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Zhang W, Han Y, Yang F, Guan L, Lu F, Mao S, Tian K, Yao M, Qin HM. A customized self-assembled synergistic biocatalyst for plastic depolymerization. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135380. [PMID: 39088944 DOI: 10.1016/j.jhazmat.2024.135380] [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: 06/17/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
The enzymatic degradation of plastic offers a green, sustainable strategy and scalable circular carbon route for solving polyester waste. Among the earlies discovered plastic-degrading enzymes are PET hydrolase (PETase) and MHET hydrolase (MHETase), which act synergistically. To promote the adsorption of enzymes on PET surfaces, increase their robustness, and enable directly depolymerization, we designed hydrophobin HFBI fused-PETase and MHETase. A customized self-assembled synergistic biocatalyst (MC@CaZn-MOF) was further developed to promote the two-step depolymerization process. The tailored catalysts showed better adhesion to the PET surface and desirable durability, retaining over 70% relative activity after incubation at pH 8.0 and 60 °C for 120 h. Importantly, MC@CaZn-MOF could directly decompose untreated AGf-PET to generate 9.5 mM TPA with weight loss over 90%. The successful implementation of a bifunctional customized catalyst makes the large-scale biocatalytic degradation of PET feasible, contributing to polymer upcycling and environmental sustainability.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Yuying Han
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Feng Yang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Lijun Guan
- Institute of Food Processing, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China
| | - Kangming Tian
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China.
| | - Mingdong Yao
- Key Laboratory of Systems Bioengineering (Ministry of Education); School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology; National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China.
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2
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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024:10.1038/s41586-024-07891-2. [PMID: 39232160 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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3
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Ogura Y, Hashino Y, Nakamura A. Direct Screening of PET Hydrolase Activity in Culture Medium Based on Turbidity Reduction. ACS OMEGA 2024; 9:34151-34160. [PMID: 39130604 PMCID: PMC11307985 DOI: 10.1021/acsomega.4c05488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024]
Abstract
The development of an efficient screening method for the activity of PET-degrading enzymes represents a significant technological advance in the field of enzyme research, with the potential to facilitate the advancement of enzymes for PET recycling. By examining the stable conditions of PET suspension and enzyme production conditions, we developed a method to quantify PET-degrading enzyme activity in E. coli culture medium using turbidity reduction as an indicator. High PET concentration or ionic strength caused aggregation of PET, and the best condition for activity detection was 0.5 mg mL-1 PET in 50 mM sodium phosphate pH 7.0. Preculture of E. coli increased the purity of enzyme secreted in medium. To evaluate the screening method, 720 colonies of the PET2-7M-H229X-F233X mutant library were analyzed and three candidates of high-activity mutants were obtained. The thermostability of the mutants could also be easily measured by measuring the residual activity after heat treatment. The H229T-F233M mutant showed 3.4 times higher degradation rate against PET film than the template enzyme at the initial time. The molecular dynamics simulation implied that the F233M mutation makes space for making an α helix and that the H229T mutation resolved the steric hindrance with Trp199. These mutations were speculated to change the angle of the Trp199 side chain of PET2 to an angle similar to that of the Trp185 of IsPETase, making it suitable for PET binding to the active center. Screening of activity using PET suspensions is compatible with robotic automation and is expected to be useful for validating computationally predicted mutations.
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Affiliation(s)
- Yui Ogura
- Department
of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yoshihito Hashino
- Department
of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akihiko Nakamura
- Department
of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research
Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Shizuoka
Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka 422-8529, Japan
- Institute
for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi 444-8787, Japan
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4
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Ercolano C, Iacono R, Cafaro V, Pizzo E, Giovannelli D, Feuerriegel G, Streit WR, Strazzulli A, Moracci M. Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability. Int J Mol Sci 2024; 25:8120. [PMID: 39125688 PMCID: PMC11311821 DOI: 10.3390/ijms25158120] [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: 05/27/2024] [Revised: 07/12/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.
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Affiliation(s)
- Carmen Ercolano
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126 Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
- Institute for Marine Biological Resources and Biotechnologies, Italian National Research Council, CNR-IRBIM, 60125 Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ 08901, USA
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany; (G.F.); (W.R.S.)
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany; (G.F.); (W.R.S.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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5
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Méndez-Zamora A, Diaz-Vidal T, Robles-Machuca M, Pereira-Santana A, Casas-Godoy L. Unveiling potential PET degrading eukaryotes through in silico bioprospecting of PETases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174978. [PMID: 39047840 DOI: 10.1016/j.scitotenv.2024.174978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/05/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
This study addresses the environmental problem of PET plastic through in silico bioprospecting for the identification and experimental validation of novel PET degrading eukaryotes through the in silico bioprospectingI of PETases, employing a methodology that combines Hidden Markov Models (HMMs), clustering techniques, molecular docking, and dynamic simulations. A total of 424 putative PETase sequences were identified from 219 eukaryotic organisms, highlighting six sequences with low affinity energies. The Aspergillus luchuensis sequence showed the lowest Gibbs free energy and exhibited stability at different temperatures in molecular dynamics assays. Experimental validation, through a plate clearance assay and HPLC, confirmed PETase activity in three wild-type fungal strains, with A. luchuensis showing the highest efficiency. The results obtained demonstrate the effectiveness of combining computational and experimental approaches as proof of concept to discover and validate eukaryotes with PET-degrading capabilities opening new perspectives for the sustainable management of this type of waste and contributing to its environmental mitigation.
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Affiliation(s)
- Andrés Méndez-Zamora
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida Normalistas 800, Col. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, Mexico
| | - Tania Diaz-Vidal
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida Normalistas 800, Col. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, Mexico
| | - Marcela Robles-Machuca
- Tecnologia de alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n, C.P. 63000 Tepic, Nayarit, Mexico
| | - Alejandro Pereira-Santana
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Parque Científico Tecnológico de Yucatán, 97302 Mérida, Yucatán, Mexico.
| | - Leticia Casas-Godoy
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Camino Arenero 1227, El Bajío, 45019 Zapopan, Jalisco, Mexico.
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6
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Dar MA, Xie R, Zabed HM, Pawar KD, Dhole NP, Sun J. Current paradigms and future challenges in harnessing gut bacterial symbionts of insects for biodegradation of plastic wastes. INSECT SCIENCE 2024. [PMID: 38990171 DOI: 10.1111/1744-7917.13417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024]
Abstract
The ubiquitous incorporation of plastics into daily life, coupled with inefficient recycling practices, has resulted in the accumulation of millions of metric tons of plastic waste, that poses a serious threat to the Earth's sustainability. Plastic pollution, a global problem, disrupts the ecological balance and endangers various life forms. Efforts to combat plastic pollution are underway, with a promising avenue being biological degradation facilitated by certain insects and their symbiotic gut microorganisms, particularly bacteria. This review consolidates existing knowledge on plastic degradation by insects and their influence on gut microbiota. Additionally, it delves into the potential mechanisms employed by insects in symbiosis with gut bacteria, exploring the bioconversion of waste plastics into value-added biodegradable polymers through mineralization. These insights hold significant promise for the bio-upcycling of plastic waste, opening new horizons for future biomanufacturing of high-value chemicals from plastic-derived compounds. Finally, we weigh the pros and cons of future research endeavors related to the bioprospection of plastic-degrading bacteria from underexplored insect species. We also underscore the importance of bioengineering depolymerases with novel characteristics, aiming for their application in the remediation and valorization of waste plastics.
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Affiliation(s)
- Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, India
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Hossain M Zabed
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Kiran D Pawar
- School of Nanoscience and Biotechnology, Shivaji University, Vidyanagar, Kolhapur, Maharashtra, India
| | - Neeraja P Dhole
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, India
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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7
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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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8
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Kawai F, Iizuka R, Kawabata T. Engineered polyethylene terephthalate hydrolases: perspectives and limits. Appl Microbiol Biotechnol 2024; 108:404. [PMID: 38953996 PMCID: PMC11219463 DOI: 10.1007/s00253-024-13222-2] [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: 02/09/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024]
Abstract
Polyethylene terephthalate (PET) is a major component of plastic waste. Enzymatic PET hydrolysis is the most ecofriendly recycling technology. The biorecycling of PET waste requires the complete depolymerization of PET to terephthalate and ethylene glycol. The history of enzymatic PET depolymerization has revealed two critical issues for the industrial depolymerization of PET: industrially available PET hydrolases and pretreatment of PET waste to make it susceptible to full enzymatic hydrolysis. As none of the wild-type enzymes can satisfy the requirements for industrialization, various mutational improvements have been performed, through classical technology to state-of-the-art computational/machine-learning technology. Recent engineering studies on PET hydrolases have brought a new insight that flexibility of the substrate-binding groove may improve the efficiency of PET hydrolysis while maintaining sufficient thermostability, although the previous studies focused only on enzymatic thermostability above the glass transition temperature of PET. Industrial biorecycling of PET waste is scheduled to be implemented, using micronized amorphous PET. Next stage must be the development of PET hydrolases that can efficiently degrade crystalline parts of PET and expansion of target PET materials, not only bottles but also textiles, packages, and microplastics. This review discusses the current status of PET hydrolases, their potential applications, and their profespectal goals. KEY POINTS: • PET hydrolases must be thermophilic, but their operation must be below 70 °C • Classical and state-of-the-art engineering approaches are useful for PET hydrolases • Enzyme activity on crystalline PET is most expected for future PET biorecycling.
