Tools Design

The project aims to study how bacterial DNA organization can influence gene expression. In order to answer this question, we decided to create a new tool based on CRISPR/Cas9 technology to bring together two DNA regions separated in space. This new tool is expected to assess the effect of DNA structure on gene expression. We designed a bring DNA closer tool (BDC tool) and a visualization tool.

In this part, we expose our tool design, our experimental strategy is available here.

Molecular tools

In order to design our two tools, we need specific molecular tools with specific functions: DNA recognition, DNA binding function, dimerization and a fluorescence system.

DNA recognition and fixation

The two tools have to recognize a specific target sequences on DNA and then bind to it. Several options were possible, such as a protein-DNA or a RNA-DNA recognition. First of all, we thought to use engineered nuclease proteins, such as zing-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) or a RNA-guided engineered nuclease (RGEN) for their ability to target a specific sequence thanks to a specific proteic or nucleic sequence (for TALEN for instance, we speak about TALE code). We chose a based CRISPR/Cas9 recognition system but for the Cas9 protein, we chose an endonuclease deficient Cas9 (dCas9). For more information about CRISPR/Cas9 technology, click here. The CRISPR/Cas9 system is a quite new tool for synthetic biology which has many applications, such as targeting specific DNA sequences. Nevertheless, our system allows a new application of CRISPR/Cas9 technology. We chose dCas9 for three reasons :

• simplicity : to target DNA sequence, we only have to design a specific sgRNA, which takes about a week
• adaptability : the tool would be adaptable to target any sequences in the genome through the sgRNA sequence design
• specificity : the use of orthologous dCas9s allows a specific one by one sgRNA/dCas9 recognition by a specific PAM sequence for each pair

Dimerization system

Our project aims to recognize specific sequences on the genome and then induce a spatial proximity. So once we chose a system allowing a DNA targetting, we had to chose a system which could dimerize the dCas9/sgRNA, in order to get these two dCas9/sgRNA closer. We chose the induced dimerization FRB/FKBP12 system. In fact, this system allows a dimerization induced by rapamycin. To avoid any problem with rapamycin and E. coli, we decided to used an analog of rapamycin called rapalog (gratefully offered by Takara Clonethec). We then used a FRB mutated protein sequence (FRB*) to be recognized by rapalog.

Fluorescence system

For the visualization tool, we needed a fluorescence system to asses a spatial proximity due to our system. We chose the tripartite split-GFP, which is divided in three different parts: two twenty amino acids parts corresponding to the 10^th and 11^th beta-sheets and a third part corresponding to the other beta-sheets of the GFP. This solution avoids poor folding and/or self-assembly background fluorescence. With this system, only two sgRNAs/dCas9s fused to their specific GFP tags are necessary to obtain an accurate fluorescence.

Bring DNA Closer tool construction

We have designed a tool based on CRISPR/Cas9 property to target a specific DNA sequence. We imagined a system using dCas9 that dimerizes under an induction signal to bring two DNA sequence closer.

A dCas9 is a protein which recognizes precisely a DNA sequence without nuclease activity. We chose this system for it high adaptability, as it targets DNA through a sgRNA which could be easily designed. But as we need to target two different sequences we also need to work with dCas9s which will not interfere with each other, we chose two orthologous dCas9s which expressed different organisms as T. denticola (TD) and S. pyogenes (SP). As they come from different organisms, they recognize different sgRNAs thanks to their PAM sequence. We ordered from Addgene the plasmid coding for each one of these dCas9s and their sgRNAs.

To dimerize this two dCas9s, we chose an inducible system using FRB and FKBP12 proteins. Originally found in mammals, these two proteins form an heterodimer when rapamycin is added in the middle, it is particularly used in protein interaction studies (Cui et al., 2014). However, rapamycin is toxic for bacteria, but studies showed that a mutated FRB (FRB*) still allows dimerization with an analog of rapamycin non toxic called rapalog. The mutations implied are: T2098L, K2095P, W2101F.(Bayle et al., 2006; Liberles, Diver, Austin, & Schreiber, 1997).

