PET水解酶传统与智能分子设计研究进展

doi:10.19586/j.2095-2341.2022.0160

生物技术进展 ›› 2023, Vol. 13 ›› Issue (1): 46-54.DOI: 10.19586/j.2095-2341.2022.0160

PET水解酶传统与智能分子设计研究进展

苗瑞菊¹^,²(), 丁尊丹², 田健², 张红兵¹(), 关菲菲²()

^1.河北经贸大学生物科学与工程学院，石家庄 050061
^2.中国农业科学院生物技术研究所，北京 100081

收稿日期:2022-09-20 接受日期:2022-10-09 出版日期:2023-01-25 发布日期:2023-02-07
通讯作者: 张红兵,关菲菲
作者简介:苗瑞菊E-mail: 1225718255@qq.com
基金资助:
国家重点研发计划项目(2021YFC2100301)

Research Advances on Traditional and Intelligent Molecular Design of PET Hydrolases

Ruiju MIAO¹^,²(), Zundan DING², Jian TIAN², Hongbing ZHANG¹(), Feifei GUAN²()

^1.College of Bioscience and Engineering，Hebei University of Economics and Business，Shijiazhuang 050061，China
^2.Biotechnology Research Institute，Chinese Academy of Agricultural Sciences，Beijing 100081，China

Received:2022-09-20 Accepted:2022-10-09 Online:2023-01-25 Published:2023-02-07
Contact: Hongbing ZHANG,Feifei GUAN

摘要/Abstract

摘要：

塑料由于其耐久性和耐降解性造成的环境污染日趋严重，而塑料废弃物的处理回收方法存在着缺陷。聚对苯二甲酸乙二醇酯（polyethylene terephthalate，PET）是应用最广泛的塑料类型之一，但在自然条件下很难被降解。近年来，虽然多种具有PET降解活性的酶被发现，但这些酶的催化活性和热稳定性难以支撑实际工业所需，因此提高PET水解酶的降解能力已成为研究热点而备受关注。脂肪酶、角质酶、IsPETase和IsMHETase是目前研究最为广泛的PET水解酶，就这几种酶的结构、活性特征进行了总结，重点阐述了传统蛋白质工程和人工智能分子设计在增强PET水解酶应用性能方面的研究进展。期望塑料降解酶可以进一步发展优化，为循环塑料经济做出有价值的贡献。

关键词: PET水解酶, 蛋白质工程, 智能分子设计, 机器学习

Abstract:

Environmental pollution caused by plastic is becoming more and more serious due to its durability and degradation resistance， and there are defects in the treatment and recycling methods of plastic waste. Polyethylene terephthalate （PET） is one of the most widely used types of plastic， but it is difficult to degrade under natural conditions. In recent years， although a variety of enzymes with PET degradation activities have been discovered， the catalytic activity and thermal stability of these enzymes are difficult to support practical industrial needs. Therefore， improving the degradation ability of PET hydrolase has become a research hotspot and has received attention. Lipase， cutinase， IsPETase and IsMHETase are the most widely studied PET hydrolases. The structure and activity characteristics of these enzymes were summarized， with emphasis on the research progress of traditional protein engineering and artificial intelligence molecular design in enhancing the application performance of PET hydrolase. It was expected that plastic-degrading enzymes could be further developed and optimized to make valuable contributions to the circular plastics economy.

Key words: PET hydrolase, protein engineering, intelligent molecular design, machine learning

中图分类号:

苗瑞菊, 丁尊丹, 田健, 张红兵, 关菲菲. PET水解酶传统与智能分子设计研究进展[J]. 生物技术进展, 2023, 13(1): 46-54.

Ruiju MIAO, Zundan DING, Jian TIAN, Hongbing ZHANG, Feifei GUAN. Research Advances on Traditional and Intelligent Molecular Design of PET Hydrolases[J]. Current Biotechnology, 2023, 13(1): 46-54.