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Affiliation(s)
- Fusako Kawai
- Graduate School of Environmental and Life Sciences, Okayama University, 1-1-1 Tsushima-Naka, Kita-Ku, Okayama, 700-8530, Japan.
| | - Ryo Iizuka
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Takeshi Kawabata
- Graduate School of Information Sciences, Tohoku University, Aoba 6-3-09, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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9
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Carr CM, Göttsch F, de Oliveira BFR, Murcia PAS, Jackson SA, Wei R, Clarke DJ, Bornscheuer UT, Dobson ADW. Identification and expression of MarCE, a marine carboxylesterase with synthetic ester-degrading activity. Microb Biotechnol 2024; 17:e14479. [PMID: 38881500 PMCID: PMC11180994 DOI: 10.1111/1751-7915.14479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Carboxylic ester hydrolases with the capacity to degrade polyesters are currently highly sought after for their potential use in the biological degradation of PET and other chemically synthesized polymers. Here, we describe MarCE, a carboxylesterase family protein identified via genome mining of a Maribacter sp. isolate from the marine sponge Stelligera stuposa. Based on phylogenetic analysis, MarCE and its closest relatives belong to marine-associated genera from the Cytophaga-Flavobacterium-Bacteroides taxonomic group and appear evolutionarily distinct to any homologous carboxylesterases that have been studied to date in terms of structure or function. Molecular docking revealed putative binding of BHET, a short-chain PET derivative, onto the predicted MarCE three-dimensional structure. The synthetic ester-degrading activity of MarCE was subsequently confirmed by MarCE-mediated hydrolysis of 2 mM BHET substrate, indicated by the release of its breakdown products MHET and TPA, which were measured, respectively, as 1.28 and 0.12 mM following 2-h incubation at 30°C. The findings of this study provide further insight into marine carboxylic ester hydrolases, which have the potential to display unique functional plasticity resulting from their adaptation to complex and fluctuating marine environmentsw.
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Affiliation(s)
- Clodagh M. Carr
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
| | - Frederike Göttsch
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | | | - Pedro A. Sánchez Murcia
- Laboratory of Computer‐Aided Molecular Design, Division of Medicinal Chemistry, Otto‐Loewi Research CenterMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Stephen A. Jackson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - David J. Clarke
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Alan D. W. Dobson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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10
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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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11
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Salam LB. Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment. World J Microbiol Biotechnol 2024; 40:172. [PMID: 38630153 DOI: 10.1007/s11274-024-03972-6] [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: 02/18/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.
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Affiliation(s)
- Lateef B Salam
- Microbiology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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12
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Frey B, Aiesi M, Rast BM, Rüthi J, Julmi J, Stierli B, Qi W, Brunner I. Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach. PLoS One 2024; 19:e0300503. [PMID: 38578779 PMCID: PMC10997104 DOI: 10.1371/journal.pone.0300503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 04/07/2024] Open
Abstract
Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.
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Affiliation(s)
- Beat Frey
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Margherita Aiesi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Facoltà de Science Agrarie e Alimentari, University Degli Studi di Milano, Milano, Italy
| | - Basil M. Rast
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Joel Rüthi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jérôme Julmi
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zürich, ETH Zürich and University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Ivano Brunner
- Swiss Federal Institute for Forest, Forest Soils and Biogeochemistry, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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13
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Tan Q, Chen W, Liu H, Yan W, Huang X, Li Y. The programmed sequence-based oxygenase screening for polypropylene degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133173. [PMID: 38061126 DOI: 10.1016/j.jhazmat.2023.133173] [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: 10/06/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 02/08/2024]
Abstract
Enzymatic degradation of plastic is an effective means of plastic recycling and pollution control. However, the strong chemical inertness of polypropylene plastic (PP) severely impedes its oxidative cleavage, making it resistant to degradation. In this study, based on sequence screening of Hidden Markov Model (HMM), a dioxygenase (HIS1) was identified and characterized to be effective in PP oxidation. Various kinds of PP products, including plastic films, microplastics, and disposable water cups or bags, were HIS1-degraded with cracks and holes on the surface. The hydrophobic binding was the primary force driving oxidative degradation in the specific cavity of HIS1. The discovery of HIS1 achieved a zero breakthrough in PP biodegradation, providing a promising candidate for the selection and evolution of degrading enzymes.
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Affiliation(s)
- Qianlong Tan
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Wentao Chen
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Hong Liu
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China
| | - Wende Yan
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Xiu Huang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Li
- Life and Science Department, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha, Hunan 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China.
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14
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Shah MZ, Quraishi M, Sreejith A, Pandit S, Roy A, Khandaker MU. Sustainable degradation of synthetic plastics: A solution to rising environmental concerns. CHEMOSPHERE 2024; 352:141451. [PMID: 38368957 DOI: 10.1016/j.chemosphere.2024.141451] [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: 06/07/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Plastics have a significant role in various sectors of the global economy since they are widely utilized in agriculture, architecture, and construction, as well as health and consumer goods. They play a crucial role in several industries as they are utilized in the production of diverse things such as defense materials, sanitary wares, tiles, plastic bottles, artificial leather, and various other household goods. Plastics are utilized in the packaging of food items, medications, detergents, and cosmetics. The overconsumption of plastics presents a significant peril to both the ecosystem and human existence on Earth. The accumulation of plastics on land and in the sea has sparked interest in finding ways to breakdown these polymers. It is necessary to employ suitable biodegradable techniques to decrease the accumulation of plastics in the environment. To address the environmental issues related to plastics, it is crucial to have a comprehensive understanding of the interaction between microorganisms and polymers. A wide range of creatures, particularly microbes, have developed techniques to survive and break down plastics. This review specifically examines the categorization of plastics based on their thermal and biodegradable properties, as well as the many types of degradation and biodegradation. It also discusses the various types of degradable plastics, the characterization of biodegradation, and the factors that influence the process of biodegradation. The plastic breakdown and bioremediation capabilities of these microbes make them ideal for green chemistry applications aimed at removing hazardous polymers from the ecosystem.
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Affiliation(s)
- Masirah Zahid Shah
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Marzuqa Quraishi
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Anushree Sreejith
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201306, India.
| | - Arpita Roy
- Department of Biotechnology, Sharda School of Engineering & Technology, Sharda University, Greater Noida, India.
| | - Mayeen Uddin Khandaker
- Applied Physics and Radiation Technologies Group, CCDCU, School of Engineering and Technology, Sunway University, 47500, Bandar Sunway, Selangor, Malaysia; Faculty of Graduate Studies, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka, 1216, Bangladesh
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15
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Parida D, Katare K, Ganguly A, Chakraborty D, Konar O, Nogueira R, Bala K. Molecular docking and metagenomics assisted mitigation of microplastic pollution. CHEMOSPHERE 2024; 351:141271. [PMID: 38262490 DOI: 10.1016/j.chemosphere.2024.141271] [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: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.
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Affiliation(s)
- Dinesh Parida
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Konica Katare
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Atmaadeep Ganguly
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, West Bengal State University, Kolkata, 700118, India.
| | - Disha Chakraborty
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Oisi Konar
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Regina Nogueira
- Institute of Sanitary Engineering and Waste Management, Leibniz Universität, Hannover, Germany.
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
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16
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Li Z, Feng C, Lei J, He X, Wang Q, Zhao Y, Qian Y, Zhan X, Shen Z. Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3654-3664. [PMID: 38318812 DOI: 10.1021/acs.est.3c07717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.
