Team:OUC-China/Improve
Improve
Overview
This year, we create a brand new family called Csy4 family on the basis of an existing part, Csy4 BBa_K1062004. We redesign four Csy4 mutants by point mutation. The members in Csy4 family have different capabilities of cleavage and recognition. As an important role in project, we tested them by several ways. The Csy4 family works well as expectationn. Csy4 family is an improvement based on existing part and is proved work well in our system.
Proof of functions about Csy4 family
We did three kinds of experiments to help us confirm the function of the Csy4 family. The aim is to get some new Csy4 mutants with different capabilities. Superfolder green fluorescent protein (sfGFP) is target gene for test experiments. Our expectation is that the fluorescence intensities of sfGFP change upon various activity of Csy4 mutants. It means we have improved four new parts which present various expression of target genes.
Prediction
Before the experiments, model proved our ideas. The predication shows the possibilities of different expression levels by different Csy4 mutants. It is not difficult to predict that the cleavage rate has an influence in the expression of sfGFP.
Fig.1 The predication: the fluorescence intensities by different Csy4 mutants along with time.
We designed three kinds experiments to test the capabilities of five Csy4 mutants by putting them into miniToe system. So the recombination strains for test both have same pReporter but different Csy4 mutants plasmids in the following. The recombination strains to test the functions of Csy4 are strain-Csy4 (pCsy4&pReporter), strain-Csy4-Q104A (pCsy4-Q104A&pReporter), strain-Csy4-Y176F (pCsy4-Y176F&pReporter), strain-Csy4-F155A (pCsy4-F155A&pReporter), strain-Csy4-H29A (pCsy4-H29A&pReporter). At the same time, we have a control strain named strain-miniToe-only which only has pReporter.
The qualitative experiments by fluorescent microscope
First, we have tested five different groups by Fluorescent Stereo Microscope Leica M165 FC. The sfGFP accumulated during the cultivation period so the fluorescence can be observed by microscope after 8 hours. Because the five Csy4 mutants have different capabilities of cleavage, the distinguishing intensities of fluorescent can be seen by naked eyes. The five test strains have same miniToe part but different Csy4 mutant genes. From top to bottom in Fig.2, there are fluorescence images by fluorescent microscope which indicate strain-Csy4, strain-Csy4-Q104A, strain-Csy4-Y176F, strain-Csy4-F155A and strain-Csy4-H29A in sequence. The visible distinctions have shown in these images. The fluorescence intensities decrease one by one from top to bottom which means the Csy4s' capabilities of cleavage decrease one by one. The Csy4-WT has the strongest capability of cleavage when the Csy4-H29A is a kind of dead-Csy4 (dCsy4) which is hardly to find the fluorescence by microscope. The qualitative experiment is a basis of further experiments.
Fig.2-1. The expression of sfGFP by Csy4-WT&miniToe.
Fig.2-2. The expression of sfGFP by Csy4-Q104A&miniToe.
Fig.2-3. The expression of sfGFP by Csy4-Y176F&miniToe.
Fig.2-4. The expression of sfGFP by Csy4-F155A&miniToe.
Fig.2-5. The expression of sfGFP by Csy4-H29A&miniToe.
Fig.2 The fluorescence images by fluorescent microscope. From top to bottom, the images shows the expression of sfGFP by strain-Csy4, strain-Csy4-Q104A, strain-Csy4-Y176F, strain-Csy4-F155A and strain-Csy4-H29A in sequence. The plotting scale is on the right corner of images. The images on the left shows E. coli without fluorescence excitation. The images on the right represent situation when fluorescence excitation.
The result by flow cytometer
The qualitative experiment is not enough to analyze the Csy4 mutants. So we tested miniToe family system by flow cytometer. The expression of sfGFP by strain-Csy4, strain-Csy4-Q104A, strain-Csy4-Y176F, strain-Csy4-F155A and strain-Csy4-H29A is showed in Fig.3. We find that 5 groups' fluorescence intensities have an obvious order from Csy4-WT to Csy4-H29A, which means the capabilities decrease one by one. Their order goes from strong to weak is Csy4-WT, Csy4-Q104A, Csy4-Y176F,Csy4-F155A and Csy4-H29A.
Fig.3 The fluorescence intensities of sfGFP about Csy4 mutants by flow cytometer. Histograms show distribution of fluorescence in samples with strain-Csy4 (Black), strain-Csy4-Q104A (Orange), strain-Csy4-Y176F (Red), strain-Csy4-F155A (Blue), strain-Csy4-H29A (Green). Crosscolumn number shows fold increase of sfGFP fluorescence.
