Difference between revisions of "Part:BBa K322921"

Revision as of 11:48, 12 October 2022

B. subtilis levansucrase. Lethal to E. coli in presence of sucrose.

sacB encodes the Bacillus subtilis levansucrase, which catalyses hydrolysis of sucrose and synthesis of levans (high molecular weight fructose polymers). It is lethal to gram-negative bacteria E-coli.

It works with cat as an alternative method for inserting BioBricks into the genome by using homologous recombination rather than restriction digestion. SacB is used as a negative selection marker, which allows to insert genes onto the chromosomes without leaving a selection marker. The method can thus be reused indefinitely.

The protocol for BRIDGE can be found on the Edinburgh 2010 igem wiki.

http://2010.igem.org/Team:Edinburgh/Project/Protocol

Measurement of SacB promoter:

SacB promoter is the starting sequence of part BBa K322921. It is separately documented as BBa_K2224001 [1] by SMS_Shenzhen team in 2017.

We, SMS_Shenzhen Team, tested the strength of this promoter by comparing it with J23100. According to our measurement,SacB promoter is a functional promoter in E.coli expression system.

For detailed information about SacB promoter, please see the ‘measurement’subtitle on page [2].

Sequence and Features

Contribution: iGEM22_WHU-China

This is a sucrose lethal gene that encodes the enzyme levosucrase, which catalyzes the production of high molecular weight fructose polymers called Levans. Given that heterologous expression of SacB is lethal in the presence of sucrose in many Gram-negative bacteria, SacB is widely used as a genetic engineering tool.

In our project of directed evolution , we added SacB in our constructed vector as a counter-selection element , and we collected some related information from the past papers to verify our experiment.

Fig.1 SacB addition in our constructed vector , which serves as a counter-selection element.

Fig.2 In the process of counter-selection,we add sucrose on the surface of solid culture medium . (A): No colonies are found on the medium supplemented with sucrose;(B):There are many colonies on the medium without added sucrose.

Reference:
[1] Ambrosis N, Fernández J, Sisti F. Counter-Selection Method for Markerless Allelic Exchange in Bordetella bronchiseptica Based on sacB Gene From Bacillus subtilis. Curr Protoc Microbiol. 2020 Dec;59(1):e125.
[2] Chen W, Li Y, Wu G, Zhao L, Lu L, Wang P, Zhou J, Cao C, Li S. Simple and efficient genome recombineering using kil counter-selection in Escherichia coli. J Biotechnol. 2019 Mar 20;294:58-66.
[3] Logue CA, Peak IR, Beacham IR. Facile construction of unmarked deletion mutants in Burkholderia pseudomallei using sacB counter-selection in sucrose-resistant and sucrose-sensitive isolates. J Microbiol Methods. 2009 Mar;76(3):320-3.
[4] Tan Y, Xu D, Li Y, Wang X. Construction of a novel sacB-based system for marker-free gene deletion in Corynebacterium glutamicum. Plasmid. 2012 Jan;67(1):44-52.

Contribution: iGEM22_DUT_China

1. We have compiled the information about sacB in the literature, such as the structure and function of the protein, to facilitate the follow-up investigation of this protein by other teams.

2. We developed a CRISPR-based purification system "strainer" in Escherichia coli, which can remove the unsuccessfully edited cells, and then improve the overall editing efficiency. This system can be used on most scenes.

1 New information learned from literature

The description of BBa_K322921 has briefly introduced the lethal effect of sacB, and the DUT_China team will add information on its structure and function.

The sacB gene encodes the secreted enzyme levansucrase. The enzyme catalyzes hydrolysis of sucrose and synthesis of levans, which are high-molecular-weight fructose polymers. In the gram-negative bacteria E. coli, E. chrysanthemi, and L. pneumophila, expression of sacB in the presence of sucrose is lethal. In E. coli, levansucrase activity is mostly located in the periplasm. The molecular basis of the toxicity is still unclear, but the toxicity could be due to an accumulation of levans which might encumber the periplasm because of their high molecular weight or a transfer of fructose residues to inappropriate acceptor molecules, which could thereafter have toxic effects on the bacterial cells.[1]

We learned that, modification of the tuned interplay among the ten residues that originate the sucrose-binding site (first layer comprising subsites -1 and +1) has generally a drastic effect on the enzyme’s 1activity and often reduces transfructosylation/hydrolysis and HMW levan/FOS partitions.