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Affiliation(s)
- Zhenling Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Chenghong Feng
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Jinming Lei
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaokang He
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Qixuan Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue Zhao
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yibin Qian
- National Plot Zone for Ecological Conservation (Hainan) Research Center, Hainan Research Academy of Environmental Sciences, Haikou 571127, P. R. China
| | - Xinmin Zhan
- Civil Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
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17
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Bell EL, Rosetto G, Ingraham MA, Ramirez KJ, Lincoln C, Clarke RW, Gado JE, Lilly JL, Kucharzyk KH, Erickson E, Beckham GT. Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization. Nat Commun 2024; 15:1217. [PMID: 38336849 PMCID: PMC10858056 DOI: 10.1038/s41467-024-45523-5] [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: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Successes in biocatalytic polyester recycling have raised the possibility of deconstructing alternative polymers enzymatically, with polyamide (PA) being a logical target due to the array of amide-cleaving enzymes present in nature. Here, we screen 40 potential natural and engineered nylon-hydrolyzing enzymes (nylonases), using mass spectrometry to quantify eight compounds resulting from enzymatic nylon-6 (PA6) hydrolysis. Comparative time-course reactions incubated at 40-70 °C showcase enzyme-dependent variations in product distributions and extent of PA6 film depolymerization, with significant nylon deconstruction activity appearing rare. The most active nylonase, a NylCK variant we rationally thermostabilized (an N-terminal nucleophile (Ntn) hydrolase, NylCK-TS, Tm = 87.4 °C, 16.4 °C higher than the wild-type), hydrolyzes 0.67 wt% of a PA6 film. Reactions fail to restart after fresh enzyme addition, indicating that substrate-based limitations, such as restricted enzyme access to hydrolysable bonds, prohibit more extensive deconstruction. Overall, this study expands our understanding of nylonase activity distribution, indicates that Ntn hydrolases may have the greatest potential for further development, and identifies key targets for progressing PA6 enzymatic depolymerization, including improving enzyme activity, product selectivity, and enhancing polymer accessibility.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gloria Rosetto
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Clarissa Lincoln
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Ryan W Clarke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Japheth E Gado
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Jacob L Lilly
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | | | - Erika Erickson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
- BOTTLE Consortium, Golden, CO, 80401, USA.
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18
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Oda K, Wlodawer A. Development of Enzyme-Based Approaches for Recycling PET on an Industrial Scale. Biochemistry 2024. [PMID: 38285602 DOI: 10.1021/acs.biochem.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Pollution by plastics such as polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), polyurethane (PUR), polyamide (PA), polystyrene (PS), and poly(ethylene terephthalate) (PET) is now gaining worldwide attention as a critical environmental issue, closely linked to climate change. Among them, PET is particularly prone to hydrolysis, breaking down into its constituents, ethylene glycol (EG) and terephthalate (TPA). Biorecycling or bioupcycling stands out as one of the most promising methods for addressing PET pollution. For dealing with pollution by the macrosize PET, a French company Carbios has developed a pilot-scale plant for biorecycling waste PET beverage bottles into new bottles using derivatives of thermophilic leaf compost cutinase (LCC). However, this system still provides significant challenges in its practical implementation. For the micro- or nanosize PET pollution that poses significant human health risks, including cancer, no industrial-scale approach has been established so far, despite the need to develop such technologies. In this Perspective, we explore the enhancement of the low activity and thermostability of the enzyme PETase to match that of LCC, along with the potential application of microbes and enzymes for the treatment of waste PET as microplastics. Additionally, we discuss the shortcomings of the current biorecycling protocols from a life cycle assessment perspective, covering aspects such as the diversity of PET-hydrolyzing enzymes in nature, the catalytic mechanism for crystallized PET, and more. We also provide an overview of the Ideonella sakaiensis system, highlighting its ability to operate and grow at moderate temperatures, in contrast to high-temperature processes.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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19
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Xu L, Li K, Bai X, Zhang G, Tian X, Tang Q, Zhang M, Hu M, Huang Y. Microplastics in the atmosphere: Adsorb on leaves and their effects on the phyllosphere bacterial community. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132789. [PMID: 37862903 DOI: 10.1016/j.jhazmat.2023.132789] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Phyllosphere is the largest interface between the atmosphere and terrestrial ecosystems and serves as a major sink for atmospheric microplastics (MPs). It is also a unique habitat for microbiota with diverse ecological functions. This field study investigated the characteristics of atmospheric MPs adsorbed on leaves with automatic technology, and found their abundance was 3.62 ± 1.29 items cm-2. MPs on leaves were mainly below 80 µm, and dominated by polyamide, polyethene, and rubber. MPs on leaves correlated significantly with the structure and functions of the phyllosphere bacterial community (PBC). Both the MPs abundance and size distribution (MSD) were positively correlated with the α diversity and negatively correlated with the β diversity and network complexity of PBC. PBC functions of environmental and genetic information process were negatively correlated with MPs abundance, and functions related to human diseases and cellular process were positively correlated with MSD significantly. The relative abundance of Sphingomonas was significantly correlated with the MSD, suggesting that Sphingomonas might emerge as the key genus involved in the pathogenicity of PBC mediated by MPs. These results highlighted the ecological health risks of atmospheric MPs as they can be transferred anywhere and potentially increase the pathogenicity of local phyllosphere microflora.
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Affiliation(s)
- Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xinyi Bai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Guangbao Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xudong Tian
- Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control of Zhejiang, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Qian Tang
- Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control of Zhejiang, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China
| | - Mengjun Zhang
- Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China; PKU-HKUST Shenzhen-Hongkong Institution, Shenzhen, Guangdong 518057, China.
| | - Min Hu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
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20
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Shi L, Zhu L. Recent Advances and Challenges in Enzymatic Depolymerization and Recycling of PET Wastes. Chembiochem 2024; 25:e202300578. [PMID: 37960968 DOI: 10.1002/cbic.202300578] [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: 08/16/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/15/2023]
Abstract
Poly (ethylene terephthalate) (PET) is one of the most commonly used plastics in daily life and various industries. Enzymatic depolymerization and recycling of post-consumer PET (pc-PET) provides a promising strategy for the sustainable circular economy of polymers. Great protein engineering efforts have been devoted to improving the depolymerization performance of PET hydrolytic enzymes (PHEs). In this review, we first discuss the mechanisms and challenges of enzymatic PET depolymerization. Subsequently, we summarize the state-of-the-art engineering of PHEs including rational design, machine learning, and directed evolution for improved depolymerization performance, and highlight the advances in screening methods of PHEs. We further discuss several factors that affect the enzymatic depolymerization efficiency. We conclude with our perspective on the opportunities and challenges in bio-recycling and bio-upcycling of PET wastes.
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Affiliation(s)
- Lixia Shi
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Leilei Zhu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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21
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Zhou H, Shi S, You Q, Zhang K, Chen Y, Zheng D, Sun J. Polyethylene Terephthalate Hydrolases in Human Gut Microbiota and Their Implications for Human Health. Microorganisms 2024; 12:138. [PMID: 38257965 PMCID: PMC10820491 DOI: 10.3390/microorganisms12010138] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Polyethylene terephthalate (PET), primarily utilized for food and beverage packaging, consistently finds its way into the human gut, thereby exerting adverse effects on human health. PET hydrolases, critical for the degradation of PET, have been predominantly sourced from environmental microbial communities. Given the fact that the human gut harbors a vast and intricate consortium of microorganisms, inquiry into the presence of potential PET hydrolases within the human gut microbiota becomes imperative. In this investigation, we meticulously screened 22,156 homologous sequences that could potentially encode PET hydrolases using the hidden Markov model (HMM) paradigm, drawing from 4984 cultivated genomes of healthy human gut bacteria. Subsequently, we methodically validated the hydrolytic efficacy of five selected candidate PET hydrolases on both PET films and powders composed of micro-plastics (MPs). Notably, our study also unveiled the influence of both diverse PET MP powders and their resultant hydrolysates on the modulation of cytokine expression in macrophages. In summary, our research underscores the ubiquitous prevalence and considerable potential of the human gut microbiota in PET hydrolysis. Furthermore, our study significantly contributes to the holistic evaluation of the potential health hazards posed by PET MPs to human well-being.
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Affiliation(s)
- Heqi Zhou
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Songbiao Shi
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;
| | - Qiuhong You
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Kaikai Zhang
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Yuchuan Chen
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Dekai Zheng
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Jian Sun
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
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22
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Qiu J, Chen Y, Zhang L, Wu J, Zeng X, Shi X, Liu L, Chen J. A comprehensive review on enzymatic biodegradation of polyethylene terephthalate. ENVIRONMENTAL RESEARCH 2024; 240:117427. [PMID: 37865324 DOI: 10.1016/j.envres.2023.117427] [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: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023]
Abstract
Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.
