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Wang T, Yang WT, Gong YM, Zhang YK, Fan XX, Wang GC, Lu ZH, Liu F, Liu XH, Zhu YS. Molecular engineering of PETase for efficient PET biodegradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116540. [PMID: 38833982 DOI: 10.1016/j.ecoenv.2024.116540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
The widespread utilization of polyethylene terephthalate (PET) has caused a variety of environmental and health problems. Compared with traditional thermomechanical or chemical PET cycling, the biodegradation of PET may offer a more feasible solution. Though the PETase from Ideonalla sakaiensis (IsPETase) displays interesting PET degrading performance under mild conditions; the relatively low thermal stability of IsPETase limits its practical application. In this study, enzyme-catalysed PET degradation was investigated with the promising IsPETase mutant HotPETase (HP). On this basis, a carbohydrate-binding module from Bacillus anthracis (BaCBM) was fused to the C-terminus of HP to construct the PETase mutant (HLCB) for increased PET degradation. Furthermore, to effectively improve PET accessibility and PET-degrading activity, the truncated outer membrane hybrid protein (FadL) was used to expose PETase and BaCBM on the surface of E. coli (BL21with) to develop regenerable whole-cell biocatalysts (D-HLCB). Results showed that, among the tested small-molecular weight ester compounds (p-nitrophenyl phosphate (pNPP), p-Nitrophenyl acetate (pNPA), 4-Nitrophenyl butyrate (pNPB)), PETase displayed the highest hydrolysing activity against pNPP. HP displayed the highest catalytic activity (1.94 μM(p-NP)/min) at 50 °C and increased longevity at 40 °C. The fused BaCBM could clearly improve the catalytic performance of PETase by increasing the optimal reaction temperature and improving the thermostability. When HLCB was used for PET degradation, the yield of monomeric products (255.7 μM) was ∼25.5 % greater than that obtained after 50 h of HP-catalysed PET degradation. Moreover, the highest yield of monomeric products from the D-HLCB-mediated system reached 1.03 mM. The whole-cell catalyst D-HLCB displayed good reusability and stability and could maintain more than 54.6 % of its initial activity for nine cycles. Finally, molecular docking simulations were utilized to investigate the binding mechanism and the reaction mechanism of HLCB, which may provide theoretical evidence to further increase the PET-degrading activities of PETases through rational design. The proposed strategy and developed variants show potential for achieving complete biodegradation of PET under mild conditions.
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Affiliation(s)
- Tao Wang
- School of Biological Science, Jining Medical University, Jining, China
| | - Wen-Tao Yang
- School of Biological Science, Jining Medical University, Jining, China
| | - Yu-Ming Gong
- School of Biological Science, Jining Medical University, Jining, China
| | - Ying-Kang Zhang
- School of Biological Science, Jining Medical University, Jining, China
| | - Xin-Xin Fan
- School of Biological Science, Jining Medical University, Jining, China
| | - Guo-Cheng Wang
- School of Biological Science, Jining Medical University, Jining, China
| | - Zhen-Hua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - You-Shuang Zhu
- School of Biological Science, Jining Medical University, Jining, China.
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2
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Han Z, Nina MRH, Zhang X, Huang H, Fan D, Bai Y. Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134532. [PMID: 38749251 DOI: 10.1016/j.jhazmat.2024.134532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Polyethylene terephthalate (PET) is widely used for various industrial applications. However, owing to its extremely slow breakdown rate, PET accumulates as plastic trash, which negatively affects the environment and human health. Here, we report two novel PET hydrolases: PpPETase from Pseudomonas paralcaligenes MRCP1333, identified in human feces, and ScPETase from Streptomyces calvus DSM 41452. These two enzymes can decompose various PET materials, including semicrystalline PET powders (Cry-PET) and low-crystallinity PET films (gf-PET). By structure-guided engineering, two variants, PpPETaseY239R/F244G/Y250G and ScPETaseA212C/T249C/N195H/N243K were obtained that decompose Cry-PET 3.1- and 1.9-fold faster than their wild-type enzymes, respectively. The co-expression of ScPETase and mono-(2-hydroxyethyl) terephthalate hydrolase from Ideonella sakaiensis (IsMHETase) resulted in 1.4-fold more degradation than the single enzyme system. This engineered strain degraded Cry-PET and gf-PET by more than 40% and 6%, respectively, after 30 d. The concentrations of terephthalic acid (TPA) in the Cry-PET and gf-PET degradation products were 37.7% and 25.6%, respectively. The discovery of these two novel PET hydrolases provides opportunities to create more powerful biocatalysts for PET biodegradation.
