40-2-C-SLE-PETase

IsPETase, a PET hydrolase discovered from the bacterium Ideonella sakaiensis 201-F6, has become a research favorite for its ability to efficiently degrade PET at low temperature ^[1]. It breaks PET into bis(2-hydroxyethyl) terephthalate (BHET) and 2-hydroxyethyl methyl terephthalate (MHET) by hydrolyzing the ester bond, followed by hydrolysis to the end products EG and TPA with the help of MHETase (Fig. 1). However, due to the surface hydrophobicity of PET, it is difficult for PETase to directly bind to it, which negatively affects the hydrolysis rate of PETase on PET ^[2].

Fig. 1. Schematic diagram of the PETase pathway for PET degradation.

Plastic-binding peptides are a class of short-chain peptides that can bind to PET plastic surfaces through hydrophobic binding and other forces, and are a potential solution to improve the degradability of PETase towards PET. However, the sources of PET-binding peptides are currently limited, and they are usually unearthed in a single-point trial-and-error manner, which is inefficient. In this regard, firstly, we performed PET-binding peptide prediction with the help of deep learning, and, then, fused PETase with the efficient binding peptide obtained from the prediction and screening through linker to construct a fusion protein, so as to improve the binding ability of PETase to PET microplastics with the help of PET-binding peptide, thus improving the degradation efficiency.

Linker as a fragment connecting enzyme and short peptide is categorized into flexible linker, rigid linker and cleavable linker. The selection and design of linker can affect the binding affinity between enzyme and short peptide, and may also provide many other advantages for fusion protein production, such as improving biological activity and increasing expression ^[3]. Therefore, we tried to replace the linker to optimize the spatial conformation between the enzyme and the short peptide, reducing the mutual influence between the two component proteins, thus improving the substrate catalytic efficiency as well as expression of the fusion protein. Based on the screening results, we choose to replace the flexible linker G4S with the rigid linker SLE for linker optimization.

Our fusion proteins consist of four basic components:
1) PETase
IsPETase-derived modified mutant with high catalytic performance and stability.

2) SLE linker
A short repetitive sequence selected from the region of the endogenous spacer sequence region of PETase. Molecular dynamics simulations show that it is rigid. It can be used as a rigid linker to maintain a fixed distance between the structural domains of a fusion protein and keep their independent functions ^[3].

3) PET-binding peptide
We used both LSTM and graph neural network (GCN) models to optimise the prediction of high-affinity to obtain efficient PET-binding peptides.

Since the connection of PET-binding peptides at the amino or carboxyl ends will lead to different positions and functional properties, and may also have different effects on the overall protein properties, so this composite element tries to validate the characterization at the carboxyl end of PETase.

4) His tag
The his tag added to the C-terminus of the fusion protein allows specific binding to immobilised metal ions such as Ni²⁺ by forming stable complexes, facilitating purification and testing of the fusion protein.

Fig. 2. Schematic diagram of the fusion protein gene expression cassette.

Molecular construction

The fusion protein gene was synthesised and cloned into plasmid pET-21b（with T7 promotor BBa_K4790075, lac operator BBa_K4790078, RBS BBa_K4790079, and T7 terminator BBa_K4790076) to construct recombinant plasmid pET21b-PETase-SLE-40-2-C-His tag.

Protein expression and purification

The recombinant plasmid was transformed into Escherichia coli BL21 (DE3) for expression and cultured in a 50 mL flask to express sufficient fusion protein.

After fermentation optimization with the fusion protein 50-4-N-G4S-PETase, we determined the final concentration of IPTG to be 0.05 mmol/L. After induction, the culture was incubated at 16°C and fermented for 48 h using TB medium. After culture, the fermentation broth was centrifuged, wall-broken by high-pressure homogenization, and then centrifuged again. The fermentation supernatant and supernatant of cell fragmentation were collected as the crude enzyme.

