Coding

Part:BBa_K4652008

Designed by: YUAN-AN CHEN   Group: iGEM23_Mingdao   (2023-08-15)


SpyTag-PCLase1-SpyCatcher



Polycaprolactone (PCL) is a biodegradable plastic material that has received FDA approval. It's extensively used in various applications such as tissue engineering, drug delivery, food packaging, and agricultural coverings1. Typically, products made from PCL take 2-3 years to decompose. As a result, there's a growing interest in identifying novel enzymes that can degrade PCL or in optimizing those that are currently available commercially2. However, most of them can’t tolerate at extremely high temperatures, including the boiling temperatures encountered during the thermoforming process of shaping PCL plastic.


In Prof. Fan Li's laboratory, novel PCL-degrading enzymes, PCLase I and PCLase II, were identified and purified from Pseudomonas hydrolytica3. This discovery was made possible by cultivating the bacteria in a PCL-emulsified medium. The team conducted an in-depth study of the PCLase enzymes, examining aspects such as enzyme activity, the influence of pH and temperature, substrate specificity, degradation products, as well as the associated gene sequences and protein structures. Learned with this comprehensive data and the enzymes' impressive PCL-degrading efficiency, our aim is to enhance their thermostability.


SpyRing cyclization technique to enhance enzyme thermal resilience was clarified by Dr. Mark Howarth’s team4. SpyRing harbors genetically modified SpyTag (13 amino acids) on the N-terminus and SpyCatcher (12kDa) on the C-terminus on the protein of interest. This context spontaneously reacts together through an irreversible isopeptide bond. SpyRing cyclization was demonstrated successfully to increase stress resilience of β-lactamase and some industrially important enzymes. With this synthetic biology tool, we plan to employ SpyRing cyclization techniques and expect to make PCLase thermal resistent, as demonstrated in our work with the SpyTag-GFP-SpyCatcher construct (Part:BBa_K4652002).


PLASMID CONSTRUCTION





PCLase I and PCLase II gene sequences with N-terminal SpyTag and C-terminal SpyCatcher were synthesized by Integrated DNA Technologies, Inc. (IDT) and then cloned into pSB1C3, respectively (SpyTag-PCLase1-SpyCatcher, Part:BBa_K4652008; SpyTag-PCLase2-SpyCatcher, Part:BBa_K4652012). Then, the parts were connected with a T7 promoter (Part:BBa_K1833999), a strong RBS (Part:BBa_B0030), and a double terminator (Part:BBa_B0015). The final construct was verified using colony PCR (Figure 1) and further validated through DNA sequencing. These resultant constructs were designated as T7-SpyTag-PCLase1-SpyCatcher (Part:BBa_K4652010) and T7-SpyTag-PCLase2-SpyCatcher (Part:BBa_K4652013), respectively.





Figure 1. Verification of T7-SpyTag-PCLase1-SpyCatcher (Part:BBa_K4652010) and T7-SpyTag-PCLase2-SpyCatcher (Part:BBa_K4652013) using colony PCR. PCR was performed using a CmR-specific forward primer from the vector and a PCLase-specific reverse primer from the gene. The expected size of the amplified DNA fragments is 2395 bp for T7-SpyTag-PCLase1-SpyCatcher and 2561 bp for T7-SpyTag-PCLase2-SpyCatcher, respectively. The rightmost lane displays a 1 kb DNA ladder. The numbers correspond to selected colonies, with one control (lane 7) derived from a mock pick from a clear zone on the plate.



PCL-DEGRADING LIPASE COMPARISON

To compare the lipase activities of PCLase I, PCLase II, and other commercially available PCR-degrading enzymes such as BCLA5 and CALB6, we conducted a pNPB assay. In this assay, a potential lipase breaks down the ester bond of p-nitrophenylbutyrate (pNPB), producing p-Nitrophenol. The concentration of p-Nitrophenol can be measured at 405nm, and these measurements are corresponding to the lipase activity.




Lysates from E. coli BL21, which carried the T7 promoter-driven expression plasmid with the indicated genes in the same context, were collected after being induced with 0.3 mM IPTG at 25°C for 20 hours. The lipase activities within these lysates were assessed using the pNPB assay5. As shown in Figure 2, PCLase I exhibited the significantly highest readings at 405 nm. This suggests that under our experimental conditions, PCLase I is the most effective lipase, demonstrating potential activity in decomposing PCL through the hydrolysis of the ester bonds between polymers. Consequently, we chose to investigate the characteristics of PCLase I (hereafter referred to as PCLase for short) in terms of its thermostability, protein structure, PCL degradation capability, and its potential use in real-world products.