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Affiliation(s)
- Zhengyang Han
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hanyao Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Daidi Fan
- Shaanxi R&D Centre of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China.
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3
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Saunders JW, Damry AM, Vongsouthi V, Spence MA, Frkic RL, Gomez C, Yates PA, Matthews DS, Tokuriki N, McLeod MD, Jackson CJ. Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design. Biochemistry 2024; 63:1663-1673. [PMID: 38885634 DOI: 10.1021/acs.biochem.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The mono(2-hydroxyethyl) terephthalate hydrolase (MHETase) from Ideonella sakaiensis carries out the second step in the enzymatic depolymerization of poly(ethylene terephthalate) (PET) plastic into the monomers terephthalic acid (TPA) and ethylene glycol (EG). Despite its potential industrial and environmental applications, poor recombinant expression of MHETase has been an obstacle to its industrial application. To overcome this barrier, we developed an assay allowing for the medium-throughput quantification of MHETase activity in cell lysates and whole-cell suspensions, which allowed us to screen a library of engineered variants. Using consensus design, we generated several improved variants that exhibit over 10-fold greater whole-cell activity than wild-type (WT) MHETase. This is revealed to be largely due to increased soluble expression, which biochemical and structural analysis indicates is due to improved protein folding.
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Affiliation(s)
- Jake W Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Adam M Damry
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Patrick A Yates
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dana S Matthews
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Malcolm D McLeod
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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4
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Orr G, Niv Y, Barakat M, Boginya A, Dessau M, Afriat-Jurnou L. Streamlined screening of extracellularly expressed PETase libraries for improved polyethylene terephthalate degradation. Biotechnol J 2024; 19:e2400021. [PMID: 38987219 DOI: 10.1002/biot.202400021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024]
Abstract
Enzyme-mediated polyethylene terephthalate (PET) depolymerization has recently emerged as a sustainable solution for PET recycling. Towards an industrial-scale implementation of this technology, various strategies are being explored to enhance PET depolymerization (PETase) activity and improve enzyme stability, expression, and purification processes. Recently, rational engineering of a known PET hydrolase (LCC-leaf compost cutinase) has resulted in the isolation of a variant harboring four-point mutations (LCC-ICCG), presenting increased PETase activity and thermal stability. Here, we revealed the enzyme's natural extracellular expression and used it to efficiently screen error-prone genetic libraries based on LCC-ICCG for enhanced activity toward consumer-grade PET. Following multiple rounds of mutagenesis and screening, we successfully isolated variants that exhibited up to a 60% increase in PETase activity. Among other mutations, the improved variants showed a histidine to tyrosine substitution at position 218, a residue known to be involved in substrate binding and stabilization. Introducing H218Y mutation on the background of LCC-ICCG (named here LCC-ICCG/H218Y) resulted in a similar level of activity improvement. Analysis of the solved structure of LCC-ICCG/H218Y compared to other known PETases featuring different amino acids at the equivalent position suggests that H218Y substitution promotes enhanced PETase activity. The expression and screening processes developed in this study can be further used to optimize additional enzymatic parameters crucial for efficient enzymatic degradation of consumer-grade PET.