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Affiliation(s)
- Jiarong Qiu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China; Development Center of Science and Education Park of Fuzhou University, Jinjiang, 362251, China
| | - Yuxin Chen
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Liangqing Zhang
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China; Development Center of Science and Education Park of Fuzhou University, Jinjiang, 362251, China.
| | - Jinzhi Wu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Xianhai Zeng
- College of Energy, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Lemian Liu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Jianfeng Chen
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
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23
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Liu YN, Bairoliya S, Zaiden N, Cao B. Establishment of plastic-associated microbial community from superworm gut microbiome. ENVIRONMENT INTERNATIONAL 2024; 183:108349. [PMID: 38039945 DOI: 10.1016/j.envint.2023.108349] [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: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Gut microbial communities of plastic-munching worms provide novel insights for the development of plastic-processing biotechnologies. Considering the complexity of worm maintenance and the gut microbial communities, it is challenging to apply the worms directly in plastic processing. Harnessing the power of microbial communities derived from the worm gut microbiomes in vitro may enable a promising bioprocess for plastic degradation. Here, we established stable and reproducible plastic-associated biofilm communities derived from the gut microbiome of a superworm, Zophobas atratus, through a two-stage enrichment process: feeding with plastics (HDPE, PP, and PS) and in vitro incubation of gut microbiomes obtained from the plastic-fed worms. Plastic feeding exhibited marginal influence on bacterial diversity but substantially changed the relative abundance of different bacterial groups, and intriguingly, enriched potential plastic degraders. More prominent shifts of microbial communities were observed during the in vitro incubation of the gut microbiomes. Taxa containing plastic-degrading strains were further enriched, while other taxa represented by lactic acid bacteria were depleted. Additionally, the plastic characterization confirmed the degradation of the incubated plastics by the plastic-associated microbial communities. Community functional inference for both gene abundance and community phenotype suggested that the in vitro incubation enhanced plastic-degrading potential. Deterministic ecological effects, in particular, selection processes, were identified as the main driving force of the observed community shifts. Our findings provide novel insights into plastic-munching-worm-inspired bioprocessing of plastic wastes.
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Affiliation(s)
- Yi-Nan Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Sakcham Bairoliya
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Norazean Zaiden
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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24
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Buhari SB, Nezhad NG, Normi YM, Shariff FM, Leow TC. Insight on recently discovered PET polyester-degrading enzymes, thermostability and activity analyses. 3 Biotech 2024; 14:31. [PMID: 38178895 PMCID: PMC10761646 DOI: 10.1007/s13205-023-03882-8] [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: 07/04/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
The flexibility and the low production costs offered by plastics have made them crucial to society. Unfortunately, due to their resistance to biological degradation, plastics remain in the environment for an extended period of time, posing a growing risk to life on earth. Synthetic treatments of plastic waste damage the environment and may cause damage to human health. Bacterial and fungal isolates have been reported to degrade plastic polymers in a logistic safe approach with the help of their microbial cell enzymes. Recently, the bacterial strain Ideonella sakaiensis (201-F6) was discovered to break down and assimilate polyethylene terephthalate (PET) plastic via metabolic processes at 30 °C to 37 °C. PETase and MHETase enzymes help the bacterium to accomplish such tremendous action at lower temperatures than previously discovered enzymes. In addition to functioning at low temperatures, the noble bacterium's enzymes have amazing qualities over pH and PET plastic degradation, including a shorter period of degradation. It has been proven that using the enzyme PETase, this bacterium hydrolyzes the ester linkages of PET plastic, resulting in production of terephthalic acid (TPA), nontoxic compound and mono-2-hydroxyethyl (MHET), along with further depolymerization of MHET to release ethylene glycogen (EG) and terephthalic acid (TPA) by the second enzyme MHETase. Enzymatic plastic degradation has been proposed as an environmentally friendly and long-term solution to plastic waste in the environment. As a result, this review focuses on the enzymes involved in hydrolyzing PET plastic polymers, as well as some of the other microorganisms involved in plastic degradation.
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Affiliation(s)
- Sunusi Bataiya Buhari
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
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25
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Díaz-García L, Chuvochina M, Feuerriegel G, Bunk B, Spröer C, Streit WR, Rodriguez-R LM, Overmann J, Jiménez DJ. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes. Syst Appl Microbiol 2024; 47:126485. [PMID: 38211536 DOI: 10.1016/j.syapm.2023.126485] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
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Affiliation(s)
- Laura Díaz-García
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia; Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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26
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Zhang H, Dierkes RF, Perez-Garcia P, Costanzi E, Dittrich J, Cea PA, Gurschke M, Applegate V, Partus K, Schmeisser C, Pfleger C, Gohlke H, Smits SHJ, Chow J, Streit WR. The metagenome-derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate (PET). FEBS J 2024; 291:70-91. [PMID: 37549040 DOI: 10.1111/febs.16924] [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: 01/31/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Polyethylene terephthalate (PET) is a widely used synthetic polymer and known to contaminate marine and terrestrial ecosystems. Only few PET-active microorganisms and enzymes (PETases) are currently known, and it is debated whether degradation activity for PET originates from promiscuous enzymes with broad substrate spectra that primarily act on natural polymers or other bulky substrates, or whether microorganisms evolved their genetic makeup to accepting PET as a carbon source. Here, we present a predicted diene lactone hydrolase designated PET40, which acts on a broad spectrum of substrates, including PET. It is the first esterase with activity on PET from a GC-rich Gram-positive Amycolatopsis species belonging to the Pseudonocardiaceae (Actinobacteria). It is highly conserved within the genera Amycolatopsis and Streptomyces. PET40 was identified by sequence-based metagenome search using a PETase-specific hidden Markov model. Besides acting on PET, PET40 has a versatile substrate spectrum, hydrolyzing δ-lactones, β-lactam antibiotics, the polyester-polyurethane Impranil® DLN, and various para-nitrophenyl ester substrates. Molecular docking suggests that the PET degradative activity is likely a result of the promiscuity of PET40, as potential binding modes were found for substrates encompassing mono(2-hydroxyethyl) terephthalate, bis(2-hydroxyethyl) terephthalate, and a PET trimer. We also solved the crystal structure of the inactive PET40 variant S178A to 1.60 Å resolution. PET40 is active throughout a wide pH (pH 4-10) and temperature range (4-65 °C) and remarkably stable in the presence of 5% SDS, making it a promising enzyme as a starting point for further investigations and optimization approaches.
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Affiliation(s)
- Hongli Zhang
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Germany
| | - Elisa Costanzi
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Pablo A Cea
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Kristina Partus
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), John von Neumann Institute for Computing and Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
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27
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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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28
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He Y, Deng X, Jiang L, Hao L, Shi Y, Lyu M, Zhang L, Wang S. Current advances, challenges and strategies for enhancing the biodegradation of plastic waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167850. [PMID: 37844647 DOI: 10.1016/j.scitotenv.2023.167850] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Due to its highly recalcitrant nature, the growing accumulation of plastic waste is becoming an urgent global problem. Biodegradation is one of the best possible approaches for the treatment of plastic waste in an environmentally friendly manner, but our current knowledge on the underlying mechanisms, as well as strategies for the development and enhancement of plastic biodegradation are still limited. This review aims to provide an updated and comprehensive overview of current research on plastic waste biodegradation, focusing on enhancement strategies with ongoing research significance, including the mining of highly efficient plastic-degrading microorganisms/enzymes, utilization of synergistic additives, novel pretreatment approaches, modification via molecular engineering, and construction of bacterial/enzyme consortia systems. Studying these strategies can (i) enrich the high-performance microbial/enzymes toolbox for plastic degradation, (ii) provide methods for recycling and upgrading plastics, as well as (iii) enable further molecular modification and functional optimization of plastic-degrading enzymes to realize economically viable biodegradation of plastics. To the best of our knowledge, this is the first review to discuss in detail strategies to enhance biodegradation of plastics. Finally, some recommendations for future research on plastic biodegradation are listed, hoping to provide the best direction for tackling the plastic waste dilemma in the future.
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Affiliation(s)
- Yuehui He
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xilong Deng
- College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lei Jiang
- College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lijuan Hao
- College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yong Shi
- College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine, Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; College of Marine Food and Bioengineering, Jiangsu Ocean University, Lianyungang 222005, China.