Figure 2. Comparison between lipase activities of BCLA, CALB, PCLase I, and PCLase II using pNPB assay. E. coli BL21 was transformed using the indicated T7 promoter-driven gene expression plasmid. The bacteria were induced by 0.3 mM of IPTG at 25°C for 20 hours. Subsequently, the lysates were harvested using 0.1 mm Disruptor Beads (Scientific Industries, Inc). A 20 µL aliquot of these lysates was combined with 175 µL of Tris-HCl buffer (20mM, pH=8) and 5 µL of pNPB (40 mM dissolved in 2-methyl-2-butanol). Lipase activity was read at 405 nm based on p-Nitrophenol production. The obtained readings were normalized with the OD600 values at the time of bacterial lysate collection.



THERMOSTABILITY

To assess the thermostability of PCLase, the bacterial lysates, prepared as described earlier, were exposed to a 100°C treatment followed by a pNPB assay to measure lipase activity. PCLase activity decreased to 20% in 5 min but remained stable for up to 30 minutes (Figure 3). The phenomena were consistent with the observations made in lysates containing cyclized GFP (Part:BBa_K4652002), but, notably, PCLase exhibited much more prolonged heat resistance at the boiling temperature (i.e., cyclized GFP is tolerate for 5 min, while cyclized PLCase is for 30 min).






Figure 3. Thermostability of PCLase lipase activity. E. coli BL21 was transformed with T7-SpyTag-PCLase1-SpyCatcher (Part:BBa_K4652010). The bacteria were induced by 0.3 mM of IPTG at 25°C for 20 hours. Subsequently, the lysates were harvested using 0.1 mm Disruptor Beads (Scientific Industries, Inc). After treated at 100°C for the indicated time, a 20 µL aliquot of these lysates was combined with 175 µL of Tris-HCl buffer (20mM, pH=8) and 5 µL of pNPB (40 mM dissolved in 2-methyl-2-butanol). Lipase activity was read at 405 nm based on p-Nitrophenol production. All values were divided by the average of the untreated control, with the resulting ratio representing the lipase activity fold change.



PROTEIN STRUCTURE & ACTIVITY







The mechanism in SpyRing for the spontaneous cyclization reaction involves Asp7 on the SpyTag at the N-terminus forming double hydrogen bonds with Glu77 on the SpyCatcher at the C-terminus. This interaction strengthens the creation of an irreversible isopeptide bond between Asp7 on SpyTag and Lys31 on SpyCatcher. As a result, the protein is seamlessly cyclized, enhancing its resistance to chemical, thermal, or enzymatic degradation7.





To verify the protein structure and its correlation to thermal tolerance, in a similar approach on T7-RBS-SpyTag (D7A)-GFP-SpyCatcher-Tr (Part:BBa_K4652003), we engineered a SpyTag mutation of PCLase and designated as T7-RBS-SpyTag (D7A)-PCLase1-SpyCatcher-Tr (Part:BBa_K4652011). The lysates, as collected previously, were subject to SDS-PAGE and Coomassie Blue staining. In Figure 4, the result showed a distinct band corresponding to the linear form of SpyTag (D7A)-PCLase1-SpyCatcher, with an expected size of 46.53 kDa. However, the lysates from SpyTag-PCLase1-SpyCatcher displayed somewhat fuzzy bands representing incomplete cyclized or fully cyclized forms. This ambiguity might arise from aggregation or polymerization due to isopeptide bond formation8. It's worth noting that the presence of incompletely cyclized PCLase could partially account for the reduced lipase activity after heating observed in the experiment in Figure 3.










Figure 4. Protein structure analysis of cyclized form and linear form of SpyTag-PCLase1-SpyCatcher. 15 µg of IPTG-induced lysates were run on a 4-12% gradient SDS-PAGE (BIO-RAD) and stained with standard Coomassie Blue. The AceColor Prestained Protein Marker (10 - 180 kDa) was used for size reference. Lane 1 refers to the linear proteins derived from lysates of SpyTag (D7A)-PCLase1-SpyCatcher (BBa_K4652011). Lane 2 refers to the cyclized proteins derived from lysates of SpyTag-PCLase1-SpyCatcher (BBa_K4652010). The predicted molecular weight for the SpyTag-PCLase1-SpyCatcher protein is 46.53 kDa.



