Design and Construction of Alk-Selector

Firstly, we will design a new device Alk-Selector. Although Alk-Sensor can also be regarded as a selector, we don’t want to select just according our eyes which is a tough work. Instead, the special function of antibiotic resistant gene will help select the gene with better property automatically in the condition of antibiotic pressure.

So based on the construction of Alk-Sensor, we substituted the RFP reporter to tetracycline resistant gene TetA which is a transporter to pump tetracycline outward the cell. Other components of the Alk-Selector are same to Alk-Sensor. The final construction of Alk-Selector and its working mechanism can be seen in Figure 1. The Alkane modular expressed NPDC and AAR to biosynthesis alkane in E. coli, the alkane can activate the expression of tetA through AlkR-PalkM system, and the transporter TetA will give tetracycline resistance to E. coli and survive it in the environment with tetracycline.

Figure 1.

Characterization of Alk-Selector

To verify the our Alk-Selector will produce more tetracycline resistance when more alkane is produced, we cotransform the Alk-Selector and an alkane producing modular to the E. coli BL21. The control strain just had Alk-Selector. These two strains were cultured in M9 media with 12ug/ml tetracycline. After 48h, we can find the growth of strain with alkane producing modular is higher than the control just as Figure 2 showed.

It means that our Alk-Selector can work.

[[Image:#.png|thumb|600px|center|Figure 2.]]

Library Construction

For library construction, we reconstructed the alkane producing modular of low productivity by adding restriction site BamHI and SacI at the two ends of gene NPDC for library construction. The workflow of the library construction is showed in Figure 3.

[[Image:#.png|thumb|600px|center|Figure 3.]]

We amplified NPDC by error-prone PCR, and ligand on the plasmid. The production of the ligation is transformed into competent cell with high efficiency, to get the library of alkane producing modular. Because of the limitation of time, the size of the library is just 20,000. Just as Figure 4 shows, every plate had about 3000 colonies, more than 90% colonies can be amplified fragment with correct length (~2000bp) by colony PCR(Figure 5), and 8 plates like this had been made. Then, the colonies were washed out and got together and then whole plasmids were extracted from it to get the amplified plasmid library of alkane producing modular. This library will be used to transform the E. coli BL21 containing Alk-Selector.

[[Image:#.png|thumb|600px|center|Figure 4.]]

[[Image:#.png|thumb|600px|center|Figure 5.]]

Process of Selection and Analyze

The whole process of selection has been showed in Figure6. The amplified plasmid library was transformed to E. coli with Alk-Selector. To guarantee this library’s diversity, we think that the number of the strain which has successfully taken the alkane producing modular was at least 60,000. To verify this requirement, all the strain will be plated on the M9 solid medium, and the numbers of the colonies will be estimated. As Figure 6 showed that the number of 1/10 of all transformants is about 6500 which has satisfied the requirement. At the same time, the strain didn’t take the plasmid would eliminate under the pressure of antibiotic in this process. Then, all the colonies were washed out by M9 medium with antibiotics of proper concentration. The mix culture will inoculated into M9 medium with 12ug/ml tetracycline by 1:1000 for seclection. For the control experiment, this culture will inoculated in the M9 medium without tetracycline. After fermentation about 12 hours, E. coli began to growth very slowly, and after 36h, the OD600 of culture beyond 2.0 which is enough to analyze.

[[Image:#.png|thumb|600px|center|Figure 6.]]

Because of the high copy number of Alk-Selector, directly separate the colonies that survived during the selection process failed in the sequencing, so we extracted whole plasmid from the culture and retransform to the E. coli without any modular to discard the plasmid of Alk-Selector. The colonies will be picked up and sequencing. After aligning the sequence, we can find the key animo acid which influent the function of the enzyme, and get the better modular of alkane producing.

Result

We picked 50 colonies for sequencing. Limited by the size of the library, only 2 mutation has been found which is F133Y and E144G. Figure 7 and Figure 8 shows this result. About 80% strains contained both of the mutation (No strain from control experiment is enriched). Among two of the mutation, E144G is just nearby the key amino residue E145 which is responsible to stabilize the iron ions of the active center, so this mutation may influent the activity of the enzyme. F133Y is far away to the active center, but may affect the entrance of the substrate to the pocket. Limited by the time, we didn’t test the function of the alkane producing modular.

Anyway, we successfully finish our selection process from a library under the help of Alk-Selector. And we had proved this favorite biobrick can work.

[[Image:#.png|thumb|600px|center|Figure 7.]]

[[Image:#.png|thumb|600px|center|Figure 8.]]