we acquired BBa_K592024 by transforming wild-type Escherichia coli K-12 with plasmid in well 17C of Distribution Kit Plate 1, isolating the plasmid, and performing restriction with EcoRI and PstI restricton enzymes. Our “Improved BFP” and BBa_K592024 were separately cloned into plasmid pQE80L using EcoRI and PstI according to our laboratory protocol. The resultant ligation products were subsequently transformed into wild-type E. coli K-12, along with empty pQE80L as control. Transformation products were spread into Luria-Bertani (LB) agar medium containing ampicillin with ratio 1000:1. On the following day, the fluorescence was assessed qualitatively under ultraviolet (UV) light (Figure 3).

Figure 3. Colony of transformed wild-type Escherichia coli K-12 with empty pQE80L (yellow arrow), pQE80L with “Improved BFP” (green arrow), and pQE80L with BBa_K592024 (orange arrow) in plasmid pQE80L under ultraviolet (UV) illumination.

Qualitatively, higher fluorescence was observed in transformed E. coli with “Improved BFP” compared with others. The probable explanation is that our “Improved BFP” has its own promoter. When our part is cloned into pQE80L with EcoRI and PstI, there are two promoters in the upstream of BFP coding region, theoretically leading to more BFP mRNA and protein being produced. However, to further investigate this hypothesis, we performed quantitative BFP fluorescence measurement from three samples (E. coli K-12 with empty pQE80L, pQE80L + “Improved BFP, and pQE80L + BBa_K592024), as will be explained later.

Fluorescence Assay
Fluorescence assay was conducted according to 5^th InterLab protocol with some modifications. From each transformation plates, two colonies were picked and let to be grown in LB medium with ampicillin (1000:1). Two colonies of E. coli containing empty plasmid pQE80L were also inoculated for control. After 18 hours, each overnight culture was diluted until optical density at 600 nm (OD₆₀₀) of 0.02 and final volume of 12 mL in 50 mL centrifuge tube covered with foil. At t = 0 hour, 1 mL from each tube was sampled to be measured for its OD₆₀₀ and fluorescence. The measurement was conducted with GloMax^®-Multi Detection System with “UV” settings: 365 nm excitation and 410-460 nm emission. The data obtained were recorded and analyzed in Excel. The rest of dilutions were incubated in shaker under 37^oC, 220 rotations per minute (rpm). We repeated the same procedure after t = 6 hour and overnight (t = 14 hour) incubation.

Figure 4. Fluorescence/OD₆₀₀ measurement (in mean arbitrary units ± standard deviation) of transformed E. coli with one of three plasmids (empty pQE80L, pQE80L with “Improved BFP”, and pQE80L with BBa_K592024) at t = 0 hour, 6 hour, and 14 hour. * and ** indicate statistically significant differences (p = 0.005 and < 0.001, respectively).

The fluorescence assay result is visualized in Figure 4. At t = 0, 6, and 14 hour, although not shown in Figure 4, fluorescence/OD₆₀₀ of transformed E. coli with pQE80L + “Improved BFP” and pQE80L + BBa_K592024 were significantly higher than negative control (transformed E. coli with empty pQE80L). At t = 6 hour, fluorescence/OD₆₀₀ of E. coli with “Improved BFP” was significantly higher than E. coli with BBa_K592024 (p = 0.005). Similar result was found after overnight incubation (p < 0.001). These results support previous qualitative observation of fluorescence and may be explained by ‘double promoter’ of “Improved BFP” in pQE80L. In addition, from Figure 4 it is also observed that fluorescence/OD₆₀₀ was decreasing along with time. The probable explanation of this result is higher bacterial concentration in medium over time, resulting in larger denominator and reducing fluorescence/OD₆₀₀. Moreover, it is also probable that the bacteria underwent cessation, causing decline in BFP production and resulting in lower fluorescence/OD₆₀₀. Nevertheless, from this experiment, it can be inferred that E. coli transformed with “Improved BFP” retains significantly higher fluorescence/OD₆₀₀ than BBa_K592024 under plasmid pQE80L expression system.

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