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Liu X, Park H, Ackermann YS, Avérous L, Ballerstedt H, Besenmatter W, Blázquez B, Bornscheuer UT, Branson Y, Casey W, de Lorenzo V, Dong W, Floehr T, Godoy MS, Ji Y, Jupke A, Klankermayer J, León DS, Liu L, Liu X, Liu Y, Manoli MT, Martínez-García E, Narancic T, Nogales J, O'Connor K, Osterthun O, Perrin R, Prieto MA, Pollet E, Sarbu A, Schwaneberg U, Su H, Tang Z, Tiso T, Wang Z, Wei R, Welsing G, Wierckx N, Wolter B, Xiao G, Xing J, Zhao Y, Zhou J, Tan T, Blank LM, Jiang M, Chen GQ. Exploring biotechnology for plastic recycling, degradation and upcycling for a sustainable future. Biotechnol Adv 2025; 81:108544. [PMID: 40024585 DOI: 10.1016/j.biotechadv.2025.108544] [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: 12/01/2024] [Revised: 02/19/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
Abstract
The persistent demand for plastic commodities, inadequate recycling infrastructure, and pervasive environmental contamination due to plastic waste present a formidable global challenge. Recycling, degradation and upcycling are the three most important ways to solve the problem of plastic pollution. Sequential enzymatic and microbial degradation of mechanically and chemically pre-treated plastic waste can be orchestrated, followed by microbial conversion into value-added chemicals and polymers through mixed culture systems. Furthermore, plastics-degrading enzymes can be optimized through protein engineering to enhance their specific binding capacities, stability, and catalytic efficiency across a broad spectrum of polymer substrates under challenging high salinity and temperature conditions. Also, the production and formulation of enzyme mixtures can be fine-tuned to suit specific waste compositions, facilitating their effective deployment both in vitro, in vivo and in combination with chemical technologies. Here, we emphasized the comprehensive strategy leveraging microbial processes to transform mixed plastics of fossil-derived polymers such as PP, PE, PU, PET, and PS, most notably polyesters, in conjunction with potential biodegradable alternatives such as PLA and PHA. Any residual material resistant to enzymatic degradation can be reintroduced into the process loop following appropriate physicochemical treatment.
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Affiliation(s)
- Xu Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; PhaBuilder Biotechnology Co. Ltd, Shunyi District, Beijing 101309, China; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing 100084, China; EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M1 7DN, UK
| | | | - Luc Avérous
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Hendrik Ballerstedt
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | | | - Blas Blázquez
- Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Yannick Branson
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - William Casey
- Bioplastech Ltd., Nova UCD, Belfield Innovation Park, University College Dublin, Belfield, Dublin 4, Ireland
| | - Víctor de Lorenzo
- Environmental Synthetic Biology Laboratory, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Tilman Floehr
- Everwave GmbH, Strüverweg 116, 52070 Aachen, Germany
| | - Manuel S Godoy
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - Yu Ji
- Institute of Biotechnology (BIOTEC), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Andreas Jupke
- Fluid Process Engineering, Aachen Process Technology (AVT), RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Jürgen Klankermayer
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - David San León
- Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Luo Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Xianrui Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yizhi Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Maria T Manoli
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - Esteban Martínez-García
- Environmental Synthetic Biology Laboratory, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Tanja Narancic
- BiOrbic Bioeconomy SFI Research Centre, and School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Juan Nogales
- Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Kevin O'Connor
- BiOrbic Bioeconomy SFI Research Centre, and School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Ole Osterthun
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Rémi Perrin
- SOPREMA, Direction R&D, 14 Rue Saint Nazaire, 67100 Strasbourg, France
| | - M Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - Eric Pollet
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Alexandru Sarbu
- SOPREMA, Direction R&D, 14 Rue Saint Nazaire, 67100 Strasbourg, France
| | - Ulrich Schwaneberg
- Institute of Biotechnology (BIOTEC), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Haijia Su
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zequn Tang
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Till Tiso
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Zishuai Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Ren Wei
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Gina Welsing
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Birger Wolter
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Gang Xiao
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jianmin Xing
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering (IPE), Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Beijing 100190, PR China
| | - Yilin Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; State Key Lab of Green Biomanufacturing, Beijing, China.
