Part:BBa_K2839006

Theo27 theophylline riboswitch controlling fused sfGFP expression

1.Short Description

This part consists of Pupsp1 promoter, the 12.1 Theophylline Riboswitch and the sfGFP fluorescent protein fused with the first 99 nucleotides of luciferase. This part is an improvement of Part:BBa_K784005 and can be used to achieve the desired expression of the marker, depending on the concentration of externally added Theophylline.

2.Biology and Functionality

Aptamers are oligonucleotides or peptide molecules that change their conformation when bound to the target molecule. They can be used for the regulation of gene expression, which becomes dependent of the inducer’s concentration. We use a Theophylline aptamer which achieves translational control of protein production. Gene expression is off when Theophylline is absent, because the RBS and start codon are hidden inside the aptamer’s loop. When theophylline is added, the aptamer’s conformation changes, the RBS is revealed and the ribosomes can initiate translation.

3.Usage in our Project

As we wanted to expand on the TAL Effector stabilized promoters system, we designed a tool that would allow, on top of the stabilization of a promoter, its induction and activation to the desired expression level. As a chassis we used DH5a E.coli cells for hosting the system’s devices. We implemented a Theophylline riboswitch, 12.1, which is completely orthogonal and shows high dynamic range, which is essential in order to allow for precise control of the expression level. As a marker, we use a fusion sfGFP protein that consists of the 99 first deoxyribonucleotides of luciferase followed by the sfGFP sequence. We were planning on using this riboswitch in the TAL Effector Stabilized promoters, but since it showed low activation ratio, we opted for Part:BBa_K2839017 instead.

5. RFC[10] compatibility

This part is RFC[10] compatible since the sequence was optimized to eliminate illegal restriction sites.

6.Cloning Strategy

The final plasmids containing the Riboswitch Theo27 fusion sfGFP cassette consist of three individual parts: A(Pupsp1 promoter fused with Theo27 riboswitch), B(sfGFP marker) and C.

Each part’s sequence is flanked by BsaI recognition sites and after digestion with BsaI restriction enzyme, part A has sticky ends with part B and part C, while part B has sticky ends with part A and part C.In order to successfully clone the Riboswitch Theo27 fusion sfGFP cassette into pSB1C3 vector we followed this procedure:

• PCR amplification of psb1c3 vector with a set of standardized primers. These primers amplify the plasmid backbone without the insert, incorporate BsaI sites at prefix and suffix, forming the amplified pSB1C3 vector (part C).
• Design and synthesis of the part A, part B fragments with the appropriate flanking regions.
• Golden Gate assembly between part A, part B and the amplified pSB1C3 Vector (part C). This reaction forms the final plasmid RiboT27-pSB1C3 containing the riboswitch characterization device.

7.Characterization

• Sample preparation:

In order to prepare the cultures for flow cytometry analysis we followed the protocol created by Adam Mayer et al [1]. In particular the correct colonies were inoculated into 1 ml Lb + antibiotics and grown overnight at 37 °C in a shaking incubator adjusted to 250 rpm.The overnight growths were diluted 1:200 into 1 ml LB + antibiotics and grown at 37 °C into shaking incubator .After 2 hours the growths were diluted 1:500 into prewarmed LB + antibiotics + inducer where necessary and grown at 37 °C, 250 rpm for 5 hours.After growth, 20 μl of culture sample was diluted into 180 μl PBS + 200 μg/ml kanamycin to inhibit translation. The samples were stored at 4°C for 1 hour and then measurements were performed using the CyFlow Cube8 Sysmex Partec Flow Cytometer.

• Measurement:

Fig1: Performance of Theo27 Riboswirtch in Different theophylline concentrations. Error Bars represent Standard Deviation from three biological replicates.

7.References [1]A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Research, 37(1), 184–192. https://doi.org/10.1093/nar/gkn924 [2]Espah Borujeni, A., Mishler, D. M., Wang, J., Huso, W., & Salis, H. M. (2016). Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Research, 44(1), 1–13. https://doi.org/10.1093/nar/gkv1289

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 787
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]