In addition, we compared the thermostabilities between lipase activities in lysates with linear PCLase (SpyTag (D7A)-PCLase1-SpyCatcher) and cyclized PCLase (SpyTag-PCLase1-SpyCatcher) using the pNPB assay. After being treated at temperatures ranging from 70°C to 100°C for 10 min, the cyclized lipase retained higher activity compared to the linear form of PCLase (Figure 5). It maintained over 50% activity up to 90°C and retained up to 20% at 100°C. It's worth exploring whether purifying and concentrating the fully cyclized PCLase could enhance the lipase activity in the lysates for thermal testing. Taken together, the experimental data demonstrated successfully making a thermostable PCLase by cyclization through SpyRing technique.




Figure 5. Thermostability of PCLase lipase activities between cyclized PCLase (SpyTag-PCLase1-SpyCatcher, Part:BBa_K4652010) and linear PCLase (SpyTag (D7A)-PCLase1-SpyCatcher, Part:BBa_K4652011). E. coli BL21 was transformed with the indicated plasmid and then was induced by 0.3 mM of IPTG at 25°C for 20 hours. Subsequently, the lysates were harvested using 0.1 mm Disruptor Beads (Scientific Industries, Inc). After treated at 100°C for the indicated time, a 20 µL aliquot of these lysates was combined with 175 µL of Tris-HCl buffer (20mM, pH=8) and 5 µL of pNPB (40 mM dissolved in 2-methyl-2-butanol). Lipase activity was read at 405 nm based on p-Nitrophenol production. All values were divided by the average of the untreated control, with the resulting ratio representing the lipase activity fold change.



PCL GRANULE DECOMPOSITION

To evaluate PCLase's degradation potential on PCL plastic, we purchased polycaprolactone raw materials in granule form (Mn 80,000, #440744, SIGMA-ALDRICH). Measuring weight loss over days is a feasible approach to assess enzyme degradation efficiency9. Around 10 mg of PCL granules were placed in 5 ml of Tris-HCl at a pH of 8 and mixed with 500 µl of bacterial lysates containing PCLase. Incubate at 50°C for 24 hrs, the granules were taken out, oven-dried, and weighed. These granules were introduced again in the fresh buffer and fresh enzymes. This process was monitored over a span of 5 days. As shown in Figure 6, when compared to controls without any enzyme treatment, PCLase resulted in a daily weight loss of approximately 10-20%. By the final day of observation, the PCL granule had lost nearly half its weight. The findings suggest that the PCLase produced in our lab is effective in degrading PCL plastics.



Figure 6. PCL granule degradation by PCLase. PCL granules (Mn 80,000) were obtained from Sigma-Aldrich. Around 10 mg of the granules were immersed in 5 ml of Tris-HCL buffer (100mM, pH = 8) supplemented with 500 µl of PCLase or without any enzyme as a control. After a 24-hour incubation at 50°C, the granules were removed, dried and weighed, followed by replaced with fresh buffer and fresh enzymes. The cycle continued for 5 days. Weight loss was determined relative to the average weight on Day 1. Data represents the mean and standard error from three independent sets.



PCL NANOFIBER FILM DEGRADATION

Electrospun PCL nanofiber films are prevalent in medical care, especially for applications like wound dressings10. While PCL materials have FDA approval, their 2-3 year degradation time appears too long. Consequently, enzymes that degrade PCL have gained significant research interest. Prof. Hsiao-Chun Yang from the Department of Fiber and Composite Materials at Feng Chia University is a renowned expert in this field. We consulted him for guidance on our PCLase and obtained some PCL films for testing. To increase the PCLase protein concentration, we passed the sonicated bacterial lysates through 0.45 µm PES (Polyethersulfone) Syringe Filters (HYUNDAI MICRO CO.,LTD.) and subsequently concentrated the proteins using 30K Microsep™ Advance Centrifugal Devices (Pall Corporation). We then submerged 1-cm x 1-cm PCL films in 3 ml of Tris-HCl buffer (pH = 8) with 30 µl of the concentrated lysates, incubating at 50°C for 24 hrs. As demonstrated in Figure 7, PCLase significantly and efficiently degraded PCL film compared to controls without enzyme treatment or those with GFP. In sum, the PCLase we developed exhibits lipase activity in the pNPB assay and is also capable of breaking down PCL granules and films.