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Affiliation(s)
- Guy Orr
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Yoav Niv
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Maya Barakat
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Moshe Dessau
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
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5
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Joho Y, Royan S, Caputo AT, Newton S, Peat TS, Newman J, Jackson C, Ardevol A. Enhancing PET Degrading Enzymes: A Combinatory Approach. Chembiochem 2024; 25:e202400084. [PMID: 38584134 DOI: 10.1002/cbic.202400084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Plastic waste has become a substantial environmental issue. A potential strategy to mitigate this problem is to use enzymatic hydrolysis of plastics to depolymerize post-consumer waste and allow it to be reused. Over the last few decades, the use of enzymatic PET-degrading enzymes has shown promise as a great solution for creating a circular plastic waste economy. PsPETase from Piscinibacter sakaiensis has been identified as an enzyme with tremendous potential for such applications. But to improve its efficiency, enzyme engineering has been applied aiming at enhancing its thermal stability, enzymatic activity, and ease of production. Here, we combine different strategies such as structure-based rational design, ancestral sequence reconstruction and machine learning to engineer a more highly active Combi-PETase variant with a melting temperature of 70 °C and optimal performance at 60 °C. Furthermore, this study demonstrates that these approaches, commonly used in other works of enzyme engineering, are most effective when utilized in combination, enabling the improvement of enzymes for industrial applications.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Santana Royan
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Alessandro T Caputo
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Sophia Newton
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Thomas S Peat
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Janet Newman
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
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6
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Jones BS, Ross CM, Foley G, Pozhydaieva N, Sharratt JW, Kress N, Seibt LS, Thomson RES, Gumulya Y, Hayes MA, Gillam EMJ, Flitsch SL. Engineering Biocatalysts for the C-H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angew Chem Int Ed Engl 2024; 63:e202314869. [PMID: 38163289 DOI: 10.1002/anie.202314869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids, but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions of fatty acids. Herein we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multidomain, self-sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from subterminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multidomain enzymes to develop active, self-sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation.
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Affiliation(s)
- Bethan S Jones
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Connie M Ross
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Nadiia Pozhydaieva
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Joseph W Sharratt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Nico Kress
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Lisa S Seibt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Sabine L Flitsch
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
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7
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Meger AT, Spence MA, Sandhu M, Matthews D, Chen J, Jackson CJ, Raman S. Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors. Cell Syst 2024; 15:374-387.e6. [PMID: 38537640 PMCID: PMC11299162 DOI: 10.1016/j.cels.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/08/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
How a protein's function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as commonly seen in enzymes and binding proteins. On the other hand, rugged landscapes are poorly understood because of the inherent unpredictability of how sequence changes affect function. Here, we experimentally characterize the entire sequence phylogeny, comprising 1,158 extant and ancestral sequences, of the DNA-binding domain (DBD) of the LacI/GalR transcriptional repressor family. Our analysis revealed an extremely rugged landscape with rapid switching of specificity, even between adjacent nodes. Further, the ruggedness arises due to the necessity of the repressor to simultaneously evolve specificity for asymmetric operators and disfavors potentially adverse regulatory crosstalk. Our study provides fundamental insight into evolutionary, molecular, and biophysical rules of genetic regulation through the lens of fitness landscapes.
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Affiliation(s)
- Anthony T Meger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mahakaran Sandhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dana Matthews
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Jackie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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8
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Franceus J, Rivas-Fernández JP, Lormans J, Rovira C, Desmet T. Evolution of Phosphorylase Activity in an Ancestral Glycosyltransferase. ACS Catal 2024; 14:3103-3114. [PMID: 38449530 PMCID: PMC10913872 DOI: 10.1021/acscatal.3c05819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of molecular evolution by exposing the adaptive pathways that shape the proteins found in nature today. Here, we track the evolution of the carbohydrate-active enzymes responsible for the synthesis and turnover of mannogen, a critical carbohydrate reserve in Leishmania parasites. Biochemical characterization of resurrected enzymes demonstrated that mannoside phosphorylase activity emerged in an ancestral bacterial mannosyltransferase, and later disappeared in the process of horizontal gene transfer and gene duplication in Leishmania. By shuffling through plausible historical sequence space in an ancestral mannosyltransferase, we found that mannoside phosphorylase activity could be toggled on through various combinations of mutations at positions outside of the active site. Molecular dynamics simulations showed that such mutations can affect loop rigidity and shield the active site from water molecules that disrupt key interactions, allowing α-mannose 1-phosphate to adopt a catalytically productive conformation. These findings highlight the importance of subtle distal mutations in protein evolution and suggest that the vast collection of natural glycosyltransferases may be a promising source of engineering templates for the design of tailored phosphorylases.