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Lab of Green Biomanufacturing, Beijing, China.
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Chavez‐Linares P, Hoppe S, Chevalot I. Recycling and Degradation Pathways of Synthetic Textile Fibers such as Polyamide and Elastane. GLOBAL CHALLENGES (HOBOKEN, NJ) 2025; 9:2400163. [PMID: 40255241 PMCID: PMC12003217 DOI: 10.1002/gch2.202400163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2025] [Revised: 01/17/2025] [Indexed: 04/22/2025]
Abstract
Synthetic textile production is a major contributor to global waste growth, a phenomenon exacerbated by population growth and increased consumption. Global fiber production is expected to reach 147 million tons by 2030. New insights into recycling solutions are being developed. For example, progress has been made in recycling fibers such as polyester, including polyethylene terephthalate (PET), through the use of enzymes that can break specific bonds and return the material to its original state. However, this process must be carried out according to the nature of the polymer in question. In addition, the mixing of different synthetic fibers and the use of dyes make it difficult to develop a complete recycling process that separates the fibers and returns them to their original raw material. This review focuses on two types of fibers widely used in the textile industry, Nylon or polyamide (PA) and elastane (Spandex or Lycra), and explores the challenges and opportunities associated with their recycling.
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de Witt J, Luthe T, Wiechert J, Jensen K, Polen T, Wirtz A, Thies S, Frunzke J, Wynands B, Wierckx N. Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida. Nat Microbiol 2025; 10:667-680. [PMID: 39929973 PMCID: PMC11879879 DOI: 10.1038/s41564-025-01929-5] [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: 09/10/2024] [Accepted: 01/08/2025] [Indexed: 03/06/2025]
Abstract
Aliphatic polyamides, or nylons, are widely used in the textile and automotive industry due to their high durability and tensile strength, but recycling rates are below 5%. Chemical recycling of polyamides is possible but typically yields mixtures of monomers and oligomers which hinders downstream purification. Here, Pseudomonas putida KT2440 was engineered to metabolize C6-polyamide monomers such as 6-aminohexanoic acid, ε-caprolactam and 1,6-hexamethylenediamine, guided by adaptive laboratory evolution. Heterologous expression of nylonases also enabled P. putida to metabolize linear and cyclic nylon oligomers derived from chemical polyamide hydrolysis. RNA sequencing and reverse engineering revealed the metabolic pathways for these non-natural substrates. To demonstrate microbial upcycling, the phaCAB operon from Cupriavidus necator was heterologously expressed to enable production of polyhydroxybutyrate (PHB) from PA6 hydrolysates. This study presents a microbial host for the biological conversion, in combination with chemical hydrolysis, of polyamide monomers and mixed polyamids hydrolysates to a value-added product.
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Affiliation(s)
- Jan de Witt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Tom Luthe
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Johanna Wiechert
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Thies
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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Jahanshahi DA, Barzani MRR, Bahram M, Ariaeenejad S, Kavousi K. Metagenomic exploration and computational prediction of novel enzymes for polyethylene terephthalate degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025; 289:117640. [PMID: 39793291 DOI: 10.1016/j.ecoenv.2024.117640] [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: 06/29/2024] [Revised: 12/13/2024] [Accepted: 12/29/2024] [Indexed: 01/13/2025]
Abstract
As a global environmental challenge, plastic pollution raises serious ecological and health concerns owing to the excessive accumulation of plastic waste, which disrupts ecosystems, harms wildlife, and threatens human health. Polyethylene terephthalate (PET), one of the most commonly used plastics, has contributed significantly to this growing crisis. This study offers a solution for plastic pollution by identifying novel PET-degrading enzymes. Using a combined approach of computational analysis and metagenomic workflow, we identified a diverse array of genes and enzymes linked to plastic degradation. Our study identified 1305,282 unmapped genes, 36,000 CAZymes, and 317 plastizymes in the soil samples were heavily contaminated with plastic. We extended our approach by training machine learning models to discover candidate PET-degrading enzymes. To overcome the scarcity of known PET-degrading enzymes, we used a Generative Adversarial Network (GAN) model for dataset augmentation and a pretrained deep Evolutionary Scale Language Model (ESM) to generate sequence embeddings for classification. Finally, 21 novel PET-degrading enzymes were identified. These enzymes were further validated through active site analysis, amino acid composition analysis, and 3D structure comparison. Additionally, we isolated bacterial strains from contaminated soils and extracted plastizymes to demonstrate their potential for environmental remediation. This study highlights the importance of biotechnological solutions for plastic pollution, emphasizing scalable, cost-effective processes and the integration of computational and metagenomic methods.