Figure 7. PCL electrospun film degradation by PCLase. PCL films were obtained from Prof. Yang’s laboratory. A 1-cm x 1-cm PCL films was immersed in 3 ml of Tris-HCL buffer (100mM, pH = 8) either supplemented with 30 µl of concentrated PCLase, 30 µl of concentrated GFP, or left enzyme-free as a control. After a 24-hour incubation at 50°C, the film decomposition was observed. The pictures were representative data from 3 independent experiments.



APPLICATION OF PCLase-EMBEDDED PCL PRODUCT

Although many researches are working on lipase-embedded PCL materials11,12,13, they often utilize existing PCL-degrading enzymes that are not able to endure the thermoforming process typical in standard PCL plastic production. We're wondering if our cyclized PCLase can address this issue. Traditionally, PCL granules are dissolved in organic solvents such as chloroform, dimethylformamide, or toluene14. Besides their inherent toxicity, these solvents often impair and deactivate any bioactive enzyme intended for mixing. To blend seamlessly with PCL without using organic solvents, we freeze-dried the concentrated PCLase into a powder form, facilitating its mixture with PCL powder (Figure 8).









Figure 8. PCL, GFP, PCLase materials in our studies. PCL granules were purchased from SIGMA-ALDRICH (Mn 80,000, #440744). PCL powder was purchased from MAGERIAL SCIENCE (100 mesh size, #24980-41-4). GFP powder and PCLase powder were prepared by ourselves using a freeze dryer (KINGMECH Freeze Dryers System #FD4.5-8P-L).


The PCL-PCLase composite containing 10 mg of PCL powder and 2 mg of PCLase powder in a glass bottle was heated to a pliable state at 100°C for 1min in a water bath. Once cooled, the PCLase-embedded PCL plastic resembled a raw fibrous membrane. Then, the bottle was filled with 3 ml of 100mM Tris-HCl buffer (pH = 8), followed by incubation at 50°C for 1 week. Compared to the GFP-embedded PCL plastic used as a control, the size of the PCLase-embedded plastics reduced to half by Day 3, to a tenth by Day 5, and had nearly vanished by Day 7 (Figure 9).

Notably, the buffer from the GFP-embedded membrane exhibits green fluorescence, likely due to excess GFP on the membrane's surface. It also could be a concern that GFP or any embedded protein might be released from the membrane, that warrants further refinement in protein embedding techniques. However, the membrane's distinct green fluorescence remains vivid under blue LED exposure even after 30 days of incubation in the buffer at 50°C (Figure 9, inset panel). This indicates that the protein retains its structural integrity and biological function in challenging conditions, making it promising for storage and transportation. Altogether, the results highlight the potential of thermostable PCLase-embedded PCL materials, suggesting their suitability for standard biodegradable plastic manufacturing processes worldwide.



Figure 9. GFP or PCLase-embedded PCL fibrous membrane. Each membrane was made by mixing and heating at 100°C for 1min with 10 mg of PCL powder and 2 mg of either GFP or PCLase protein powder. The membranes were submerged in 3 ml of Tris-HCL buffer (100mM, pH = 8) at 50°C and observed daily for a month. The images depict results from Days 1, 3, 5, and 7. The inset panel highlights GFP activity of GFP-embedded membrane on Day 30, captured under blue LED light. The pictures were representative data from 3 independent experiments.



CONCLUSION

Polycaprolactone (PCL), a widely-used biodegradable plastic, typically takes 2-3 years to decompose. To address this, our team identified PCL-degrading enzymes, PCLase, according to the research of Prof. Fan Li. Using the Dr. Mark Howarth’s SpyRing cyclization technique, we enhanced PCLase's thermostability, allowing it to retain activity at high temperatures. In practical tests, PCLase significantly reduced the weight of PCL granules within five days and similarly degraded PCL nanofiber films. Traditional PCL processing uses toxic solvents, but our freeze-drying method allowed PCLase to mix directly with PCL powder, leading to rapid degradation of the resulting composite. This implies that such a thermostable PCLase-PCL composite material is primed for integration into standard thermoforming plastic production processes in the real world.


Interestingly, the buffer containing the GFP-embedded membrane emitted a fluorescent signal, indicating potential protein leaching and underscoring the need for further refinement. However, our GFP-embedded membrane demonstrated remarkable stability of the embedded protein, enduring for 30 days or more in a challenging 50°C environment. In summary, our research presents a groundbreaking approach to faster biodegradable plastics, offering a sustainable solution to a global environmental challenge.