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Affiliation(s)
- Jorick Franceus
- Centre
for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - José Pablo Rivas-Fernández
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Jolien Lormans
- Centre
for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Tom Desmet
- Centre
for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
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9
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Cui Y, Chen Y, Sun J, Zhu T, Pang H, Li C, Geng WC, Wu B. Computational redesign of a hydrolase for nearly complete PET depolymerization at industrially relevant high-solids loading. Nat Commun 2024; 15:1417. [PMID: 38360963 PMCID: PMC10869840 DOI: 10.1038/s41467-024-45662-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Biotechnological plastic recycling has emerged as a suitable option for addressing the pollution crisis. A major breakthrough in the biodegradation of poly(ethylene terephthalate) (PET) is achieved by using a LCC variant, which permits 90% conversion at an industrial level. Despite the achievements, its applications have been hampered by the remaining 10% of nonbiodegradable PET. Herein, we address current challenges by employing a computational strategy to engineer a hydrolase from the bacterium HR29. The redesigned variant, TurboPETase, outperforms other well-known PET hydrolases. Nearly complete depolymerization is accomplished in 8 h at a solids loading of 200 g kg-1. Kinetic and structural analysis suggest that the improved performance may be attributed to a more flexible PET-binding groove that facilitates the targeting of more specific attack sites. Collectively, our results constitute a significant advance in understanding and engineering of industrially applicable polyester hydrolases, and provide guidance for further efforts on other polymer types.
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Affiliation(s)
- Yinglu Cui
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yanchun Chen
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chunli Li
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Chao Geng
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Chemistry, Nankai University, Tianjin, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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10
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DeMars MD, O’Connor SE. Evolution and diversification of carboxylesterase-like [4+2] cyclases in aspidosperma and iboga alkaloid biosynthesis. Proc Natl Acad Sci U S A 2024; 121:e2318586121. [PMID: 38319969 PMCID: PMC10873640 DOI: 10.1073/pnas.2318586121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a large and diverse class of plant natural products, and their biosynthetic construction has been a subject of intensive study for many years. The enzymatic basis for the production of aspidosperma and iboga alkaloids, which are produced exclusively by members of the Apocynaceae plant family, has recently been discovered. Three carboxylesterase (CXE)-like enzymes from Catharanthus roseus and Tabernanthe iboga catalyze regio- and enantiodivergent [4+2] cycloaddition reactions to generate the aspidosperma (tabersonine synthase, TS) and iboga (coronaridine synthase, CorS; catharanthine synthase, CS) scaffolds from a common biosynthetic intermediate. Here, we use a combined phylogenetic and biochemical approach to investigate the evolution and functional diversification of these cyclase enzymes. Through ancestral sequence reconstruction, we provide evidence for initial evolution of TS from an ancestral CXE followed by emergence of CorS in two separate lineages, leading in turn to CS exclusively in the Catharanthus genus. This progression from aspidosperma to iboga alkaloid biosynthesis is consistent with the chemotaxonomic distribution of these MIAs. We subsequently generate and test a panel of chimeras based on the ancestral cyclases to probe the molecular basis for differential cyclization activity. Finally, we show through partial heterologous reconstitution of tabersonine biosynthesis using non-pathway enzymes how aspidosperma alkaloids could have first appeared as "underground metabolites" via recruitment of promiscuous enzymes from common protein families. Our results provide insight into the evolution of biosynthetic enzymes and how new secondary metabolic pathways can emerge through small but important sequence changes following co-option of preexisting enzymatic functions.