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Affiliation(s)
- Donya Afshar Jahanshahi
- Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran; Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Mohammad Reza Rezaei Barzani
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005, Tartu, Estonia; Department of Agroecology, Aarhus University, Forsøgsvej 1 4200, Slagelse, Denmark
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Zhang Q, Song J, Wu H, Wang L, Zhuo G, Li H, He S, Pan Y, Liu G. Intratumoral microbiota associates with systemic immune inflammation state in nasopharyngeal carcinoma. Int Immunopharmacol 2024; 141:112984. [PMID: 39173404 DOI: 10.1016/j.intimp.2024.112984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/07/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND The nasopharynx serves as a crucial niche for the microbiome of the upper respiratory tract. However, the association between the intratumoral microbiota and host systemic inflammation and immune status in nasopharyngeal carcinoma (NPC) remain uncertain. METHODS We performed 5R 16S rDNA sequencing on NPC tissue samples, followed by diversity analysis, LEfSe differential analysis, and KEGG functional prediction. The analyses were based on indices such as AISI, SIRI, PAR, PLR, and NAR. Correlation analyses between microbes and these indices were performed to identify microbes associated with inflammation and immune status. Additionally, regression analysis based on tumor TNM stage was performed to identify key microbes linked to tumor progression. The head and neck squamous cell carcinoma (HNSC) transcriptome and the paired HNSC microbiome data from TCGA were utilized to validate the analyses. RESULTS The Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the most enriched phyla in NPC tissues. Microbes within these phyla demonstrated high sensitivity to changes in host systemic inflammation and immune status. Proteobacteria and Firmicutes showed significant differences between inflammation groups. Actinobacteria varied specifically with platelet-related inflammatory indices, and Bacteroidetes genera exhibited significant differences between NAR groups. Corynebacterium and Brevundimonas significantly impacted the T stage of tumors, with a high load of Corynebacterium within tumors associated with a better prognosis CONCLUSION: Our analysis indicates that Proteobacteria play a crucial role in the inflammatory state of NPC, while Bacteroidetes are more sensitive to the tumor immune status.
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Affiliation(s)
- Qian Zhang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Jiangqin Song
- Department of Laboratory Medicine, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Huiqing Wu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Liping Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Guangzheng Zhuo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Huashun Li
- Department of Pathology, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Siyu He
- Department of Laboratory Medicine, The First People's Hospital of Tianmen City, Tianmen, Hubei 431700, China
| | - Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China; Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China.
| | - Guohong Liu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China.