图/表 1

参考文献 75

1	THOMPSON R C, MOORE C J, VOM S F, et al.. Plastics, the environment and human health: current consensus and future trends[J]. Philos. Trans. R. Soc. Lond B Biol. Sci., 2009, 364(1526): 2153-2166.
2	MAGALHAES R P, CUNHA J M, SOUSA S F. Perspectives on the role of enzymatic biocatalysis for the degradation of plastic PET[J/OL]. Int. J. Mol. Sci., 2021, 22(20): 11257[2022-08-05]. .
3	ALLEN S, ALLEN D, PHOENIX V R, et al.. Atmospheric transport and deposition of microplastics in a remote mountain catchment[J]. Nat. Geosci., 2019, 12(5): 339-344.
4	THOMPSON R C, OLSEN Y, MITCHELL R P, et al.. Lost at sea: where is all the plastic?[J]. Science, 2004, 304(5672): 838-838.
5	刘鑫蓓, 董旭晟, 解志红, 等. 土壤中微塑料的生态效应与生物降解[J]. 土壤学报, 2022, 59(2): 349-363.
6	GAO R, PAN H, LIAN J. Recent advances in the discovery, characterization, and engineering of poly(ethylene terephthalate) (PET) hydrolases[J/OL]. Enzyme Microb. Technol., 2021, 150: 109868[2022-08-10]. .
7	GEWERT B, PLASSMANN M M, MACLEOD M. Pathways for degradation of plastic polymers floating in the marine environment[J]. Environ. Sci. Proc. Impacts, 2015, 17(9): 1513-1521.
8	LEBRETON L, SLAT B, FERRARI F, et al.. Evidence that the great pacific garbage patch is rapidly accumulating plastic[J/OL]. Sci. Rep., 2018, 8(1): 4666[2022-08-10]. .
9	LI C T, ZHUANG H K, HSIEH L T, et al.. PAH emission from the incineration of three plastic wastes[J]. Environ. Int., 2001, 27(1): 61-67.
10	RAGAERT K, DELVA L, VAN GEEM K. Mechanical and chemical recycling of solid plastic waste[J]. Waste Manag., 2017, 69: 24-58.
11	GRIGORE M. Methods of recycling, properties and applications of recycled thermoplastic polymers[J/OL]. Recycling, 2017, 2(4): 24[2022-08-10]. .
12	SCALENGHE R. Resource or waste? A perspective of plastics degradation in soil with a focus on end-of-life options[J/OL]. Heliyon, 2018, 4(12): e941[2022-08-10]. .
13	PARK S H, KIM S H. Poly (ethylene terephthalate) recycling for high value added textiles[J/OL]. Fashion Textiles, 2014, 1(1): 1[2022-08-11]. .
14	AL-SABAGH A M, YEHIA F Z, ESHAQ G, et al.. Greener routes for recycling of polyethylene terephthalate[J]. Egyptian J. Petrol., 2016, 25(1): 53-64.
15	SCHYNS Z, SHAVER M P. Mechanical recycling of packaging plastics: a review[J/OL]. Macromol. Rapid Commun., 2021, 42(3): e2000415[2022-08-11]. .
16	WEBB H, ARNOTT J, CRAWFORD R, et al.. Plastic degradation and its environmental implications with special reference to poly(ethylene terephthalate)[J]. Polymers, 2013, 5(1): 1-18.
17	KAUSHAL J, KHATRI M, ARYA S K. Recent insight into enzymatic degradation of plastics prevalent in the environment: a mini - review[J/OL]. Cleaner Engin. Technol., 2021, 2: 100083[2022-08-15]. .
18	ROSE R S, RICHARDSON K H, LATVANEN E J, et al.. Microbial degradation of plastic in aqueous solutions demonstrated by CO₂ evolution and quantification[J/OL]. Int. J. Mol. Sci., 2020, 21(4): 1176 [2022-08-15]. .
19	AMOBONYE A, BHAGWAT P, SINGH S, et al.. Plastic biodegradation: frontline microbes and their enzymes[J/OL]. Sci. Total Environ., 2021, 759: 143536[2022-08-15]. .
20	张彤, 刘盼, 王倩, 等. 降解石油基塑料的微生物及微生物菌群[J]. 生物工程学报, 2021, 37(10): 3520-3534.
21	MÜLLER R, SCHRADER H, PROFE J, et al. Enzymatic degradation of poly(ethylene terephthalate): rapid hydrolyse using a hydrolase from T. fusca [J]. Macromol. Rapid Comm., 2005, 26(17): 1400-1405.
