Computational redesign of a PETase for plastic biodegradation by the GRAPE strategy

Y, Cui; Chen, Y; Liu, Xiaoyu; Dong, Shujun; Tian, Ying; Qiao, Yuxin; Mitra, Ruchira; Han, Junqiang; C, Li; Han, Xingwei; W, Liu; Chen, Q; Du, Wei; Tang, Shuang-Yan; Xiang, Hua; H, Liu; Wu, Botao

doi:10.1101/787069

Cited by 20 publications

(47 citation statements)

References 45 publications

(53 reference statements)

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“…Moreover, Cui and coworkers developed a computational strategy for the mutational analysis of PETase and the design of a multiple mutant with enhanced thermostability when compared with the wild-type protein. This mutant designated as “duraPETase” contains the substitutions S214H-I168R-W159HS188Q-R280A-A180I-G165A-Q119Y-L117F-T140D, and it was able to degrade amorphous PET, but also longer polymers such as PBT with an optimum reaction temperature of 40 °C [ 60 ]. However, both engineered PETase mutants showed low efficiency in the degradation of crystalline high-density polymers, suggesting that the compactness of the material limits the protein access to the free chemical groups.…”

Section: Discussionmentioning

confidence: 99%

Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors

Leitão

Enguita

2021

IJMS

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Esters are organic compounds widely represented in cellular structures and metabolism, originated by the condensation of organic acids and alcohols. Esterification reactions are also used by chemical industries for the production of synthetic plastic polymers. Polyester plastics are an increasing source of environmental pollution due to their intrinsic stability and limited recycling efforts. Bioremediation of polyesters based on the use of specific microbial enzymes is an interesting alternative to the current methods for the valorization of used plastics. Microbial esterases are promising catalysts for the biodegradation of polyesters that can be engineered to improve their biochemical properties. In this work, we analyzed the structure-activity relationships in microbial esterases, with special focus on the recently described plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. Our analysis, based on structure-alignment, molecular docking, coevolution of amino acids and surface electrostatics determined the specific characteristics of some polyester hydrolases that could be related with their efficiency in the degradation of aromatic polyesters, such as phthalates.

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Section: Discussionmentioning

confidence: 99%

Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors

Leitão

Enguita

2021

IJMS

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“…Engineering the formation of hydrogen bonds at the region responsible for a more stable enzyme structure is another method to gain enhanced thermostability [49]. The hydrogen bond can maintain protein higher-order structures, which can promote structural stability and improve resistance to high temperature.…”

Section: Trends Trends In In Biotechnology Biotechnologymentioning

confidence: 99%

“…For example, the formation of a water-mediated hydrogen bond between S121E and N172 residues at the highly flexible β6-β7 connecting loop region of PETase could increase the regional rigidity and lead to substantially enhanced thermostability [50]. In another study, multiple mutations including T140D, W159H, I168R, and S188Q were implemented to introduce new hydrogen bonds in PETase, and the engineered PETase had a melting temperature 31°C higher than that of the wild-type enzyme [49].…”

Section: Trends Trends In In Biotechnology Biotechnologymentioning

confidence: 99%

“…To avoid such negative impact, profound understanding and analyses of enzyme structure-function relationships are needed. In fact, in most of the published studies, enzymes engineered with enhanced thermostability also had improved or unchanged plastic degradation efficiency [45,46,49,54,58]. For example, the engineered LCC variants exhibited both enhanced thermostability and increased PET degradation efficiency compared with wild-type LCC [58].…”

Section: Trends Trends In In Biotechnology Biotechnologymentioning

confidence: 99%

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Enzyme discovery and engineering for sustainable plastic recycling