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Guo W, Li D, Zhai Y, Xu X, Qiu H, Miao A, Cao X, Zhao L. Differential interaction modes of As(III)/As(V) with microbial cell membrane induces opposite effects on organic contaminant biodegradation in groundwater. ENVIRONMENT INTERNATIONAL 2024; 193:109074. [PMID: 39426033 DOI: 10.1016/j.envint.2024.109074] [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: 07/13/2024] [Revised: 09/09/2024] [Accepted: 10/10/2024] [Indexed: 10/21/2024]
Abstract
Arsenic, a widespread toxic metalloid in groundwater, derives both from natural geological environment and industrial discharge, is extensively detected to be coexisting with organic contaminants, such as 2,4,6-trichlorophenol (TCP), a prior concerned pollutant. During biological remediation of groundwater, arsenic potentially intervenes microbial behaviors. This study found an opposite interference of arsenic in its two different valences (III and V) on the degradation of TCP by the functional bacteria, Sphingomonas fennica K101. As(III) inhibited TCP degradation in a concentration-dependent manner (from 0.1-10 mg/L), with a maximum inhibition rate of 35.5%, whereas As(V) exhibited promoting effects by 13.8% and 33.2% at 1 mg/L and 10 mg/L, respectively. Employing field emission transmission electron microscopy, quantum chemical calculations, fourier-transform ion cyclotron resonance mass spectrometry and metabolomic analysis, we unveil distinct interactions between cell membranes and arsenic in two valence states. Exposure to As(III) led to significant accumulation of As(III) in the cytoplasm, followed by interaction with intracellular ferritin (ferritin heavy chain 1), releasing iron ions and generating ROS. Subsequently, it induced ferroptosis and disrupted bacterial basal metabolism, thereby inhibiting TCP biodegradation. Oppositely, As(V) bound to a critical component sphingosine and triggered sphingosine polymerization, increasing membrane permeability, which was evidenced by measuring lactate dehydrogenase release. This process facilitated TCP transmembrane permeation by reducing membrane or extracellular secretion resistance. As(V) concurrently upregulated energy metabolism and accelerated TCP degradation. Our study elucidates the influence of prevalent arsenic on biodegradation efficacy, particularly amidst changing redox conditions associated with varying arsenic valences.
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Affiliation(s)
- Wenbo Guo
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Deping Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Zhai
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyun Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aijun Miao
- School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xinde Cao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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Roth S, Gandomkar S, Rossi F, Hall M. Mild hydrolysis of chemically stable valerolactams by a biocatalytic ATP-dependent system fueled by metaphosphate. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2024; 26:4498-4505. [PMID: 38654979 PMCID: PMC11033972 DOI: 10.1039/d3gc04434c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 04/26/2024]
Abstract
Medium-sized 5- and 6-membered ring lactams are molecules with remarkable stability, in contrast to smaller β-lactams. As monomers, they grant access to nylon-4 and nylon-5, which are alternative polyamides to widespread caprolactam-based nylon-6. Chemical hydrolysis of monocyclic γ- and δ-lactams to the corresponding amino acids requires harsh reaction conditions and up to now, no mild (enzymatic) protocol has been reported. Herein, the biocatalytic potential of a pair of heterologously expressed bacterial ATP-dependent oxoprolinases - OplA and OplB - was exploited. Strong activity in the presence of excess of ATP was monitored on δ-valerolactam and derivatives thereof, while trace activity was detected on γ-butyrolactam. An ATP recycling system based on cheap Graham's salt (sodium metaphosphate) and a polyphosphate kinase allowed the use of catalytic amounts of ATP, leading to up to full conversion of 10 mM δ-valerolactam at 30 °C in aqueous medium. Further improvements were obtained by co-expressing OplA and OplB using the pETDuet1 vector, a strategy which enhanced the soluble expression yield and the protein stability. Finally, a range of phosphodonors was investigated in place of ATP. With acetyl phosphate and carbamoyl phosphate, turnover numbers up to 176 were reached, providing hints on a possible mechanism, which was studied by 31P-NMR.
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Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Somayyeh Gandomkar
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Federico Rossi
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- BioHealth, University of Graz Heinrichstrasse 28 8010 Graz Austria
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Jahanshahi DA, Ariaeenejad S, Kavousi K. A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins. Sci Rep 2023; 13:16029. [PMID: 37749380 PMCID: PMC10519993 DOI: 10.1038/s41598-023-43042-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research.