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Degli-Innocenti F, Breton T, Chinaglia S, Esposito E, Pecchiari M, Pennacchio A, Pischedda A, Tosin M. Microorganisms that produce enzymes active on biodegradable polyesters are ubiquitous. Biodegradation 2023; 34:489-518. [PMID: 37354274 DOI: 10.1007/s10532-023-10031-8] [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: 01/20/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Biodegradability standards measure ultimate biodegradation of polymers by exposing the material under test to a natural microbial inoculum. Available tests developed by the International Organization for Standardization (ISO) use inoculums sampled from different environments e.g. soil, marine sediments, seawater. Understanding whether each inoculum is to be considered as microbially unique or not can be relevant for the interpretation of tests results. In this review, we address this question by consideration of the following: (i) the chemical nature of biodegradable plastics (virtually all biodegradable plastics are polyesters) (ii) the diffusion of ester bonds in nature both in simple molecules and in polymers (ubiquitous); (iii) the diffusion of decomposers capable of producing enzymes, called esterases, which accelerate the hydrolysis of esters, including polyesters (ubiquitous); (iv) the evidence showing that synthetic polyesters can be depolymerized by esterases (large and growing); (v) the evidence showing that these esterases are ubiquitous (growing and confirmed by bioinformatics studies). By combining the relevant available facts it can be concluded that if a certain polyester shows ultimate biodegradation when exposed to a natural inoculum, it can be considered biodegradable and need not be retested using other inoculums. Obviously, if the polymer does not show ultimate biodegradation it must be considered recalcitrant, until proven otherwise.
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Affiliation(s)
| | - Tony Breton
- Novamont S.p.A., via Fauser 8, 28100, Novara, Italy
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30
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Yahiaoui B, Bounabi H, Boukerb AM, Gasmi M. Insights into Genomic Features and Potential Biotechnological Applications of Bacillus halotolerans Strain HGR5. Pol J Microbiol 2023; 72:477-490. [PMID: 38103009 PMCID: PMC10725166 DOI: 10.33073/pjm-2023-045] [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: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Algeria is one of the wealthiest countries in terms of hydrothermal sources, with more than two hundred hot springs. However, diverse and little-described microbial communities colonize these habitats, making them an intriguing research subject. This work reports the isolation of bacteria from two hot springs water samples in northeastern Algeria, evaluating their enzymatic activities and effect on plant pathogens. Out of the obtained 72 bacterial isolates and based on the 16S rRNA gene sequence analysis, the strain HGR5 belonging to Bacillus halotolerans had the most interesting activity profile. Interestingly, HGR5 was substantially active against Fusarium graminearum, Phytophthora infestans, and Alternaria alternata. Furthermore, this strain presented a high ability to degrade casein, Tween 80, starch, chitin, cellulose, and xylan. The genome sequence of HGR5 allowed taxonomic validation and screening of specific genetic traits, determining its antagonistic and enzymatic activities. Genome mining revealed that strain HGR5 encloses several secondary metabolite biosynthetic gene clusters (SM-BGCs) involved in metabolite production with antimicrobial properties. Thus, antimicrobial metabolites included bacillaene, fengycin, laterocidine, bacilysin, subtilosin, bacillibactin, surfactin, myxovirescin, dumulmycin, and elansolid A1. HGR5 strain genome was also mined for CAZymes associated with antifungal activity. Finally, the HGR5 strain exhibited the capacity to degrade polycaprolactone (PCL), a model substrate for polyester biodegradation. Overall, these results suggest that this strain may be a promising novel biocontrol agent with interesting plastic-degradation capability, opening the possibilities of its use in various biotechnological applications.
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Affiliation(s)
- Bilal Yahiaoui
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, Setif, Algeria
| | - Hadjira Bounabi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
| | - Amine M. Boukerb
- Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, CBSA UR 4312, Rouen, France
| | - Meriem Gasmi
- Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
- Laboratory of Biotechnology, Higher National School of Biotechnology Taoufik Khaznadar, Constantine, Algeria
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31
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Howard SA, Carr CM, Sbahtu HI, Onwukwe U, López MJ, Dobson ADW, McCarthy RR. Enrichment of native plastic-associated biofilm communities to enhance polyester degrading activity. Environ Microbiol 2023; 25:2698-2718. [PMID: 37515381 PMCID: PMC10947123 DOI: 10.1111/1462-2920.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Plastic pollution is an increasing worldwide problem urgently requiring a solution. While recycling rates are increasing globally, only 9% of all plastic waste has been recycled, and with the cost and limited downstream uses of recycled plastic, an alternative is needed. Here, we found that expanded polystyrene (EPS) promoted high levels of bacterial biofilm formation and sought out environmental EPS waste to characterize these native communities. We demonstrated that the EPS attached communities had limited plastic degrading activity. We then performed a long-term enrichment experiment where we placed a robust selection pressure on these communities by limiting carbon availability such that the waste plastic was the only carbon source. Seven of the resulting enriched bacterial communities had increased plastic degrading activity compared to the starting bacterial communities. Pseudomonas stutzeri was predominantly identified in six of the seven enriched communities as the strongest polyester degrader. Sequencing of one isolate of P. stutzeri revealed two putative polyesterases and one putative MHETase. This indicates that waste plastic-associated biofilms are a source for bacteria that have plastic-degrading potential, and that this potential can be unlocked through selective pressure and further in vitro enrichment experiments, resulting in biodegradative communities that are better than nature.
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Affiliation(s)
- Sophie A. Howard
- Centre for Inflammation Research and Translational Medicine, Division of Biosciences, Department of Life Sciences, College of Health and Life SciencesBrunel University LondonUxbridgeUK
| | - Clodagh M. Carr
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
| | - Habteab Isaack Sbahtu
- Centre for Inflammation Research and Translational Medicine, Division of Biosciences, Department of Life Sciences, College of Health and Life SciencesBrunel University LondonUxbridgeUK
| | - Uchechukwu Onwukwe
- Experimental Techniques Centre, College of Engineering, Design and Physical SciencesBrunel University LondonUxbridgeUK
| | - Maria J. López
- Department of Biology and Geology, CITE II‐BUniversity of Almería, Agrifood Campus of International Excellence ceiA3, CIAIMBITALAlmeriaSpain
| | - Alan D. W. Dobson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
| | - Ronan R. McCarthy
- Centre for Inflammation Research and Translational Medicine, Division of Biosciences, Department of Life Sciences, College of Health and Life SciencesBrunel University LondonUxbridgeUK
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Porter R, Černoša A, Fernández-Sanmartín P, Cortizas AM, Aranda E, Luo Y, Zalar P, Podlogar M, Gunde-Cimerman N, Gostinčar C. Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae. Microbiol Res 2023; 277:127507. [PMID: 37793281 DOI: 10.1016/j.micres.2023.127507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
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Affiliation(s)
- Rachel Porter
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Černoša
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Paola Fernández-Sanmartín
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Antonio Martínez Cortizas
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Elisabet Aranda
- University of Granada, Institute of Water Research, Environmental Microbiology Group, Ramón y Cajal n4, 18071 Granada, Spain
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 266555, China
| | - Polona Zalar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Matejka Podlogar
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Cene Gostinčar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia.
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Qi X, Ji M, Yin CF, Zhou NY, Liu Y. Glacier as a source of novel polyethylene terephthalate hydrolases. Environ Microbiol 2023; 25:2822-2833. [PMID: 37775503 DOI: 10.1111/1462-2920.16516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Polyethylene terephthalate (PET) is a major component of microplastic contamination globally, which is now detected in pristine environments including Polar and mountain glaciers. As a carbon-rich molecule, PET could be a carbon source for microorganisms dwelling in glacier habitats. Thus, glacial microorganisms may be potential PET degraders with novel PET hydrolases. Here, we obtained 414 putative PET hydrolase sequences by searching a global glacier metagenome dataset. Metagenomes from the Alps and Tibetan glaciers exhibited a higher relative abundance of putative PET hydrolases than those from the Arctic and Antarctic. Twelve putative PET hydrolase sequences were cloned and expressed, with one sequence (designated as GlacPETase) proven to degrade amorphous PET film with a similar performance as IsPETase, but with a higher thermostability. GlacPETase exhibited only 30% sequence identity to known active PET hydrolases with a novel disulphide bridge location and, therefore may represent a novel PET hydrolases class. The present work suggests that extreme carbon-poor environments may harbour a diverse range of known and novel PET hydrolases for carbon acquisition as an environmental adaptation mechanism.
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Affiliation(s)
- Xiaoyan Qi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Chao-Fan Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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34
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Zhao S, Liu R, Wang J, Lv S, Zhang B, Dong C, Shao Z. Biodegradation of polyethylene terephthalate (PET) by diverse marine bacteria in deep-sea sediments. Environ Microbiol 2023; 25:2719-2731. [PMID: 37421171 DOI: 10.1111/1462-2920.16460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/19/2023] [Indexed: 07/09/2023]
Abstract
PET plastic waste entering the oceans is supposed to take hundreds of years to degrade and tends to accumulate in the deep sea. However, we know little about the bacteria capable of plastic degradation therein. To determine whether PET-degrading bacteria are present in deep-sea sediment, we collected the samples from the eastern central Pacific Ocean and initiated microbial incubation with PET as the carbon source. After enrichment with PET for 2 years, we gained all 15 deep-sea sediment communities at five oceanic sampling sites. Bacterial isolation for pure culture and further growth tests confirmed that diverse bacteria possess degradation ability including Alcanivorax xenomutans BC02_1_A5, Marinobacter sediminum BC31_3_A1, Marinobacter gudaonensis BC06_2_A6, Thalassospira xiamenensis BC02_2_A1 and Nocardioides marinus BC14_2_R3. Furthermore, four strains were chosen as representatives to reconfirm the PET degradation capability by SEM, weight loss and UPLC-MS. The results showed that after 30-day incubation, 1.3%-1.8% of PET was lost. De-polymerization of PET by the four strains was confirmed by the occurrence of the PET monomer of MHET and TPA as the key degradation products. Bacterial consortia possessing PET-degrading potential are prevalent and diverse and might play a key role in the removal of PET pollutants in deep oceans.