Fig.4 The Gate Mean of flow cytometer. Histograms show the relative expression of sfGFP. The five test groups present different fluorescence intensities from high to low which prove that they have different capabilities of cleavage.
The result by microplate reader
Besides all the works before, we also need to know more information about the Csy4 mutants in entire cultivation period. Even though we known that our Csy4 mutants have differentiated expression level in ten-hour-culture, the expression of whole cultivation period is also a reference for us to know if our system can work as expectations.
So we tested five test stains individually (strain-Csy4, strain-Csy4-Q104A, strain-Csy4-Y176F, strain-Csy4-F155A and strain-Csy4-H29A) by microplate reader every two hours. The green lines in all the images represents strain-miniToe-only group keep stable. It means the miniToe structure fold well and lock the process of translation without Csy4. And the five test groups show different characteristics. In Fig.5-A, the group strain-Csy4 shows the same result with the first system. The switch turns off without IPTG (as the blue line shows). And the expression level is the highest among all the test groups which indicates the Csy4-WT has strongest capabilities (Fig.5-F). In the Fig.5-B, the tendency of fluorescence intensities by Csy4-Q104A is similar with Csy4-WT. And the expression level is lower than Csy4-WT. The Csy4-Y176F’s capabilities ranks the third. What is special is Csy4-H29A. The active site of Csy4 contains an essential histidine residue (H29) that functions as a general base during RNA strand scission. Mutation of H29 to alanine inactivates Csy4 without affecting substrate binding affinity or specificity. So Csy4-H29A is a dead-Csy4 which has high binding affinity but has lowest capabilities of cleavage as we can see in Fig.5-E. In summary, we put all the test groups together in Fig.5-F, the picture shows our prediction by model matchs the result perfectly in Fig.6.
Fig.5 The fluorescence intensities of sfGFP by microplate reader. A. strain-Csy4. B. strain-Csy4-Q104A. C. strain-Csy4-Y176F. D. strain-Csy4-F155A. E. strain-Csy4-H29A. A-E. The blue line is test group with IPTG. The yellow line is test group without IPTG. The green line is a control group which only has miniToe structure without Csy4s. F. The summary of different test groups which indicates the capabilities of Csy4 mutants. The results are listed in the order: Csy4-WT>Csy4-Q104A>Csy4-Y176F>Csy4-F155A>Csy4-H29A.
Fig.6 The comparison about model and result by microplate reader.
In summary
This year, we redesign four mutants on the basis of Csy4(BBa_K1062004) which are Csy4-Q104A(BBa_K2615004), Csy4-Y176F(BBa_K2615005),Csy4-F155A(BBa_K2615006) and Csy4-H29A(BBa_K2615007). The capabilities of cleavage and recognition are different for each Csy4 mutants, and we name them the Csy4 family. The combination of the Csy4 family members and the miniToe family members constitute a post-transcriptional regulatory toolkit for achieving different expression levels of target genes.
Csy4-WT, the wild type, is a member of the CRISPR family, and also the core member of our project. Csy4-WT can specifically recognize and cleave a 22nt hairpin structure, known as the miniToe-WT. We confirmed that Csy4-WT is the strongest of the Csy4 family through the analysis of the results of our fluorescence microscopy, flow cytometry and microplate reader experiments. And the strength of the remaining members of the Csy4 family shows a staircase pattern.
Csy4-Q104A, which is second only to Csy4-WT in strength in the Csy4 family, coming from point mutation, and we change the CAG(encoding Gln) to GCG(encoding Ala) on the 104th site based on Csy4-WT. It can also recognize and cleave the 22nt miniToe, regulating the expression of downstream genes. When we conducted experiments with the miniToe-WT combination and used sfGFP as the downstream target gene, we could see the experimental results that the sfGFP expression level of Csy4-Q104A was about half that of Csy4-WT.
Csy4-Y176F, the third-strongest in the Csy4 family. It is designed in the same way as Csy4-Q104A, but with the 176th site changed from TAC(encoding Tyr) to TTT(encoding Phe). It can be seen from the experimental results that the expression of downstream genes regulated by Csy4-Y176F is correlated with the stepwise decline of Csy4-WT and Csy4-Q104A.
Csy4-F155A, strength is the fourth in the Csy4 family. At point mutation, we changed its 155th site from TTC(encoding Phe) to GCG(encoding Ara). It has a weaker cleavage and recognition capability..
Csy4-H29A, the most special one of our Csy4 family, whose 29th site is changed from CAC(encoding His ) to GCG(encoding Ara). Csy4-H29A has a high binding affinity but has the lowest capacity of cleavage, so we call it dead-Csy4. There is no doubt that its downstream gene expression is the lowest in the family.