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Affiliation(s)
- Matthew D. DeMars
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena07745, Germany
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena07745, Germany
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11
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Naidu G, Nagar N, Poluri KM. Mechanistic Insights into Cellular and Molecular Basis of Protein-Nanoplastic Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305094. [PMID: 37786309 DOI: 10.1002/smll.202305094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Plastic waste is ubiquitously present across the world, and its nano/sub-micron analogues (plastic nanoparticles, PNPs), raise severe environmental concerns affecting organisms' health. Considering the direct and indirect toxic implications of PNPs, their biological impacts are actively being studied; lately, with special emphasis on cellular and molecular mechanistic intricacies. Combinatorial OMICS studies identified proteins as major regulators of PNP mediated cellular toxicity via activation of oxidative enzymes and generation of ROS. Alteration of protein function by PNPs results in DNA damage, organellar dysfunction, and autophagy, thus resulting in inflammation/cell death. The molecular mechanistic basis of these cellular toxic endeavors is fine-tuned at the level of structural alterations in proteins of physiological relevance. Detailed biophysical studies on such protein-PNP interactions evidenced prominent modifications in their structural architecture and conformational energy landscape. Another essential aspect of the protein-PNP interactions includes bioenzymatic plastic degradation perspective, as the interactive units of plastics are essentially nano-sized. Combining all these attributes of protein-PNP interactions, the current review comprehensively documented the contemporary understanding of the concerned interactions in the light of cellular, molecular, kinetic/thermodynamic details. Additionally, the applicatory, economical facet of these interactions, PNP biogeochemical cycle and enzymatic advances pertaining to plastic degradation has also been discussed.
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Affiliation(s)
- Goutami Naidu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
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12
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Joho Y, Vongsouthi V, Gomez C, Larsen JS, Ardevol A, Jackson CJ. Improving plastic degrading enzymes via directed evolution. Protein Eng Des Sel 2024; 37:gzae009. [PMID: 38713696 PMCID: PMC11091475 DOI: 10.1093/protein/gzae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/09/2024] Open
Abstract
Plastic degrading enzymes have immense potential for use in industrial applications. Protein engineering efforts over the last decade have resulted in considerable enhancement of many properties of these enzymes. Directed evolution, a protein engineering approach that mimics the natural process of evolution in a laboratory, has been particularly useful in overcoming some of the challenges of structure-based protein engineering. For example, directed evolution has been used to improve the catalytic activity and thermostability of polyethylene terephthalate (PET)-degrading enzymes, although its use for the improvement of other desirable properties, such as solvent tolerance, has been less studied. In this review, we aim to identify some of the knowledge gaps and current challenges, and highlight recent studies related to the directed evolution of plastic-degrading enzymes.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Joachim S Larsen
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
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13
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Faber A, Fritz G. Seek and you shall find-news on the quest for novel PET-degrading enzymes. FEBS J 2024; 291:57-60. [PMID: 37731192 DOI: 10.1111/febs.16958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Plastic-degrading enzymes hold immense potential for eco-friendly recycling methods. However, the catalytic rates of current enzymes do not stack up against the mammoth task of degrading millions of tons of plastic waste per year. In the quest for more efficient polyethylene terephthalate (PET)-degrading enzymes, Zhang et al. report the discovery and characterization of PET40, a versatile PET-hydrolyzing esterase that is divergent from most characterized PETases. While PET40 has comparably low hydrolytic activity on PET, Zhang et al. demonstrate its broad activity on an expanded substrate pool. This sheds light on the potential ecological role of these esterases and suggests that PET might be only a recent addition to their substrate spectrum.