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Affiliation(s)
- Sufang Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
| | - Juan Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
| | - Shiwei Lv
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
| | - Benjuan Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Fisheries and Life, Shanghai Ocean University, Shanghai, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, China
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
- School of Environmental Science, Harbin Institute of Technology, Harbin, China
- School of Fisheries and Life, Shanghai Ocean University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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35
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Zeng C, Ding F, Zhou J, Dong W, Cui Z, Yan X. Biodegradation of Poly(ethylene terephthalate) by Bacillus safensis YX8. Int J Mol Sci 2023; 24:16434. [PMID: 38003625 PMCID: PMC10671283 DOI: 10.3390/ijms242216434] [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: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Due to the extensive utilization of poly (ethylene terephthalate) (PET), a significant amount of PET waste has been discharged into the environment, endangering both human health and the ecology. As an eco-friendly approach to PET waste treatment, biodegradation is dependent on efficient strains and enzymes. In this study, a screening method was first established using polycaprolactone (PCL) and PET nanoparticles as substrates. A PET-degrading strain YX8 was isolated from the surface of PET waste. Based on the phylogenetic analysis of 16S rRNA and gyrA genes, this strain was identified as Bacillus safensis. Strain YX8 demonstrated the capability to degrade PET nanoparticles, resulting in the production of terephthalic acid (TPA), mono (2-hydroxyethyl) terephthalic acid (MHET), and bis (2-hydroxyethyl) terephthalic acid (BHET). Erosion spots on the PET film were observed after incubation with strain YX8. Furthermore, the extracellular enzymes produced by strain YX8 exhibited the ability to form a clear zone on the PCL plate and to hydrolyze PET nanoparticles to generate TPA, MHET, and BHET. This work developed a method for the isolation of PET-degrading microorganisms and provides new strain resources for PET degradation and for the mining of functional enzymes.
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Affiliation(s)
- Caiting Zeng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Fanghui Ding
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Jie Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (J.Z.); (W.D.)
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (J.Z.); (W.D.)
| | - Zhongli Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Xin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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36
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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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37
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Xu L, Li K, Zhang M, Guo J, Jia W, Bai X, Tian X, Huang Y. Plastic substrate and residual time of microplastics in the urban river shape the composition and structure of bacterial communities in plastisphere. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118710. [PMID: 37536136 DOI: 10.1016/j.jenvman.2023.118710] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The widespread secondary microplastics (MPs) in urban freshwater, originating from plastic wastes, have created a new habitat called plastisphere for microorganisms. The factors influencing the structure and ecological risks of the microbial community within the plastisphere are not yet fully understood. We conducted an in-site incubation experiment in an urban river, using MPs from garbage bags (GB), shopping bags (SB), and plastic bottles (PB). Bacterial communities in water and plastisphere incubated for 2 and 4 weeks were analyzed by 16S high-throughput sequencing. The results showed the bacterial composition of the plastisphere, especially the PB, exhibited enrichment of plastic-degrading and photoautotrophic taxa. Diversity declined in GB and PB but increased in SB plastisphere. Abundance analysis revealed distinct bacterial species that were enriched or depleted in each type of plastisphere. As the succession progressed, the differences in community structure was more pronounced, and the decline in the complexity of bacterial community within each plastisphere suggested increasing specialization. All the plastisphere exhibited elevated pathogenicity at the second or forth week, compared to bacterial communities related to natural particles. These findings highlighted the continually evolving plastisphere in urban rivers was influenced by the plastic substrates, and attention should be paid to fragile plastic wastes due to the rapidly increasing pathogenicity of the bacterial community attached to them.
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Affiliation(s)
- Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Mengjun Zhang
- Peking University Shenzhen Institute, Shenzhen, Guangdong, 518057, China; PKU-HKUST Shenzhen-Hongkong Institution, Shenzhen, Guangdong, 518057, China
| | - Jiabao Guo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xinyi Bai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xudong Tian
- Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control of Zhejiang, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou, 310012, China.
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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38
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Howard SA, McCarthy RR. Modulating biofilm can potentiate activity of novel plastic-degrading enzymes. NPJ Biofilms Microbiomes 2023; 9:72. [PMID: 37788986 PMCID: PMC10547765 DOI: 10.1038/s41522-023-00440-1] [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: 04/16/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Plastic pollution is an increasing global issue desperately requiring a solution. Only 9% of all plastic waste has been recycled, and whilst recycling gives a second life to plastic, it is costly and there are limited downstream uses of recycled plastic, therefore an alternative is urgently needed. Biodegradation of plastic by microorganisms is a developing field of interest with the potential for bioreactors to be used alongside recycling to degrade plastic that may otherwise be sent to landfill. Here, we have identified two novel polyethylene terephthalate (PET) degrading enzymes through genomic mining and characterised their activity, including their ability to degrade PET. One of the main roadblocks facing the development of microbial enzymes as a plastic biodegradation solution, is that their efficiency is too low to facilitate development as bioremediation tools. In an innovative approach to tackle this roadblock, we hypothesised that enhancing a bacteria's ability to attach to and form a biofilm on plastic could maximise the local concentration of the enzyme around the target substrate, therefore increasing the overall rate of plastic degradation. We found that increasing biofilm levels, by manipulating the levels of the second messenger, Cyclic-di-GMP, led to increased levels of polyester degradation in cells expressing novel and well characterised polyester-degrading enzymes. This indicates that modulating biofilm formation is a viable mechanism to fast track the development of bacterial plastic bioremediation solutions.
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Affiliation(s)
- Sophie A Howard
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Ronan R McCarthy
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK.
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39
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Duan S, Zhang N, Chao T, Wu Y, Wang M. The structural and molecular mechanisms of type II PETases: a mini review. Biotechnol Lett 2023; 45:1249-1263. [PMID: 37535135 DOI: 10.1007/s10529-023-03418-3] [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: 03/21/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
The advent of plastics has led to significant advances for humans, although the accompanying pollution has also been a source of concern for countries globally. Consequently, a biological method to effectively degrade polyethylene terephthalate (PET) has been an area of significant scientific interest. Following the report of the highly efficient PET hydrolase from the bacterium Ideonella sakaiensis strain 201-F6 (i.e., IsPETase) in 2016, its structure has been extensively studied, showing that it belongs to the type II PETase group. Unlike type I PETases that include most known cutinases, structural investigations of type II PETases have only been conducted since 2017. Type II PETases are further divided into type IIa and IIb enzymes. Moreover, even less research has been conducted on type IIa plastic-degrading enzymes. Here, we present a review of recent studies of the structure and mechanism of type II PETases, using the known structure of the type IIa PETase PE-H from the marine bacterium Pseudomonas aestusnigri in addition to the type IIb enzyme IsPETase as representatives. These studies have provided new insights into the structural features of type II PETases that exhibit PET catalytic activity. In addition, recent studies investigating the rational design of IsPETases are reviewed and summarized alongside a discussion of controversies surrounding PETase investigations.
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Affiliation(s)
- Shuyan Duan
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China.
| | - Nan Zhang
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Tianzhu Chao
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Yaoyao Wu
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Mengying Wang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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40
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Perez-Garcia P, Chow J, Costanzi E, Gurschke M, Dittrich J, Dierkes RF, Molitor R, Applegate V, Feuerriegel G, Tete P, Danso D, Thies S, Schumacher J, Pfleger C, Jaeger KE, Gohlke H, Smits SHJ, Schmitz RA, Streit WR. An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate. Commun Chem 2023; 6:193. [PMID: 37697032 PMCID: PMC10495362 DOI: 10.1038/s42004-023-00998-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Elisa Costanzi
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Violetta Applegate
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Prince Tete
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Dominik Danso
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
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41
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James-Pearson LF, Dudley KJ, Te'o VSJ, Patel BKC. A hot topic: thermophilic plastic biodegradation. Trends Biotechnol 2023; 41:1117-1126. [PMID: 37121828 DOI: 10.1016/j.tibtech.2023.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023]
Abstract
Biological degradation of plastic waste is an environmentally and economically friendlier alternative to current recycling practices and enables the cycling of plastic monomers back into virgin-quality plastics. However, due to slow reaction rates, there is a lack of an industrially viable biodegradation strategy for most plastics. Here, we highlight the applicability of a thermophilic biodegradation strategy over a mesophilic approach, to enhance enzyme accessibility and catalyze plastic biodegradation. Thus, at reactions closer to the melting temperature or glass transition temperature of plastics, thermophilic reactions can offer an alternative direction to conventional plastic biodegradation strategies.