22	CARNIEL A, VALONI É, NICOMEDES J, et al.. Lipase from Candida antarctica (CALB) and cutinase from Humicola insolens act synergistically for PET hydrolysis to terephthalic acid[J]. Proc. Biochem., 2017, 59: 84-90.
23	SULAIMAN S, YAMATO S, KANAYA E, et al.. Isolation of a novel cutinase homolog with polyethylene terephthalate-degrading activity from leaf-branch compost by using a metagenomic approach[J]. Appl. Environ. Microbiol., 2012, 78(5): 1556-1562.
24	ROTH C, WEI R, OESER T, et al.. Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca [J]. Appl. Microbiol. Biotechnol., 2014, 98(18): 7815-7823.
25	YOSHIDA S, HIRAGA K, TAKEHANA T, et al.. A bacterium that degrades and assimilates poly(ethylene terephthalate)[J]. Science, 2016, 351(6278): 1196-1199.
26	SALVADOR M, ABDULMUTALIB U, GONZALEZ J, et al. Microbial genes for a circular and sustainable bio-PET economy[J/OL]. Genes (Basel), 2019, 10(5): 373 [2022-08-21]. .
27	DISSANAYAKE L, JAYAKODY L N. Engineering microbes to bio-upcycle polyethylene terephthalate[J/OL]. Front. Bioeng. Biotechnol., 2021, 9: 656465 [2022-08-21]. .
28	RORRER N A, NICHOLSON S, CARPENTER A, et al.. Combining reclaimed PET with bio-based monomers enables plastics upcycling[J]. Joule, 2019, 3(4): 1006-1027.
29	URBANEK A K, RYMOWICZ W, MIRONCZUK A M. Degradation of plastics and plastic-degrading bacteria in cold marine habitats[J]. Appl. Microbiol. Biotechnol., 2018, 102(18): 7669-7678.
30	蒋迎迎, 曲戈, 孙周通. 机器学习助力酶定向进化[J]. 生物学杂志, 2020, 37(4): 1-11.
31	CHANDRA P, ENESPA, SINGH R, et al.. Microbial lipases and their industrial applications: a comprehensive review[J/OL]. Microb. Cell Fact., 2020, 19(1): 169 [2022-08-22]. .
32	STAUCH B, FISHER S J, CIANCI M. Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation[J]. J. Lipid Res., 2015, 56(12): 2348-2358.
33	EBERL A, HEUMANN S, BRUCKNER T, et al.. Enzymatic surface hydrolysis of poly(ethylene terephthalate) and bis(benzoyloxyethyl) terephthalate by lipase and cutinase in the presence of surface active molecules[J]. J. Biotechnol., 2009, 143(3): 207-212.
34	KAWAI F, KAWABATA T, ODA M. Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields[J]. Appl. Microbiol. Biotechnol., 2019, 103(11): 4253-4268.
35	CARVALHO C M, AIRES-BARROS M R, CABRAL J M. Cutinase: from molecular level to bioprocess development[J]. Biotechnol. Bioeng., 1999, 66(1): 17-34.
36	ZIMMERMANN W, BILLIG S. Enzymes for the biofunctionalization of poly(ethylene terephthalate)[J]. Adv. Biochem. Eng. Biotechnol., 2011, 125: 97-120.
37	NICOLAS A, EGMOND M, VERRIPS C T, et al. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state[J]. Biochemistry, 1996, 35(2): 398-410.
38	TOURNIER V, TOPHAM C M, GILLES A, et al.. An engineered PET depolymerase to break down and recycle plastic bottles[J].Nature, 2020, 580(7802): 216-219.
39	JOO S, CHO I J, SEO H, et al.. Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation[J/OL]. Nat. Commun., 2018, 9(1): 382[2022-08-25]. .
40	AUSTIN H P, ALLEN M D, DONOHOE B S, et al.. Characterization and engineering of a plastic-degrading aromatic polyesterase[J].Proc. Natl. Acad. Sci. USA, 2018, 115(19): E4350-E4357.
41	HAN X, LIU W, HUANG J W, et al.. Structural insight into catalytic mechanism of PET hydrolase[J/OL]. Nat. Commun., 2017, 8(1): 2106[2022-08-25]. .