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Affiliation(s)
- Donya Afshar Jahanshahi
- Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Cui D, Cox J, Mejias E, Ng B, Gardinali P, Bagner DM, Quinete N. Evaluating non-targeted analysis methods for chemical characterization of organic contaminants in different matrices to estimate children's exposure. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2023:10.1038/s41370-023-00547-9. [PMID: 37120701 PMCID: PMC10148696 DOI: 10.1038/s41370-023-00547-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Children are vulnerable to environmental exposure of contaminants due to their small size, lack of judgement skills, as well as their proximity to dust, soil, and other environmental sources. A better understanding about the types of contaminants that children are exposed to or how their bodies retain or process these compounds is needed. OBJECTIVE In this study, we have implemented and optimized a methodology based on non-targeted analysis (NTA) to characterize chemicals in dust, soil, urine, and in the diet (food and drinking water) of infant populations. METHODS To evaluate potential toxicological concerns associated with chemical exposure, families with children between 6 months and 6 years of age from underrepresented groups were recruited in the greater Miami area. Samples of soil, indoor dust, food, water, and urine were provided by the caregivers, prepared by different techniques (involving online SPE, ASE, USE, QuEChERs), and analyzed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Data post-processing was performed using the small molecule structure identification software, Compound Discoverer (CD) 3.3, and identified features were plotted using Kendrick mass defect plot and Van Krevelen diagrams to show unique patterns in different samples and regions of anthropogenic compound classifications. RESULTS The performance of the NTA workflow was evaluated using quality control standards in terms of accuracy, precision, selectivity, and sensitivity, with an average of 98.2%, 20.3%, 98.4% and 71.1%, respectively. Sample preparation was successfully optimized for soil, dust, water, food, and urine. A total of 30, 78, 103, 20 and 265 annotated features were frequently identified (detection frequency >80%) in the food, dust, soil, water, and urine samples, respectively. Common features detected in each matrix were prioritized and classified, providing insight on children's exposure to organic contaminants of concern and their potential toxicities. IMPACT STATEMENT Current methods to assess the ingestion of chemicals by children have limitations and are generally restricted by specific classes of targeted organic contaminants of interest. This study offers an innovative approach using non-targeted analysis for the comprehensive screening of organic contaminants that children are exposed to through dust, soil, and diet (drinking water and food).
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Affiliation(s)
- Danni Cui
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Joseph Cox
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Emily Mejias
- Institute of Environment, Florida International University, Miami, FL, USA
- Department of Psychology, Center for Children and Families, Florida International University, Miami, FL, USA
| | - Brian Ng
- Institute of Environment, Florida International University, Miami, FL, USA
- Department of Chemistry and Biochemistry, Florida International University, North Miami, FL, USA
| | - Piero Gardinali
- Institute of Environment, Florida International University, Miami, FL, USA
- Department of Chemistry and Biochemistry, Florida International University, North Miami, FL, USA
| | - Daniel M Bagner
- Department of Psychology, Center for Children and Families, Florida International University, Miami, FL, USA
| | - Natalia Quinete
- Institute of Environment, Florida International University, Miami, FL, USA.
- Department of Chemistry and Biochemistry, Florida International University, North Miami, FL, USA.
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10
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Esikova TZ, Anokhina TO, Suzina NE, Shushkova TV, Wu Y, Solyanikova IP. Characterization of a New Pseudomonas Putida Strain Ch2, a Degrader of Toxic Anthropogenic Compounds Epsilon-Caprolactam and Glyphosate. Microorganisms 2023; 11:microorganisms11030650. [PMID: 36985223 PMCID: PMC10053300 DOI: 10.3390/microorganisms11030650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate (GP) as a sole source of phosphorus. Analysis of the nucleotide sequence of the 16S rRNA gene of Ch2 revealed that the strain belongs to the species Pseudomonas putida. This strain grew in the mineral medium containing CAP in a concentration range of 0.5 to 5.0 g/L and utilized 6-aminohexanoic acid and adipic acid, which are the intermediate products of CAP catabolism. The ability of strain Ch2 to degrade CAP is determined by a conjugative megaplasmid that is 550 kb in size. When strain Ch2 is cultured in a mineral medium containing GP (500 mg/L), more intensive utilization of the herbicide occurs in the phase of active growth. In the phase of declining growth, there is an accumulation of aminomethylphosphonic acid, which indicates that the C-N bond is the first site cleaved during GP degradation (glyphosate oxidoreductase pathway). Culture growth in the presence of GP during the early step of its degradation is accompanied by unique substrate-dependent changes in the cytoplasm, including the formation of vesicles of cytoplasmic membrane consisting of specific electron-dense content. There is a debate about whether these membrane formations are analogous to metabolosomes, where the primary degradation of the herbicide can take place. The studied strain is notable for its ability to produce polyhydroxyalkanoates (PHAs) when grown in mineral medium containing GP. At the beginning of the stationary growth phase, it was shown that, the amount and size of PHA inclusions in the cells drastically increased; they filled almost the entire volume of cell cytoplasm. The obtained results show that the strain P. putida Ch2 can be successfully used for the PHAs’ production. Moreover, the ability of P. putida Ch2 to degrade CAP and GP determines the prospects of its application for the biological cleanup of CAP production wastes and in situ bioremediation of soil polluted with GP.