Zhu

Wang

Wei

2022

Trends in Biotechnology

159

114

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The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plasticdegrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed. Biocatalysis as an Emerging Solution for the Global Plastic Waste ChallengePlastic materials play a revolutionary role in the modern world, although the enormous manufacture and extensive use of plastic commodities inevitably generate an extraordinary amount of post-consumer plastic waste. Around 12 000 million metric tons of plastic waste are predicted to accumulate in landfills and the natural environment by 2050 [1]. Improper handling of plastic waste has caused a grand environmental challenge. The debris of plastic waste, especially microplastics (see Glossary), can impose hazardous effects on various organisms and eventually threaten human well-being [2-5]. In addition, the degradation resistance of plastics further escalates their adverse environmental impacts [6]. Therefore, it is urgent to develop innovative technologies for treatment and recycling of post-consumer plastics, to achieve both waste valorization and environmental protection.Enzymatic biocatalysis has gained increasing attention as an eco-friendly alternative to conventional plastic treatment and recycling methods (Box 1) [7]. To date, various microbial plastic-degrading enzymes have been discovered, representing promising biocatalyst candidates for plastic depolymerization. Considering the ubiquity of plastics in different ecosystems and the tremendous metabolic and genetic diversity of microorganisms, microbial communities in various habitats have likely evolved capabilities in plastic decomposition and utilization. The plastic-degrading enzymes identified so far might only account for a small portion of the enzymes relevant to plastic depolymerization in the environment. Therefore, it is of ever-growing interest to explore diverse environments to discover new plastic-degrading enzymes with desirable properties and functionalities. However, naturally occurring plasticdegrading enzymes are not well suited for synthetic plastic degradation in industrial applications due to poor thermostability and low catalytic activity. Particularly, synthetic plastic materials usually possess distinct physical and chemical properties (e.g., high crystallinity) that render them more resistant to...

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“…Now the target is shifted for rational designing of thermo-stable PETase from I. sakaiensis [ 103 , 104 , 108 ]. To resolve the inherent instability problem of the PETase from Ideonalla sakaiensis at ambient temperature, its computational redesigning, and subsequent protein engineering is done to improve the enzymatic/ catalytic activity (400 fold), and durability (10 days) with higher crystallinity at 40ºC [ 109 ]. In spite of much progress, some technical barriers still hinder their direct physical application on a wider scale.…”

Section: Biotechnological Implication Of Metagenomic Informationmentioning

confidence: 99%

Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application

Purohit

Chattopadhyay

Teli

2020

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: Since the last few decades, the promiscuous and uncontrolled use of plastics leads to the accumulation of millions of tons of plastic waste in the terrestrial and marine environment and elevated the risk of environmental pollution and climate change. The concern arises more due to the reckless and unscientific disposal of plastics containing high molecular weight polymers, viz., polystyrene, polyamide, polyvinylchloride, polypropylene, polyurethane, and polyethylene, etc. which are very difficult to degrade. Thus, the focus is now paid to search for efficient, eco-friendly, low-cost waste management technology. Of them, degradation of non-degradable synthetic polymer using diverse microbial agents, viz., bacteria, fungi, and other extremophiles become an emerging option. So far, very few microbial agents and their secreted enzymes have been identified and characterized for plastic degradation, but with low efficiency. It might be due to the predominance of uncultured microbial species; consequently remain unexplored from the respective plastic degrading milieu. To overcome this problem, metagenomic analysis of microbial population engaged in the plastic biodegradation is advisable to decipher the microbial community structure and to predict their biodegradation potential in situ. Advancements in sequencing technologies and bioinformatics analysis allow the rapid metagenome screening that helps in the identification of total microbial community and also opens up the scope for mining genes or enzymes (hydrolases, laccase, etc.) engaged in polymer degradation. Further, the extraction of the core microbial population and their adaptation, fitness, and survivability can also be deciphered through comparative metagenomic study. It will help to engineer the microbial community and their metabolic activity to speed up the degradation process.

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Computational redesign of a PETase for plastic biodegradation by the GRAPE strategy

Cited by 20 publications

References 45 publications

Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors

Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors

Enzyme discovery and engineering for sustainable plastic recycling

Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application

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