42	PALM G J, REISKY L, BOTTCHER D, et al.. Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate[J/OL]. Nat. Commun., 2019, 10(1): 1717[2022-08-25]. .
43	SAGONG H, SEO H, KIM T, et al.. Decomposition of the PET film by MHETase using exo-PETase function[J]. Acs Catal., 2020, 10(8): 4805-4812.
44	KNOTT B C, ERICKSON E, ALLEN M D, et al.. Characterization and engineering of a two-enzyme system for plastics depolymerization[J]. Proc. Natl. Acad. Sci. USA, 2020, 117(41): 25476-25485.
45	KIKKAWA Y, FUJITA M, ABE H, et al.. Effect of water on the surface molecular mobility of poly(lactide) thin films: an atomic force microscopy study[J]. Biomacromolecules, 2004, 5(4): 1187-1193.
46	KAWAI F, ODA M, TAMASHIRO T, et al.. A novel Ca²⁺-activated, thermostabilized polyesterase capable of hydrolyzing polyethylene terephthalate from Saccharomonospora viridis AHK190[J]. Appl. Microbiol. Biotechnol., 2014, 98(24): 10053-10064.
47	ODA M, YAMAGAMI Y, INABA S, et al.. Enzymatic hydrolysis of PET: functional roles of three Ca²⁺ ions bound to a cutinase-like enzyme, Cut190*, and its engineering for improved activity[J]. Appl. Microbiol. Biotechnol., 2018, 102(23): 10067-10077.
48	ARAÚJO R, SILVA C, O'NEILL A, et al.. Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6, 6 fibers[J]. J. Biotechnol., 2007, 128(4): 849-857.
49	SILVA C, DA S, SILVA N, et al.. Engineered Thermobifida fusca cutinase with increased activity on polyester substrates[J]. Biotechnol. J., 2011, 6(10): 1230-1239.
50	KAWABATA T, ODA M, KAWAI F. Mutational analysis of cutinase-like enzyme, Cut190, based on the 3D docking structure with model compounds of polyethylene terephthalate[J]. J. Biosci. Bioeng., 2017, 124(1): 28-35.
51	WEI R, OESER T, SCHMIDT J, et al.. Engineered bacterial polyester hydrolases efficiently degrade polyethylene terephthalate due to relieved product inhibition[J]. Biotechnol. Bioeng., 2016, 113(8): 1658-1665.
52	CHEN C, HAN X, LI X, et al.. General features to enhance enzymatic activity of poly(ethylene terephthalate) hydrolysis[J]. Nat. Catal., 2021, 4(5): 425-430.
53	FURUKAWA M, KAWAKAMI N, ODA K, et al.. Acceleration of enzymatic degradation of poly(ethylene terephthalate) by surface coating with anionic surfactants[J]. ChemSusChem, 2018, 11(23): 4018-4025.
54	MA Y, YAO M, LI B, et al.. Enhanced poly(ethylene terephthalate) hydrolase activity by protein engineering[J]. Engineering, 2018, 4(6): 888-893.
55	LIU B, HE L, WANG L, et al.. Protein crystallography and site-direct mutagenesis analysis of the poly(ethylene terephthalate) hydrolase PETase from Ideonella sakaiensis [J]. Chembiochem, 2018, 19(14): 1471-1475.
56	SON H F, CHO I J, JOO S, et al.. Rational protein engineering of thermo-Stable PETase from Ideonella sakaiensis for highly efficient PET degradation[J]. Acs Catal., 2019, 9(4): 3519-3526.
57	NUMOTO N, KAMIYA N, BEKKER G, et al.. Structural dynamics of the PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190 in substrate-bound states elucidates the Ca²⁺-driven catalytic cycle[J]. Biochemistry, 2018, 57(36): 5289-5300.
58	MIYAKAWA T, MIZUSHIMA H, OHTSUKA J, et al.. Structural basis for the Ca²⁺-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190[J]. Appl. Microbiol. Biotechnol., 2015, 99(10): 4297-4307.
59	THEN J, WEI R, OESER T, et al.. A disulfide bridge in the calcium binding site of a polyester hydrolase increases its thermal stability and activity against polyethylene terephthalate[J]. FEBS Open Biol, 2016, 6(5): 425-432.