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Affiliation(s)
- Anna Faber
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- Oceans Institute, The University of Western Australia, Crawley, Australia
- The Forrest Research Foundation, Crawley, Australia
| | - Georg Fritz
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- Oceans Institute, The University of Western Australia, Crawley, Australia
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14
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Qu Z, Chen K, Zhang L, Sun Y. Computation-Based Design of Salt Bridges in PETase for Enhanced Thermostability and Performance for PET Degradation. Chembiochem 2023; 24:e202300373. [PMID: 37639367 DOI: 10.1002/cbic.202300373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Polyethylene terephthalate (PET) is one of the most widely used plastics, and the accumulation of PET poses a great threat to the environment. IsPETase can degrade PET rapidly at moderate temperatures, but its application is greatly limited by the low stability. Herein, molecular dynamics (MD) simulations combined with a sequence alignment strategy were adopted to introduce salt bridges into the flexible region of IsPETase to improve its thermal stability. In the designed variants, the Tm values of IsPETaseI168R/S188D and IsPETaseI168R/S188E were 7.4 and 8.7 °C higher than that of the wild type, respectively. The release of products degraded by IsPETaseI168R/S188E was 4.3 times that of the wild type. Tertiary structure characterization demonstrated that the structure of the variants IsPETaseI168R/S188D and IsPETaseI168R/S188E became more compact. Extensive MD simulations verified that a stable salt bridge was formed between the residue R168 and D186 in IsPETaseI168R/S188D , while in IsPETaseI168R/S188E an R168-D186-E188 salt bridge network was observed. These results confirmed that the proposed computation-based salt bridge design strategy could efficiently generate variants with enhanced thermal stability for the long-term degradation of PET, which would be helpful for the design of enzymes with improved stability.
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Affiliation(s)
- Zhi Qu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Lin Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
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15
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Sana B, Ding K, Siau JW, Pasula RR, Chee S, Kharel S, Lena JBH, Goh E, Rajamani L, Lam YM, Lim S, Ghadessy JF. Thermostability enhancement of polyethylene terephthalate degrading PETase using self- and nonself-ligating protein scaffolding approaches. Biotechnol Bioeng 2023; 120:3200-3209. [PMID: 37555384 DOI: 10.1002/bit.28523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/23/2023] [Indexed: 08/10/2023]
Abstract
Polyethylene terephthalate (PET) hydrolase enzymes show promise for enzymatic PET degradation and green recycling of single-use PET vessels representing a major source of global pollution. Their full potential can be unlocked with enzyme engineering to render activities on recalcitrant PET substrates commensurate with cost-effective recycling at scale. Thermostability is a highly desirable property in industrial enzymes, often imparting increased robustness and significantly reducing quantities required. To date, most engineered PET hydrolases show improved thermostability over their parental enzymes. Here, we report engineered thermostable variants of Ideonella sakaiensis PET hydrolase enzyme (IsPETase) developed using two scaffolding strategies. The first employed SpyCatcher-SpyTag technology to covalently cyclize IsPETase, resulting in increased thermostability that was concomitant with reduced turnover of PET substrates compared to native IsPETase. The second approach using a GFP-nanobody fusion protein (vGFP) as a scaffold yielded a construct with a melting temperature of 80°C. This was further increased to 85°C when a thermostable PETase variant (FAST PETase) was scaffolded into vGFP, the highest reported so far for an engineered PET hydrolase derived from IsPETase. Thermostability enhancement using the vGFP scaffold did not compromise activity on PET compared to IsPETase. These contrasting results highlight potential topological and dynamic constraints imposed by scaffold choice as determinants of enzyme activity.