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Affiliation(s)
- Louisa F James-Pearson
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Valentino Setoa Junior Te'o
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Bharat K C Patel
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia.
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42
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Makryniotis K, Nikolaivits E, Gkountela C, Vouyiouka S, Topakas E. Discovery of a polyesterase from Deinococcus maricopensis and comparison to the benchmark LCC ICCG suggests high potential for semi-crystalline post-consumer PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131574. [PMID: 37150100 DOI: 10.1016/j.jhazmat.2023.131574] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
Plastic pollution remains a significant environmental challenge, with conventional waste management strategies proving insufficient in addressing the problem. Enzymatic degradation has emerged as a promising alternative, with LCCICCG, an engineered metagenome-derived cutinase, being the most effective in degrading polyethylene terephthalate (PET), the most commonly produced and discarded polyester. However, more efficient PET-hydrolases are needed for the upscaling of a PET-waste biorefinery. In this regard, the study reports the characterization of a novel, phylogenetically distinct, thermophilic polyesterase from Deinococcus maricopensis (DmPETase) and its comparison to LCCICCG. DmPETase is capable of degrading various synthetic polymers, including PET, polyurethane, as well as four semi-crystalline aliphatic polyesters. DmPETase was found to be comparable to LCCICCG at 50 °C in degrading semi-crystalline sections of post-consumer PET bottles, but it appeared to be less sensitive to crystallinity degree increase. This property makes DmPETase a new template for protein engineering endeavors to create an efficient biocatalyst to be integrated into the bio-recycling process of PET waste, without the need for amorphization of the materials.
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Affiliation(s)
- Konstantinos Makryniotis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
| | - Christina Gkountela
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Stamatina Vouyiouka
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
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43
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Hong H, Ki D, Seo H, Park J, Jang J, Kim KJ. Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties. Nat Commun 2023; 14:4556. [PMID: 37507390 PMCID: PMC10382486 DOI: 10.1038/s41467-023-40233-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Excessive polyethylene terephthalate (PET) waste causes a variety of problems. Extensive research focused on the development of superior PET hydrolases for PET biorecycling has been conducted. However, template enzymes employed in enzyme engineering mainly focused on IsPETase and leaf-branch compost cutinase, which exhibit mesophilic and thermophilic hydrolytic properties, respectively. Herein, we report a PET hydrolase from Cryptosporangium aurantiacum (CaPETase) that exhibits high thermostability and remarkable PET degradation activity at ambient temperatures. We uncover the crystal structure of CaPETase, which displays a distinct backbone conformation at the active site and residues forming the substrate binding cleft, compared with other PET hydrolases. We further develop a CaPETaseM9 variant that exhibits robust thermostability with a Tm of 83.2 °C and 41.7-fold enhanced PET hydrolytic activity at 60 °C compared with CaPETaseWT. CaPETaseM9 almost completely decompose both transparent and colored post-consumer PET powder at 55 °C within half a day in a pH-stat bioreactor.
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Affiliation(s)
- Hwaseok Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dongwoo Ki
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyoung Park
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jaewon Jang
- Institute of Biotechnology, CJ CheilJedang Co., Suwon-si, Gyeonggi-do, 16495, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Zyen Co, Daegu, 41566, Republic of Korea.
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44
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Li A, Sheng Y, Cui H, Wang M, Wu L, Song Y, Yang R, Li X, Huang H. Discovery and mechanism-guided engineering of BHET hydrolases for improved PET recycling and upcycling. Nat Commun 2023; 14:4169. [PMID: 37443360 PMCID: PMC10344914 DOI: 10.1038/s41467-023-39929-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Although considerable research achievements have been made to address the plastic crisis using enzymes, their applications are limited due to incomplete degradation and low efficiency. Herein, we report the identification and subsequent engineering of BHETases, which have the potential to improve the efficiency of PET recycling and upcycling. Two BHETases (ChryBHETase and BsEst) are identified from the environment via enzyme mining. Subsequently, mechanism-guided barrier engineering is employed to yield two robust and thermostable ΔBHETases with up to 3.5-fold enhanced kcat/KM than wild-type, followed by atomic resolution understanding. Coupling ΔBHETase into a two-enzyme system overcomes the challenge of heterogeneous product formation and results in up to 7.0-fold improved TPA production than seven state-of-the-art PET hydrolases, under the conditions used here. Finally, we employ a ΔBHETase-joined tandem chemical-enzymatic approach to valorize 21 commercial post-consumed plastics into virgin PET and an example chemical (p-phthaloyl chloride) for achieving the closed-loop PET recycling and open-loop PET upcycling.
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Affiliation(s)
- Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Haiyang Cui
- RWTH Aachen University, Templergraben 55, Aachen, 52062, Germany
- University of Illinois at Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Luxuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Rongrong Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China.
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45
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Galarza–Verkovitch D, Turak O, Wiese J, Rahn T, Hentschel U, Borchert E. Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates. AIMS Microbiol 2023; 9:518-539. [PMID: 37649797 PMCID: PMC10462454 DOI: 10.3934/microbiol.2023027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 09/01/2023] Open
Abstract
Plastics have quickly become an integral part of modern life. Due to excessive production and improper waste disposal, they are recognized as contaminants present in practically all habitat types. Although there are several polymers, polyethylene terephthalate (PET) is of particular concern due to its abundance in the environment. There is a need for a solution that is both cost-effective and ecologically friendly to address this pollutant. The use of microbial depolymerizing enzymes could offer a biological avenue for plastic degradation, though the full potential of these enzymes is yet to be uncovered. The purpose of this study was to use (1) plate-based screening methods to investigate the plastic degradation potential of marine bacteria from the order Enterobacterales collected from various organismal and environmental sources, and (2) perform genome-based analysis to identify polyesterases potentially related to PET degradation. 126 bacterial isolates were obtained from the strain collection of RD3, Research Unit Marine Symbioses-GEOMAR-and sequentially tested for esterase and polyesterase activity, in combination here referred to as PETase-like activity. The results show that members of the microbial families Alteromonadaceae, Shewanellaceae, and Vibrionaceae, derived from marine sponges and bryozoans, are the most promising candidates within the order Enterobacterales. Furthermore, 389 putative hydrolases from the α/β superfamily were identified in 23 analyzed genomes, of which 22 were sequenced for this study. Several candidates showed similarities with known PETases, indicating underlying enzymatic potential within the order Enterobacterales for PET degradation.
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Affiliation(s)
| | - Onur Turak
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Jutta Wiese
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
- Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
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46
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Jayasekara SK, Joni HD, Jayantha B, Dissanayake L, Mandrell C, Sinharage MM, Molitor R, Jayasekara T, Sivakumar P, Jayakody LN. Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Comput Struct Biotechnol J 2023; 21:3513-3521. [PMID: 37484494 PMCID: PMC10362282 DOI: 10.1016/j.csbj.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 07/25/2023] Open
Abstract
Polyethylene terephthalate (PET) is the largest produced polyester globally, and less than 30% of all the PET produced globally (∼6 billion pounds annually) is currently recycled into lower-quality products. The major drawbacks in current recycling methods (mechanical and chemical), have inspired the exploration of potentially efficient and sustainable PET depolymerization using biological approaches. Researchers have discovered efficient PET hydrolyzing enzymes in the plastisphere and have demonstrated the selective degradation of PET to original monomers thus enabling biological recycling or upcycling. However, several significant hurdles such as the less efficiency of the hydrolytic reaction, low thermostability of the enzymes, and the inability of the enzyme to depolymerize crystalline PET must be addressed in order to establish techno-economically feasible commercial-scale biological PET recycling or upcycling processes. Researchers leverage a synthetic biology-based design; build, test, and learn (DBTL) methodology to develop commercially applicable efficient PET hydrolyzing enzymes through 1) high-throughput metagenomic and proteomic approaches to discover new PET hydrolyzing enzymes with superior properties: and, 2) enzyme engineering approaches to modify and optimize PET hydrolyzing properties. Recently, in-silico platforms including molecular mechanics and machine learning concepts are emerging as innovative tools for the development of more efficient and effective PET recycling through the exploration of novel mutations in PET hydrolyzing enzymes. In-silico-guided PET hydrolyzing enzyme engineering with DBTL cycles enables the rapid development of efficient variants of enzymes over tedious conventional enzyme engineering methods such as random or directed evolution. This review highlights the potential of in-silico-guided PET degrading enzyme engineering to create more efficient variants, including Ideonella sakaiensis PETase (IsPETase) and leaf-branch compost cutinases (LCC). Furthermore, future research prospects are discussed to enable a sustainable circular economy through the bioconversion of PET to original or high-value platform chemicals.