60	HERRERO A E, RIBITSCH D, DELLACHER A, et al.. Surface engineering of a cutinase from Thermobifida cellulosilytica for improved polyester hydrolysis[J]. Biotechnol. Bioeng., 2013, 110(10): 2581-2590.
61	BARTH M, OESER T, WEI R, et al.. Effect of hydrolysis products on the enzymatic degradation of polyethylene terephthalate nanoparticles by a polyester hydrolase from Thermobifida fusca [J]. Biochem. Eng. J., 2015, 93: 222-228.
62	BARTH M, WEI R, OESER T, et al.. Enzymatic hydrolysis of polyethylene terephthalate films in an ultrafiltration membrane reactor[J]. J. Membrane Sci., 2015, 494: 182-187.
63	YANG K K, WU Z, ARNOLD F H. Machine-learning-guided directed evolution for protein engineering[J]. Nat. Methods, 2019, 16(8): 687-694.
64	ALLEY E C, KHIMULYA G, BISWAS S, et al.. Unified rational protein engineering with sequence-based deep representation learning[J]. Nat. Methods, 2019, 16(12): 1315-1322.
65	WU Z, KAN S B J, LEWIS R D, et al.. Machine learning-assisted directed protein evolution with combinatorial libraries[J]. Proc. Natl. Acad. Sci. USA, 2019, 116(18): 8852-8858.
66	JANG W D, KIM G B, KIM Y, et al.. Applications of artificial intelligence to enzyme and pathway design for metabolic engineering[J]. Curr. Opin. Biotechnol., 2022, 73: 101-107.
67	BU Y, CUI Y, PENG Y, et al.. Engineering improved thermostability of the GH11 xylanase from Neocallimastix patriciarum via computational library design[J]. Appl. Microbiol. Biotechnol., 2018, 102(8): 3675-3685.
68	MU Q, CUI Y, TIAN Y, et al.. Thermostability improvement of the glucose oxidase from Aspergillus niger for efficient gluconic acid production via computational design[J]. Int. J. Biol. Macromol., 2019, 136: 1060-1068.
69	CUI Y, CHEN Y, LIU X, et al.. Computational redesign of a PETase for plastic biodegradation under ambient condition by the GRAPE strategy[J]. Acs Catal., 2021, 11(3): 1340-1350.
70	LU H, DIAZ D J, CZARNECKI N J, et al.. Machine learning-aided engineering of hydrolases for PET depolymerization[J]. Nature, 2022, 604(7907): 662-667.
71	MENG X, YANG L, LIU H, et al.. Protein engineering of stable IsPETase for PET plastic degradation by premuse[J]. Int. J. Biol. Macromol., 2021, 180: 667-676.
72	GOLDENZWEIG A, GOLDSMITH M, HILL S E, et al.. Automated structure- and sequence-based design of proteins for high bacterial expression and stability[J]. Mol. Cell, 2016, 63(2): 337-346.
73	RENNISON A, WINTHER J R, VARRONE C. Rational protein engineering to increase the activity and stability of IsPETase using the PROSS algorithm[J/OL]. Polymers, 2021, 13(22): 3884[2022-09-15]. .
74	DANSO D, SCHMEISSER C, CHOW J, et al.. New insights into the function and global distribution of polyethylene terephthalate (PET)-degrading bacteria and enzymes in marine and terrestrial metagenomes[J/OL]. Appl. Environ. Microbiol., 2018, 84(8): e02773-17 [2022-09-15]. .
75	ZHANG H, PEREZ-GARCIA P, DIERKES R F, et al.. The bacteroidetes Aequorivita sp. and Kaistella jeonii produce promiscuous esterases with PET-hydrolyzing activity[J/OL]. Front. Microbiol., 2021, 12: 803896 [2022-09-15]. .

PET水解酶传统与智能分子设计研究进展

Research Advances on Traditional and Intelligent Molecular Design of PET Hydrolases

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 1

参考文献 75

相关文章 1

编辑推荐

Metrics

本文评价