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Affiliation(s)
- Tatiana Z. Esikova
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana O. Anokhina
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Nataliya E. Suzina
- Laboratory of Cytology of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana V. Shushkova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Yonghong Wu
- Zigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Inna P. Solyanikova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
- Regional Microbiological Center, Institute of Pharmacy, Chemistry and Biology, Belgorod National Research University, 308015 Belgorod, Russia
- Correspondence:
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11
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Epsilon-Caprolactam- and Nylon Oligomer-Degrading Bacterium Brevibacterium epidermidis BS3: Characterization and Potential Use in Bioremediation. Microorganisms 2023; 11:microorganisms11020373. [PMID: 36838338 PMCID: PMC9966071 DOI: 10.3390/microorganisms11020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/16/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
epsilon-Caprolactam (Caprolactam, CAP), a monomer of the synthetic non-degradable polymer nylon-6, is the major wastewater component in the production of caprolactam and nylon-6. Biological treatment of CAP, using microbes could be a potent alternative to the current waste utilization techniques. This work focuses on the characterization and potential use of caprolactam-degrading bacterial strain BS3 isolated from soils polluted by CAP production wastes. The strain was identified as Brevibacterium epidermidis based on the studies of its morphological, physiological, and biochemical properties and 16S rRNA gene sequence analysis. This study is the first to report the ability of Brevibacterium to utilize CAP. Strain BS3 is an alcalo- and halotolerant organism, that grows within a broad range of CAP concentrations, from 0.5 up to 22.0 g/L, optimally at 1.0-2.0 g/L. A caprolactam biodegradation experiment using gas chromatography showed BS3 to degrade 1.0 g/L CAP over 160 h. In contrast to earlier characterized narrow-specific CAP-degrading bacteria, strain BS3 is also capable of utilizing linear nylon oligomers (oligomers of 6-aminohexanoic acid), CAP polymerization by-products, as sole sources of carbon and energy. The broad range of utilized toxic pollutants, the tolerance for high CAP concentrations, as well as the physiological properties of B. epidermidis BS3, determine the prospects of its use for the biological cleanup of CAP and nylon-6 production wastes that contain CAP, 6-aminohexanoic acid, and low molecular weight oligomer fractions.
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12
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Ali SS, Elsamahy T, Abdelkarim EA, Al-Tohamy R, Kornaros M, Ruiz HA, Zhao T, Li F, Sun J. Biowastes for biodegradable bioplastics production and end-of-life scenarios in circular bioeconomy and biorefinery concept. BIORESOURCE TECHNOLOGY 2022; 363:127869. [PMID: 36064080 DOI: 10.1016/j.biortech.2022.127869] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Due to global urbanization, industrialization, and economic development, biowastes generation represents negative consequences on the environment and human health. The use of generated biowastes as a feedstock for biodegradable bioplastic production has opened a new avenue for environmental sustainability from the circular (bio)economy standpoint. Biodegradable bioplastic production can contribute to the sustainability pillars (environmental, economic, and social). Furthermore, bioenergy, biomass, and biopolymers production after recycling of biodegradable bioplastic can help to maintain the energy-environment balance. Several types of biodegradable bioplastic, such as starch-based, polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate, can achieve this aim. In this review, an overview of the main biowastes valorization routes and the main biodegradable bioplastic types of production, application, and biodegradability are discussed to achieve the transition to the circular economy. Additionally, end-of-life scenarios (up-cycle and down-cycle) are reviewed to attain the maximum environmental, social, and economic benefit from biodegradable bioplastic products under biorefinery concept.