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Affiliation(s)
- Barindra Sana
- Disease Intervention Technology Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | - Ke Ding
- Disease Intervention Technology Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | - Jia Wei Siau
- Disease Intervention Technology Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | - Rupali Reddy Pasula
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological Univeristy, Singapore, Singapore
| | - Sharon Chee
- Disease Intervention Technology Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | - Sharad Kharel
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jean-Baptise Henri Lena
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Eunice Goh
- Singapore Eye Research Institute, The Academia, Singapore, Singapore
| | | | - Yeng Ming Lam
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sierin Lim
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological Univeristy, Singapore, Singapore
| | - John F Ghadessy
- Disease Intervention Technology Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
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16
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Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023; 82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Ancestral sequence reconstruction (ASR) provides insight into the changes within a protein sequence across evolution. More specifically, it can illustrate how specific amino acid changes give rise to different phenotypes within a protein family. Over the last few decades it has established itself as a powerful technique for revealing molecular common denominators that govern enzyme function. Here, we describe the strength of ASR in unveiling catalytic mechanisms and emerging phenotypes for a range of different proteins, also highlighting biotechnological applications the methodology can provide.
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Affiliation(s)
- Callum R Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marta Massari
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands. https://twitter.com/fraaije1
| | - Maria Laura Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
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17
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Liu F, Wang T, Yang W, Zhang Y, Gong Y, Fan X, Wang G, Lu Z, Wang J. Current advances in the structural biology and molecular engineering of PETase. Front Bioeng Biotechnol 2023; 11:1263996. [PMID: 37795175 PMCID: PMC10546322 DOI: 10.3389/fbioe.2023.1263996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
Poly(ethylene terephthalate) (PET) is a highly useful synthetic polyester plastic that is widely used in daily life. However, the increase in postconsumer PET as plastic waste that is recalcitrant to biodegradation in landfills and the natural environment has raised worldwide concern. Currently, traditional PET recycling processes with thermomechanical or chemical methods also result in the deterioration of the mechanical properties of PET. Therefore, it is urgent to develop more efficient and green strategies to address this problem. Recently, a novel mesophilic PET-degrading enzyme (IsPETase) from Ideonella sakaiensis was found to streamline PET biodegradation at 30°C, albeit with a lower PET-degrading activity than chitinase or chitinase-like PET-degrading enzymes. Consequently, the molecular engineering of more efficient PETases is still required for further industrial applications. This review details current knowledge on IsPETase, MHETase, and IsPETase-like hydrolases, including the structures, ligand‒protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts are highlighted, including metabolic engineering of the cell factories, enzyme immobilization or cell surface display. The information is expected to provide novel insights for the biodegradation of complex polymers.
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Affiliation(s)
- Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Wentao Yang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yingkang Zhang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yuming Gong
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Xinxin Fan
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Guocheng Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmin Wang
- School of Pharmacy, Jining Medical University, Rizhao, China
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18
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Buda K, Miton CM, Fan XC, Tokuriki N. Molecular determinants of protein evolvability. Trends Biochem Sci 2023; 48:751-760. [PMID: 37330341 DOI: 10.1016/j.tibs.2023.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
The plethora of biological functions that sustain life is rooted in the remarkable evolvability of proteins. An emerging view highlights the importance of a protein's initial state in dictating evolutionary success. A deeper comprehension of the mechanisms that govern the evolvability of these initial states can provide invaluable insights into protein evolution. In this review, we describe several molecular determinants of protein evolvability, unveiled by experimental evolution and ancestral sequence reconstruction studies. We further discuss how genetic variation and epistasis can promote or constrain functional innovation and suggest putative underlying mechanisms. By establishing a clear framework for these determinants, we provide potential indicators enabling the forecast of suitable evolutionary starting points and delineate molecular mechanisms in need of deeper exploration.