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Affiliation(s)
- Sandhya K. Jayasekara
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Hriday Dhar Joni
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Bhagya Jayantha
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lakshika Dissanayake
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Christopher Mandrell
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Manuka M.S. Sinharage
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Ryan Molitor
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Thushari Jayasekara
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Poopalasingam Sivakumar
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lahiru N. Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
- Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA
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47
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Li A, Cui H, Sheng Y, Qiao J, Li X, Huang H. Global plastic upcycling during and after the COVID-19 pandemic: The status and perspective. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110092. [PMID: 37200549 PMCID: PMC10167783 DOI: 10.1016/j.jece.2023.110092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/10/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Plastic pollution has become one of the most pressing environmental issues worldwide since the vast majority of post-consumer plastics are hard to degrade in the environment. The coronavirus disease (COVID-19) pandemic had disrupted the previous effort of plastic pollution mitigation to a great extent due to the overflow of plastic-based medical waste. In the post-pandemic era, the remaining challenge is how to motivate global action towards a plastic circular economy. The need for one package of sustainable and systematic plastic upcycling approaches has never been greater to address such a challenge. In this review, we summarized the threat of plastic pollution during COVID-19 to public health and ecosystem. In order to solve the aforementioned challenges, we present a shifting concept, regeneration value from plastic waste, that provides four promising pathways to achieve a sustainable circular economy: 1) Increasing reusability and biodegradability of plastics; 2) Transforming plastic waste into high-value products by chemical approaches; 3) The closed-loop recycling can be promoted by biodegradation; 4) Involving renewable energy into plastic upcycling. Additionally, the joint efforts from different social perspectives are also encouraged to create the necessary economic and environmental impetus for a circular economy.
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Affiliation(s)
- Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Haiyang Cui
- RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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48
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Carr CM, Keller MB, Paul B, Schubert SW, Clausen KSR, Jensen K, Clarke DJ, Westh P, Dobson ADW. Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14. Front Microbiol 2023; 14:1170880. [PMID: 37250061 PMCID: PMC10213408 DOI: 10.3389/fmicb.2023.1170880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
The successful enzymatic degradation of polyester substrates has fueled worldwide investigation into the treatment of plastic waste using bio-based processes. Within this realm, marine-associated microorganisms have emerged as a promising source of polyester-degrading enzymes. In this work, we describe the hydrolysis of the synthetic polymer PET by SM14est, a polyesterase which was previously identified from Streptomyces sp. SM14, an isolate of the marine sponge Haliclona simulans. The PET hydrolase activity of purified SM14est was assessed using a suspension-based assay and subsequent analysis of reaction products by UV-spectrophotometry and RP-HPLC. SM14est displayed a preference for high salt conditions, with activity significantly increasing at sodium chloride concentrations from 100 mM up to 1,000 mM. The initial rate of PET hydrolysis by SM14est was determined to be 0.004 s-1 at 45°C, which was increased by 5-fold to 0.02 s-1 upon addition of 500 mM sodium chloride. Sequence alignment and structural comparison with known PET hydrolases, including the marine halophile PET6, and the highly efficient, thermophilic PHL7, revealed conserved features of interest. Based on this work, SM14est emerges as a useful enzyme that is more similar to key players in the area of PET hydrolysis, like PHL7 and IsPETase, than it is to its marine counterparts. Salt-tolerant polyesterases such as SM14est are potentially valuable in the biological degradation of plastic particles that readily contaminate marine ecosystems and industrial wastewaters.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
| | - Malene B. Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bijoya Paul
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sune W. Schubert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kristine S. R. Clausen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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Palacios-Mateo C, Meng K, Legaz-Pol L, Steen Redeker E, Huerta-Lwanga E, Blank LM. Enzymes for microplastic-free agricultural soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114982. [PMID: 37156039 DOI: 10.1016/j.ecoenv.2023.114982] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/18/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
Plastic mulch films and biofertilizers (processed sewage sludge, compost or manure) have helped to increase crop yields. However, there is increasing evidence that these practices significantly contribute to microplastic contamination in agricultural soils, affecting biodiversity and soil health. Here, we draw attention to the use of hydrolase enzymes that depolymerize polyester-based plastics as a bioremediation technique for agricultural soils (in situ), biofertilizers and irrigation water (ex situ), and discuss the need for fully biodegradable plastic mulches. We also highlight the need for ecotoxicological assessment of the proposed approach and its effects on different soil organisms. Enzymes should be optimized to work effectively and efficiently under the conditions found in natural soils (typically, moist solids at an ambient temperature with low salinity). Such optimization is also necessary to ensure that already distressed ecosystems are not disrupted any further.
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Affiliation(s)
- Cristina Palacios-Mateo
- Aachen-Maastricht Institute for Biobased Materials, Faculty of Science and Engineering, Maastricht University, Urmonderbaan 22, 6167 RD Geleen, the Netherlands.
| | - Ke Meng
- Soil Physics and Land Management Group, Wageningen University & Research, Droevendaalsesteeg 3, 6708PB Wageningen, the Netherlands.
| | - Lucia Legaz-Pol
- Soil Physics and Land Management Group, Wageningen University & Research, Droevendaalsesteeg 3, 6708PB Wageningen, the Netherlands.
| | - Erik Steen Redeker
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, Paul-Henri Spaaklaan 1, PO Box 616, 6200 MD Maastricht, the Netherlands.
| | - Esperanza Huerta-Lwanga
- Soil Physics and Land Management Group, Wageningen University & Research, Droevendaalsesteeg 3, 6708PB Wageningen, the Netherlands.
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany.
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Brackmann R, de Oliveira Veloso C, de Castro AM, Langone MAP. Enzymatic post-consumer poly(ethylene terephthalate) (PET) depolymerization using commercial enzymes. 3 Biotech 2023; 13:135. [PMID: 37124991 PMCID: PMC10130296 DOI: 10.1007/s13205-023-03555-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Poly(ethylene terephthalate) (PET) is a synthetic polymer widely used globally. The high PET resistance to biotic degradation and its improper destination result in the accumulation of this plastic in the environment, largely affecting terrestrial and aquatic animals. This work investigated post-consumer PET (PC-PET) degradation using five commercial hydrolase enzymes (Novozym 51032, CalB, Palatase, Eversa, Lipozyme TL). Humicola insolens cutinase (HiC, Novozym 51032) was the most active among the enzymes studied. Several important reaction parameters (enzyme type, dual enzyme system, enzyme concentration, temperature, ultrasound treatment) were evaluated in PC-PET hydrolysis using HiC. The concentration and the proportion (molar ratio) of hydrolysis products, terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), and bis(2-hydroxyethyl) terephthalate (BHET), were significantly changed depending on the reaction temperature. The TPA released at 70 °C was 3.65-fold higher than at 50 °C. At higher temperatures, the conversion of MHET into TPA was favored. The enzymatic PET hydrolysis by HiC was very sensitive to the enzyme concentration, indicating that it strongly adsorbs on the polymer surface. The concentration of TPA, MHET, and BHET increased as the enzyme concentration increased, and a maximum was achieved using 40-50 vol % of HiC. The presented results add relevant data to optimizing enzyme-based PET recycling technologies.
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Affiliation(s)
- Rodrigo Brackmann
- Chemistry Institute, Rio de Janeiro State University (UERJ), Rua São Francisco Xavier, 524, PHLC, IQ, Sl.310, Rio de Janeiro, RJ CEP 20550-013 Brazil
- Federal University of Technology Paraná (UTFPR), Curitiba, Brazil
| | - Cláudia de Oliveira Veloso
- Chemistry Institute, Rio de Janeiro State University (UERJ), Rua São Francisco Xavier, 524, PHLC, IQ, Sl.310, Rio de Janeiro, RJ CEP 20550-013 Brazil
| | | | - Marta Antunes Pereira Langone
- Chemistry Institute, Rio de Janeiro State University (UERJ), Rua São Francisco Xavier, 524, PHLC, IQ, Sl.310, Rio de Janeiro, RJ CEP 20550-013 Brazil
- Federal Institute of Education, Science, and Technology of Rio de Janeiro (IFRJ), Rio de Janeiro, Brazil
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