Difference between revisions of "Part:BBa K4390010"

Latest revision as of 16:12, 8 October 2022

Mytilus galloprovincialis Metallothionein

This part is not compatible with BioBrick RFC10 assembly but is compatible with the iGEM Type IIS Part standard which is also accepted by iGEM.

This is a Level 0 part of type C part generating the following 4 base overhangs at upstream (TTCG) and downstream (GCTT) ends.

Usage and Biology

Metallothionein (MT) is a small protein (around 6-7 kDa) which is rich in cysteine. These thiol group in cysteines provide ability to chelate almost all heavy metal ions including Cd2+, Hg2+, Pb2+ and As3+, but had been shown that has higher binding affinity with Hg2+ (Manceau, A. et al., 2019). The ability of chelating heavy metals provides the metal tolerance for its hosts. For its ability to binding heavy metal strongly, this part can be used to build structure which can capture heavy metal ions in aqueous environment. This MT sequence was one isoform from Mytilus galloprovincialis which contains higher cysteine frequency with 23 in 72 amino acids (Vergani, L. et al., 2007). To improve the heavy metal binding affinity, Mytilus galloprovincialis MT was compared with MT from Mytilus edulis, Callinectes sapidus, Danio rerio, Pseudomonas fluorescens and Saccharomyces cerevisiae for their ability to chelate more heavy metals which lead to higher heavy metal tolerance in BL21(DE3). To express and purify the protein, the sequence was designed as a C part for JUMP assembly (Valenzuela-Ortega M and French C., 2021).

Characterization

Mytilus galloprovincialis MT part is required to be assembled into plasmid pJUMP29-1A(lacZ) along with BBa_K4390017 and BBa_K4390016. To confirm the assembly was success, we performed blue-white colony screening and colony PCR. The transformed cells were plate on Kanamycin and X-gal plates. Since pJUMP29-1A(lacZ) contains lacZ as a cloning receptor, the beta-galactosidase encoded by lacZ will cleave X-gal and forming a molecule which dimerizes and turns the colony blue when assembly is failed. It is possible that the lacZ in pJUMP29-1A(lacZ) was cut out and the non-complementary sticky ends were annealled by T4 ligase. Therefore we picked up white colonies and performed colony PCR to ensure that the assembly was correct (Figure 1).

Figure 1. Colony PCR of Mytilus galloprovincialis MT using PS1 and PS2 as primers. The 1 kb ladder (left) and colony PCR products (right) was running through a electrophresis gel to determine the molecular weight of assembled plasmid.

Result and Discussion

MT heavy metal binding affinity improvement

Ensuring Mytilus galloprovincialis MT was expressed in BL21(DE3), we performed AgNO3 gradient plate test to test the influence of Mytilus galloprovincialis MT on BL21(DE3) heavy metal tolerance. AgNO3 was used based on its high efficiency of antibacterial (Yin, I. X. et al., 2020) with low toxicity towards eukaryote. With the presence of Mytilus galloprovincialis MT, BL21(DE3) started to grew at higher AgNO3 concentration plates (Figure 2A, 2B), indicating that Mytilus galloprovincialis MT did provide heavy metal tolerance to the host bacteria. We noticed that there was one colony grew at a relatively higher AgNO3 concentration (26 mg/L) which shown almost no growth for other type of MTs (Figure 2B). This was possibly due to direct evolutionary mutation at high AgNO3 concentration environment, but the possibility of experimental error should also be considered.

Figure 2. AgNO3 gradient plate test for control, wild-type and error prone MT. 10 different concentrations were used from 16-30 mg/L for each test. The cell used in the test are A) the control BL21(DE3) with no MT expressed. B) BL21(DE3) cells expressing wild typeMytilus galloprovincialis MT. C) BL21(DE3) cells expressing error prone Mytilus galloprovincialis MT.

The result of silver tolerance test was compared between MTs from Mytilus edulis, Mytilus galloprovincialis, Callinectes sapidus, Danio rerio, Pseudomonas fluorescens and Saccharomyces cerevisiae to identify the MT which binds to the highest number of heavy metal ions. Error prone PCR of each MT was also performed with different concentration of dNTPs to increase the possibility of cysteine mutation. After error prone PCR, we did not observe any change on tolerance of BL21(DE3) (Figure 2C), indicating that the error prone did not bring new mutations that will increase the heavy metal binding affinity.

Docking simulation

Non-designed Mytilus galloprovincialis MT sequence was taken from NCBI and the Alphafold structures shown were predicted (Figure 3). These structures were docked to Ag+ using AutoDock 4.2 such that the structures were hydrated and energy minimised while allowing gamma sulphurs on the sidechains of cysteines to form coordinate covalent bonds with the metal ligand (Figure 3).The energy minimisation was done after each ligand was docked. MTs contain many cysteines however each cysteine does not carry the same binding affinity for the ligand. This was accounted for using a pass/fail metric where the passed cysteine had negative Gibbs free energy thus making the binding spontaneous. As result, there were 5 Ag+ docked with Gibbs free energy per ion binding of -0.170 kcal/mol. This data was compared with Mytilus edulis, Callinectes sapidus, Danio rerio, Pseudomonas fluorescens and Saccharomyces cerevisiae. Mytilus galloprovincialis MT contains the largest number of cysteine which might allows it to bind to more Ag+ ions.

Figure 3. 3D structure of wilt-type Mytilus galloprovincialis MT predicted by Alphafold with the metal ion binding been docked by AutoDock 4.2.

Table 1. In-silico modelled Gibbs free energy based on docking simulation

Sequence and Features

References

Manceau, A. et al. (2019) Mercury(II) Binding to Metallothionein in Mytilus edulis revealed by High Energy‐Resolution XANES Spectroscopy. Chemistry : a European journal. 25 (4), 997–1009.

Valenzuela-Ortega, M. & French, C. (2021) Joint universal modular plasmids (JUMP): a flexible vector platform for synthetic biology. Synthetic biology (Oxford University Press). 6 (1), ysab003–ysab003.

Vergani, L. et al. (2007) Molecular characterization and function analysis of MT-10 and MT-20 metallothionein isoforms from Mytilus galloprovincialis. Archives of biochemistry and biophysics. 465 (1), 247–253.

Yin, I. X. et al. (2020) The Antibacterial Mechanism of Silver Nanoparticles and Its Application in Dentistry. International journal of nanomedicine. 152555–2562.