The crude enzyme activity was measured by continuous spectrophotometry method. The reaction system was 1500 μL including 30 μL 50 mmol/L pNPB, 30 μL crude enzyme liquid and 1440 μL 100 mmol/L pH 8.0 phosphate buffer. The generation rate of p-nitrophenol during 60 s was recorded at the wavelength of 405 nm. One enzyme activity unit (U) was defined as the amount of enzyme required to hydrolyze pNPB producing 1 μmol p-nitrophenol during 60 s at 60°C.

The crude enzyme liquid of the supernatant of cell fragmentation with higher enzyme activity was subjected to Ni²⁺ column affinity chromatography. SDS-PAGE analysis showed that there wasn’t a clear band near 35 kDa (Fig. 3). Due to the hydrophobicity of the selected PET-binding peptide, it may have affected the protein conformation, resulting in the fusion protein (34kDa) being difficult to bind to Ni²⁺ ions and thus difficult to be purified. Therefore, we changed the purification method to thermal purification. We took 5 mL aforementioned crude enzyme liquid and incubated it at 50°C for 2 h, and the solution was centrifuged. Then, the supernatant was purified enzyme.

Fig. 3. SDS-PAGE analysis. M: Marker; FS: Fermentation supernatant; PC: Precipitation of cell fragmentation; SC: Supernatant of cell fragmentation; P: Purified enzyme.

Enzyme property characterization

1) Optimal pH
Enzyme activity was determined using phosphate buffer at 60°C 100 mmol/L pH 6.0-9.0 (gradient of 1.0). The relative enzyme activity at each pH was calculated using the highest enzyme activity measured as 100%. The enzyme activity of the fusion protein showed an increasing trend at pH 6.0-9.0, with the highest activity at pH 9.0 (Fig. 4).

Fig. 4. Optimum pH of PETase-SLE-40-2-C.

2) Optimal temperature
The enzyme activity was determined by preheating the pH 8.0 phosphate buffer for 10 min at different temperatures (30, 40, 50, 60, 70°C). The highest enzyme activity measured was taken as 100% and the relative enzyme activity at each temperature was calculated. The enzyme activity of the fusion protein increased gradually with increasing temperature at 30-70°C (Fig. 5).

Fig. 5. Optimum temperature for PETase-SLE-40-2-C.

3) Thermostability
The pure enzyme solution was placed in a 50°C water bath and sampled at 24 h intervals to determine the residual enzyme activity. The enzyme activity at 0 h of reaction was defined as 100%. The fusion protein possessed good stability at 50°C reaction temperature (Fig. 6).

Fig. 6. Temperature stability for PETase-SLE-40-2-C at 50°C.

Characterization of PET degradation property

PET microplastics (final concentration 2.9 g/L) were degraded by 0.01 mg/mL fusion protein under the condition of 100 mM glycine-NaOH buffer (pH 9.0) at 50°C. A total of 50 μL reaction liquid was taken mixing with 450 μL methanol after 24 h PET substrate degradation. After centrifugation, the supernatant was collected and filtered by aqueous phase filtration membrane, then the filtrate was analyzed by high performance liquid chromatography (HPLC).

Since BHET can be categorized as the incomplete degradation product of PET, and TPA and MHET can be categorized as the final degradation product of PET, we selected TPA and MHET as the indicators to calculate the product release. Compared with the original enzyme, the product release amount of was lower than PETase (Fig. 7).

Fig. 7. HPLC analysis of PET degradation of PETase and PETase-SLE-40-2-C.

PET-binding peptide 40-2 attached to the C-terminus of PETase via the SLE linker failed to promote PETase for PET degradation, so it was not studied for further modification.

References

[1] Yoshida S, Hiraga K, Takehana T, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate) [J]. Science, 2016, 351(6278): 1196-1199.
[2] Puspitasari N, Tsai S L, Lee C K. Fungal hydrophobin RolA enhanced PETase hydrolysis of polyethylene terephthalate [J]. Applied Biochemistry and Biotechnology, 2021, 193(5): 1284-1295.
[3] Chen X, Zaro J L, Shen W C. Fusion protein linkers: property, design and functionality [J]. Advanced Drug Delivery Reviews, 2013, 65(10): 1357-1369.

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