A biobrick coding FRB with mutation T2098L was already in registry (iGEM Part_ J18926) but was not available. Moreover, it contains only one mutation on the 3 described in the literature. So we decided to work with the fully mutant FRB. Rapalog and plasmid with mutant FRB and FKBP12 were offered to us by Takara Clontech. But like it was mentioned previously, this system is used in mammal cells, so we decide to optimize the sequences for an expression in E. coli with the Jcat plateforme. So we finally order gBlocks coding for the FRB* and FKBP12 optimized sequences and a linker in prevision for the fusion with their respective dCas9s.

Using these two systems (dCas9 recognition and FRB/FKBP12 dimerization) we design our new tool based on the two following BioBricks:

These two biobricks will be assembled in pSB1C3 plasmid giving us our BDC tool which would work as presented bellow:

Visualization tool construction

As every systems need an efficient control, we set up a new part of the project in order to asses our Bring DNA Closer tool: the visualization tool.

To build this new tool, two other orthologous dCas9s were used: N. meningitidis and S. thermophilus. These dCas9 were fused to fluorescent proteins. We also decided to use dCas9 system for this tool in order to have detection of a accurate and unique sequence in the genome. It will be fulfilling with a new and unreleased in the iGEM competition tripartite slip-GFP.

The tripartite split-GFP is composed of two twenty amino-acids long GFP tags (GFP 10 and GFP 11) and a third complementary subsection (GFP 1-9). The tags were fused to the two dCas9 previously quoted. A functional GFP would be formed when the tools would be close enough to allow the three slip-GFP parts reunion and the fluorescence emission. This fluorescence system avoids poor folding and/or self-assembly background fluorescence. With this system, only two sgRNAs associated with their dCas9s fused to their specific GFP tags were necessary instead of nearly 30 with mundane GFP due to background fluorescence.

We designed three biobricks to achieve this part of the project:

• BioBrick n°3 : N.meningitidis fused to GFP-10 expressed by a constitutive promoter, a RBS and a double terminator
• BioBrick n°4 : S.thermophilus fused to GFP-11 expressed by a constitutive promoter, a RBS and a double terminator
• BioBrick n°5 : The third part of the GFP 1-9 expressed by a constitutive promoter, a RBS and a double terminator

The biobricks were inserted into pSB1C3 using the iGEM process : restriction sites EcoRI and PstI.

Then, we considered to establish a composite biobrick composed of the three biobricks in the same pSB1C3 plasmid. This plasmid would have been build using the iGEM restriction site technique.

We chose to express sgRNAs on another plasmid pZA11 which is compatible with pSB1C3, as it is Amp resistant.

References

Bayle, J. H., Grimley, J. S., Stankunas, K., Gestwicki, J. E., Wandless, T. J., & Crabtree, G. R. (2006). Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity. Chemistry and Biology, 13(1), 99–107. http://doi.org/10.1016/j.chembiol.2005.10.017

Chen, Baohui et al. 2013. “Resource Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR / Cas System.” CELL 155(7): 1479–91. http://dx.doi.org/10.1016/j.cell.2013.12.001.

Church, George M. 2014. “HHS Public AccessOrthogonal Cas9 Proteins for RNA-Guided Gene Regulation and Editing.” Nat. Methods 10(11): 1116–21.

Cui, B., Wang, Y., Song, Y., Wang, T., Li, C., Wei, Y., … Shen, X. (2014). Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria. mBio, 5(3), 1–10.http://doi.org/10.1128/mBio.01050-14

Liberles, S. D., Diver, S. T., Austin, D. J., & Schreiber, S. L. (1997). Inducible gene expression and protein translocation using nontoxic ligands identified by a mammalian three-hybrid screen. Proceedings of the National Academy of Sciences of the United States of America, 94(15), 7825–7830.http://doi.org/10.1073/pnas.94.15.7825

Ma, Hanhui et al. 2015. “Multicolor CRISPR Labeling of Chromosomal Loci in Human Cells.” Proceedings of the National Academy of Sciences of the United States of America.

Nguyen, Hau B et al. 2013. “A New Protein-Protein Interaction Sensor Based on Tripartite Split-GFP Association.” Scientific Reports 10: 1–9.