REFERENCE

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  2. Urbanek AK, Mirończuk AM, García-Martín A, Saborido A, de la Mata I, Arroyo M. Biochemical properties and biotechnological applications of microbial enzymes involved in the degradation of polyester-type plastics. Biochim Biophys Acta Proteins Proteom. 2020 Feb;1868(2):140315. doi: 10.1016/j.bbapap.2019.140315. Epub 2019 Nov 16. PMID: 31740410.
  3. Li L, Lin X, Bao J, Xia H, Li F. Two Extracellular Poly(ε-caprolactone)-Degrading Enzymes From Pseudomonas hydrolytica sp. DSWY01T: Purification, Characterization, and Gene Analysis. Front Bioeng Biotechnol. 2022 Mar 18;10:835847. doi: 10.3389/fbioe.2022.835847. PMID: 35372294; PMCID: PMC8971842.
  4. Schoene C, Bennett SP, Howarth M. SpyRings Declassified: A Blueprint for Using Isopeptide-Mediated Cyclization to Enhance Enzyme Thermal Resilience. Methods Enzymol. 2016;580:149-67. doi: 10.1016/bs.mie.2016.05.004. Epub 2016 Jun 16. PMID: 27586332.
  5. Yang J, Guo D, Yan Y. Cloning, expression and characterization of a novel thermal stable and short-chain alcohol tolerant lipase from Burkholderia cepacia strain G63. Journal of Molecular Catalysis B: Enzymatic. 2007 Jan 9;45(3-4):91-96. doi:10.1016/j.molcatb.2006.12.007
  6. Ujiie A, Nakano H, Iwasaki Y. Extracellular production of Pseudozyma (Candida) antarctica lipase B with genuine primary sequence in recombinant Escherichia coli. J Biosci Bioeng. 2016 Mar;121(3):303-9. doi: 10.1016/j.jbiosc.2015.07.001. Epub 2015 Aug 10. PMID: 26272415.
  7. Reddington SC, Howarth M. Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher. Curr Opin Chem Biol. 2015 Dec;29:94-9. doi: 10.1016/j.cbpa.2015.10.002. Epub 2015 Oct 30. PMID: 26517567.
  8. Eastman D, Dworkin M. Endogenous ADP-ribosylation during development of the prokaryote Myxococcus xanthus. Microbiology (Reading). 1994 Nov;140 ( Pt 11):3167-76. doi: 10.1099/13500872-140-11-3167. PMID: 7812456.
  9. Asaduzzaman F, Salmon S. Controllable Water-Triggered Degradation of PCL Solution-Blown Nanofibrous Webs Made Possible by Lipase Enzyme Entrapment. Fibers. 2023; 11(6):49. doi: 10.3390/fib11060049.
  10. Xu H, Zhang F, Wang M, Lv H, Yu DG, Liu X, Shen H. Electrospun hierarchical structural films for effective wound healing. Biomater Adv. 2022 May;136:212795. doi: 10.1016/j.bioadv.2022.212795. Epub 2022 Apr 10. PMID: 35929294.
  11. Khan I, Nagarjuna R, Dutta JR, Ganesan R. Enzyme-Embedded Degradation of Poly(ε-caprolactone) using Lipase-Derived from Probiotic Lactobacillus plantarum. ACS Omega. 2019 Feb 7;4(2):2844-2852. doi: 10.1021/acsomega.8b02642. PMID: 31459515; PMCID: PMC6648548.
  12. DelRe C, Jiang Y, Kang P, Kwon J, Hall A, Jayapurna I, Ruan Z, Ma L, Zolkin K, Li T, Scown CD, Ritchie RO, Russell TP, Xu T. Near-complete depolymerization of polyesters with nano-dispersed enzymes. Nature. 2021 Apr;592(7855):558-563. doi: 10.1038/s41586-021-03408-3. Epub 2021 Apr 21. PMID: 33883730.
  13. Greene AF, Vaidya A, Collet C, Wade KR, Patel M, Gaugler M, West M, Petcu M, Parker K. 3D-Printed Enzyme-Embedded Plastics. Biomacromolecules. 2021 May 10;22(5):1999-2009. doi: 10.1021/acs.biomac.1c00105. Epub 2021 Apr 18. PMID: 33870685.
  14. Altun E, Ahmed J, Aydogdu MO, Harker A, Edirisinghe M. The effect of solvent and pressure on polycaprolactone solutions for particle and fibre formation. European Polymer Journal. 2022 May 31 173:111300. doi: 10.1016/j.eurpolymj.2022.111300.





Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


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Parameters
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