Difference between revisions of "Part:BBa K4176004"

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optimized sacB

This is a sequence-optimized sacB with lower toxicity

Sequence and Features

Abstract

Expression of sacB converts sucrose to levan, which accumulates in the periplasm and is toxic to E. coli. We used sacB gene as a counter-selection marker in our strainer system. However, the CFU/ug using the wild-type sacB gene (BBa_K322921) is low even using 0.01% sucrose in the media. Structural insights into the wild-type SacB reveals that S164 is important to ensure the stabilization of D86 that is the nucleophilic agent. We speculate that the S164T mutation could decrease the catalytic efficiency. Thus, we model the new hydrogen bond formation from S164T and the position of the D86 carboxyl group by molecular dynamics, and test our conjecture in our wet experiments.

Introduction

The strainer system utilizes the double stranded DNA breaks (DSBs) as a signal to start the transcription of gRNA targeting on the plasmid harboring sacB gene. Expression of sacB converts sucrose to levan, which accumulates in the periplasm and is toxic to E. coli. When the sacB plasmid is cured by CRISPR/Cas system, the successful recombined strain can survival in the media with sucrose. The strain without DSBs, still retains the plasmid harboring sacB gene, cannot survival in the media with the sucrose. In our wet-lab experiments, we found that the toxicity of sacB in our strainer system is too high. When we use original CRISPR/Cas method and the strainer method for gene editing. Although we can increase the editing efficiency by our strain compared to original CRISPR/Cas method, the CFU/ug using the strainer is much lower than that of original CRISPR/Cas method even use 0.01% sucrose. To this end, we sought to use dry-lab experiment to design a sacB mutant with lower toxicity for E. coli, and this sacB mutant can increase the CFU/μg of the strainer method with high editing efficiency.

Structural insights into the wild-type SacB reveals that S164 forms a hydrogen bond with the nucleophilic agent D86 and the 4-OH of the fructose group, and S164 is important to ensure the stabilization of D86 (Fig. 1). We speculate that the S164T mutation with an additional -methyl would change the orientation of the-OH and would effectively form new hydrogen bonds. Thus, the conformation of the D86 carboxyl group is restricted by hydrogen bonding, results in the reduced hydrolysis rate and cell toxicity. We model the new hydrogen bond formation and the position of the D86 carboxyl group by molecular dynamics, and test our conjecture in our wet experiments.

Fig. 1 The first layer means that the amino acid shown in the figure is the closest layer to the substrate (sucrose), and the distance between all amino acids and the substrate is less than 3.5 Å. W85, D86, W163, R246, D247, E342 are completely conservative in GH68 family.

Result and Discussion

Molecular dynamics (MD) simulations

MD simulations were performed using Amber software [1] and the ff99SB force field [2]. The selected docking complexes of SacB-sucrose were solvated in the OPC water model. A simulated truncated octahedral box was built for calculating protein–ligand interactions. The box size was set to avoid interactions through periodic boundaries. Nonbonded interactions were truncated at a cutoff distance of 11 Å. The system was initially equilibrated using the steepest descent method for 5000 steps twice while restraining the atoms of protein and ligand with 10 kcal/mol and 0 kcal/mol, respectively. Then, the system was gradually heated to 300K within 20 ps while maintaining the 20 kcal/mol constraint on protein–ligand. Next, a 1 ns isothermal–isobaric (NPT) ensemble and 1 ns canonical ensemble (NVT) run were performed, both with 5 kcal/mol restraint. Finally, a 20 ns MD run was adopted for equilibration and sampling. All MD simulations were performed with 2 fs time steps with the temperature maintained via a Berendsen thermostat. Protein–sucrose complexes were equilibrated by detecting the root-mean-square deviation (RMSD) of compounds and protein backbone, and reasonable and equilibrated conformations of the ligand were extracted from the MD simulations (Fig. 2). The RMSD values of SacB backbone fluctuated around 1.2 Å indicated the conformations of sucrose were stable.

Fig. 2 RMSD of SacB Wt (A) (PDB ID: 1OYG) and variant S164T (B) using sucrose as ligand. In the mutants, the fluctuating value of RMSD is large, indicating the low catalytic efficiency of the mutant.