Fig. 1. The sucrose binding site of SacB Amino acids at hydrogen bond distances (dashed purple lines) from the fructosyl- and glucosyl-moieties constitute the -1 and +1 subsites, respectively. All residues displayed are at distances ≤ 3.5 Å to sucrose hydroxyl-groups. PDB files 1oyg and 1pt2 were employed to prepare the picture. Sucrose from PDB 1pt2 is de- picted in orange/outlined sticks, highlighting either the fructosyl or the glucosyl unit.[1]

W85, D86, W163, R246, D247 and E342 are entirely conserved in such enzymes. When serine is present, its side chain can establish hydrogen bonds with sucrose. Thus, Researchers included residues 164 and 412 as part of the -1 subsite of SacB. E342, R246 and semi-conserved residues R360 and E340 are part of the +1 subsite. [2]. According to the crystallographic structure of SacB, the side chains of residues from -1/+1 subsites (excluding W163 and positions 164 and 412 when occupied by alanine) that are able to act as a donor/acceptor of the hydrogen bond are at distances ≤3.5 Å from sucrose hydroxyl-groups (Fig. 1).

R246 is an invariant residue, which participates in hydrogen bonds via its guanidinium group with the 3-OH groups of the fructosyl-moiety. So, researchers thought that the function of R246 may involve both the stabilization of sucrose binding and the support of an optimal orientation of E340 and E342 with respect to the substrate.[3]

Scientists found that S164 forms a hydrogen bond with the nucleophile D86 and the 4-OH of the fructosyl-moiety, while S412 modulates the position of the nucleophile regarding to the fructosyl-donor also via a hydrogen bond. S412 coordinates the 1-OH group of the fructosyl unit and the invariant residue R343 of the 339DxxER343 motif (Fig. 1) as well. [3]

Arginine or histidine can be found at corresponding positions to 360 in the +1 subsite of fructansucrases, respectively. These residues form hydrogen bonds with the 2- and 3-OH groups of the glucosyl-moiety (Fig. 1, right panel). Mutations at this position reduce the rate of formation of the covalent intermediate fructosyl-enzyme leaving the hydrolyzing activity unaffected and favoring the synthesis of kestose.[4]

2 New data collected from laboratory experiments

2.1 Wet lab: Improve The CFU/μg of "strainer" Method with SacB Mutant

We designed the SacB_S164T mutant which showed less toxicity for E. coli using Molecular dynamics (MD) simulations. Thus, we used Mut Express II Fast Mutagenesis Kit to construct the plasmid with the SacB_S164T mutation. Then, we tested the SacB_S164T mutant for the "strainer" method in EC85. The results showed that the editing efficiency of SacB_S164T mutant was 25% higher than the control without using "strainer" method. The CFU/μg of SacB_S164T mutant increased ~3-fold compared to the original "strainer" method while still keep the 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" method with SacB_S164T mutant was 4-fold higher than the control, although the CFU/μg of SacB_S164T mutant was still 71% lower than the control without using the "strainer" method (Fig. 2B). These results showed that our "strainer" method worked as a good purification system to remove the unedited cells.

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. (B) Used 0.01% sucrose concentration to test SacB _S164T in EC88.

2.2 Dry lab: Molecular Dynamics

Atomistic MD simulations were performed using Amber software [5] and the ff99SB force field [6]. 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 (Figure 2). The RMSD values of SacB backbone fluctuated around 1.2 Å indicated the conformations of sucrose were stable.

Fig. 3 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. 4 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 (Figure 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 (Figure 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. 5 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.

References

[1] Porras-Domínguez J, Seibel J and López-Munguía] A. A close look at the structural features and reaction conditions that modulate the synthesis of low and high molecular weight fructans by levansucrases [J]. Carbohydrate Polymers, 2019.

[2] Meng G. Structural framework of fructosyl transfer in Bacillus subtilis levansucrase [J]. Nat. Struct. Biol, 2003, 10.

[3] Homann A, Biedendieck R, Götze S, et al. Insights into polymer versus oligosaccharide synthesis: mutagenesis and mechanistic studies of a novel levansucrase fromBacillus megaterium [J]. Biochemical Journal, 2007.

[4] Chambert R and Petit-Glatron MF. Polymerase and hydrolase activities of Bacillus subtilis levansucrase can be separately modulated by site-directed mutagenesis [J]. Biochemical Journal, 1991, 279, 35-41.

[5] 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.

[6] 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.