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Affiliation(s)
- Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Xingyu Cara Fan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
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19
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Williams GB, Ma H, Khusnutdinova AN, Yakunin AF, Golyshin PN. Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays Biochem 2023; 67:715-729. [PMID: 37334661 PMCID: PMC10423841 DOI: 10.1042/ebc20220255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The steady growth in industrial production of synthetic plastics and their limited recycling have resulted in severe environmental pollution and contribute to global warming and oil depletion. Currently, there is an urgent need to develop efficient plastic recycling technologies to prevent further environmental pollution and recover chemical feedstocks for polymer re-synthesis and upcycling in a circular economy. Enzymatic depolymerization of synthetic polyesters by microbial carboxylesterases provides an attractive addition to existing mechanical and chemical recycling technologies due to enzyme specificity, low energy consumption, and mild reaction conditions. Carboxylesterases constitute a diverse group of serine-dependent hydrolases catalysing the cleavage and formation of ester bonds. However, the stability and hydrolytic activity of identified natural esterases towards synthetic polyesters are usually insufficient for applications in industrial polyester recycling. This necessitates further efforts on the discovery of robust enzymes, as well as protein engineering of natural enzymes for enhanced activity and stability. In this essay, we discuss the current knowledge of microbial carboxylesterases that degrade polyesters (polyesterases) with focus on polyethylene terephthalate (PET), which is one of the five major synthetic polymers. Then, we briefly review the recent progress in the discovery and protein engineering of microbial polyesterases, as well as developing enzyme cocktails and secreted protein expression for applications in the depolymerisation of polyester blends and mixed plastics. Future research aimed at the discovery of novel polyesterases from extreme environments and protein engineering for improved performance will aid developing efficient polyester recycling technologies for the circular plastics economy.
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Affiliation(s)
- Gwion B Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Hairong Ma
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Anna N Khusnutdinova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
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20
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Nandel V, Scadden J, Baker MAB. Ion-Powered Rotary Motors: Where Did They Come from and Where They Are Going? Int J Mol Sci 2023; 24:10601. [PMID: 37445779 PMCID: PMC10341847 DOI: 10.3390/ijms241310601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Molecular motors are found in many living organisms. One such molecular machine, the ion-powered rotary motor (IRM), requires the movement of ions across a membrane against a concentration gradient to drive rotational movement. The bacterial flagellar motor (BFM) is an example of an IRM which relies on ion movement through the stator proteins to generate the rotation of the flagella. There are many ions which can be used by the BFM stators to power motility and different ions can be used by a single bacterium expressing multiple stator variants. The use of ancestral sequence reconstruction (ASR) and functional analysis of reconstructed stators shows promise for understanding how these proteins evolved and when the divergence in ion use may have occurred. In this review, we discuss extant BFM stators and the ions that power them as well as recent examples of the use of ASR to study ion-channel selectivity and how this might be applied to further study of the BFM stator complex.
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Affiliation(s)
| | | | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW 2033, Australia; (V.N.); (J.S.)
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21
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Crnjar A, Griñen A, Kamerlin SCL, Ramírez-Sarmiento CA. Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation. ACS ORGANIC & INORGANIC AU 2023; 3:109-119. [PMID: 37035283 PMCID: PMC10080609 DOI: 10.1021/acsorginorgau.2c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 04/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at different temperatures, with the enzyme from Ideonella sakaiensis (IsPETase) having optimal catalytic activity at 30-35 °C. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between three conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218. When these residues are inserted into other PET hydrolases in place of the otherwise strictly conserved histidine and phenylalanine residues found at their respective positions, they enhance activity and decrease T opt. Herein, we combine molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S214/I218 and H214/F218 variants of IsPETase, as well as three other mesophilic and thermophilic PET hydrolases, at their respective temperature and pH optima. Our simulations show that the S214/I218 insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved tryptophan and expands the conformational plasticity of this tryptophan side chain, enabling the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PET hydrolases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.
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Affiliation(s)
- Alessandro Crnjar
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Aransa Griñen
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
| | - Shina C. L. Kamerlin
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic
Drive NW, Atlanta, Georgia 30332-0400, United
States
| | - César A. Ramírez-Sarmiento
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
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22
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Weigert S, Perez‐Garcia P, Gisdon FJ, Gagsteiger A, Schweinshaut K, Ullmann GM, Chow J, Streit WR, Höcker B. Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes. Protein Sci 2022; 31:e4500. [PMID: 36336469 PMCID: PMC9679969 DOI: 10.1002/pro.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.
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Affiliation(s)
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | | | | | | | | | - Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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