Fig. 3 Binding free energy decomposition calculated by MM/GBSA, including van der Waals energy (A) electrostatic energy (B) non-polar solvation energy (C) polar solvation energy (D) The complexes of SacB and variant S164T with sucrose are indicated in blueness and orange, respectively.

As a whole, we used the MMGBSA (Molecular Mechanics / Poisson Boltzmann (Generalized Born) Surface Area) approach (Fig. 3). The overall binding free energy of sucrose molecules is: -18.84 ± 4.10 kcal / mol. In the mutation group, this value is: -21.27 ± 3.77 kCal / mol, which doesn't change much compared to the wild-type SacB (Based on our previous experimental data, the increased binding energy per 4.5 kCal / mol corresponds to a 2 to 3-fold increase in the inhibitor inhibition capacity, which not directly correspond to the catalytic capacity). S164 plays an important role for the stabilization of sucrose molecule in the pocket, with total free energy calculated as -1.61 kcal / mol. The value of the locus in S164T mutation is only -0.41 kcal / mol. Thus, the S164T is the key mutation, which directly leads to the shift of the sucrose molecules in the catalytic pocket (Fig. 4), enhanced interaction with amino acid D53 and with E214, and diminished interaction with amino acid GLU307. This mutation breaks the delicate balance of the ternary catalytic amino acid with the ligand. Therefore, it is speculated to reduce the cytotoxicity.

Fig. 4 Comparation between variant S164T and SacB Wt. MD simulations of variant S164T (A) and SacB Wt (B) (PDB ID: 1OYG) using sucrose as ligand. The parameters of hydrogen bonds, variant S164T (C) and SacB Wt (D). Conformational change of the D86 orientation results in the partially broken hydrogen bond formed by nucleophilic agent D86 and 4-OH of fructose group , which reduced the efficiency of sucrose hydrolysis.

Improve The CFU/μg of "strainer" Method with SacB Mutant

The results showed that the editing efficiency of SacB_S164T mutant (in EC85) is 25% higher than the control without “strainer” system. The CFU/μg of SacB_S164T mutant (in EC85) increased 3-fold compared to the original “strainer” system while still keep high editing efficiency (Fig. 2A).

We also used the same condition to test SacB_S164T mutant in EC88. The results showed that the editing efficiency using “strainer” system with SacB_S164T mutant is 4-fold higher than the control, although the CFU/μg of SacB_S164T mutant (in EC88) is still 71% lower than the control without “strainer” system (Fig. 2B). We also used the same condition to test SacB_S164T mutant in EC88. However, the results showed that the toxicity of the modified SacB protein was low, and the screening effect served by the lower concentration of sucrose chosen at this point was no longer obvious, so we further optimized the sucrose concentration and found that testing the mutants at 0.1% concentration conditions, the CFU/μg using the "strainer" system with the SacB_S164T mutant was 2-fold higher than the control, although the SacB_ S164T mutant (in EC88) still had a lower CFU/μg than the control without the "strainer" system.

These results showed that our strainer system works as a good purification system to remove the unedited cells, and SacB_S164T mutant is less toxicity than the original SacB.

Fig. 2. Improve the CFU/μg of “strainer” method with SacB mutant. (A) The CFU/μg and editing efficiency of the control group, SacB and SacB_S164T under 0.01% sucrose condition in EC85. (B) The CFU/μg and editing efficiency of the control group, SacB and SacB_S164T under 0.1% sucrose and 0.2% sucrose condition in EC88.

References

[1] Case, D. A.; Belfon, K.; Ben-Shalom, I. Y.; Brozell, S. R.; Cerutti, D. S.; Cheatham, T. E., III; Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Giambasu, G.; Gilson, M. K.; Gohlke, H.; Goetz, A. W.; Harris, R.; Izadi, S.; Izmailov, S. A.; Kasavajhala, K.; Kovalenko, A.; Krasny, R.; Kurtzman, T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; Liu, J.; Luchko, T.; Luo, R.; Man, V.; Merz, K. M.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; Onufriev, A.; Pan, F.; Pantano, S.; Qi, R.; Roe, D. R.; Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Skrynnikov, N. R.; Smith, J.; Swails, J.; Walker, R. C.; Wang, J.; Wilson, L.; Wolf, R. M.; Wu, X.; Xiong, Y.; Xue, Y.; York, D. M.; Kollman, P. A. Amber20, University of California, San Francisco, 2020.

[2] Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006, 65, 712–725.