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Affiliation(s)
- Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Esraa A Abdelkarim
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece
| | - Héctor A Ruiz
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, Coahuila 25280, Mexico
| | - Tong Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Fanghua Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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13
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Zhao S, Pan C, Zhao J, Du H, Li M, Yu H, Chen X. Quantitative proteomic analysis of the microbial degradation of 3-aminobenzoic acid by Comamonas sp. QT12. Sci Rep 2022; 12:17609. [PMID: 36266292 PMCID: PMC9584955 DOI: 10.1038/s41598-022-17570-9] [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: 02/14/2022] [Accepted: 07/27/2022] [Indexed: 01/13/2023] Open
Abstract
A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to 3-aminobenzoic acid remains unclear. In this study, label-free quantitative proteome analysis based on LC-MS/MS was used to study the protein expression difference of strain QT12 under the condition of using 3AB (3AB) and citric acid/ammonium chloride as substrates (3ABCon). A total of 2068 proteins were identified, of which 239 were significantly up-regulated in 3AB group, 124 were significantly down-regulated in 3AB group, 624 were expressed only in 3AB group, and 216 were expressed only in 3ABCon group in 3AB group. KEGG pathway analysis found that 83 pathways were up-regulated and 49 pathways were down-regulated, In GO analysis, 315 paths were up-regulated and 156 paths were down-regulated. There were 6 genes in the mab cluster that were only detected in the 3AB group.The mab cluster was found to be related to degradation of 3AB. By knockout, it was found that the growth rate of the mutant △orf7 and △orf9 were slowed down. HPLC results showed that the mutant △orf7 and △orf9 could still degrade 3AB, it was found that orf7, orf9 were not key genes about 3AB degradation and they could be replaced by other genes in strain QT12. These findings improve our understanding of the molecular mechanisms underlying the cellular response of 3AB degradation in Comamonas bacterium.
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Affiliation(s)
- Shuxue Zhao
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China ,grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Chao Pan
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Junxing Zhao
- Qingdao Water Administration Bureau, Qingdao, 266071 China
| | - Haiyan Du
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Min Li
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Hao Yu
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Xi Chen
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
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14
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Lopes AR, Bunin E, Viana AT, Froufe H, Muñoz-Merida A, Pinho D, Figueiredo J, Barroso C, Vaz-Moreira I, Bellanger X, Egas C, Nunes OC. In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T. Sci Rep 2022; 12:15502. [PMID: 36109598 PMCID: PMC9477822 DOI: 10.1038/s41598-022-18732-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Abstract
Gulosibacter molinativorax ON4T is the only known organism to produce molinate hydrolase (MolA), which catalyses the breakdown of the thiocarbamate herbicide into azepane-1-carboxylic acid (ACA) and ethanethiol. A combined genomic and transcriptomic strategy was used to fully characterize the strain ON4T genome, particularly the molA genetic environment, to identify the potential genes encoding ACA degradation enzymes. Genomic data revealed that molA is the only catabolic gene of a novel composite transposon (Tn6311), located in a novel low copy number plasmid (pARLON1) harbouring a putative T4SS of the class FATA. pARLON1 had an ANI value of 88.2% with contig 18 from Agrococcus casei LMG 22410T draft genome. Such results suggest that pARLON1 is related to genomic elements of other Actinobacteria, although Tn6311 was observed only in strain ON4T. Furthermore, genomic and transcriptomic data demonstrated that the genes involved in ACA degradation are chromosomal. Based on their overexpression when growing in the presence of molinate, the enzymes potentially involved in the heterocyclic ring breakdown were predicted. Among these, the activity of a protein related to caprolactone hydrolase was demonstrated using heterologous expression. However, further studies are needed to confirm the role of the other putative enzymes.
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15
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Tiso T, Winter B, Wei R, Hee J, de Witt J, Wierckx N, Quicker P, Bornscheuer UT, Bardow A, Nogales J, Blank LM. The metabolic potential of plastics as biotechnological carbon sources - Review and targets for the future. Metab Eng 2021; 71:77-98. [PMID: 34952231 DOI: 10.1016/j.ymben.2021.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022]
Abstract
The plastic crisis requires drastic measures, especially for the plastics' end-of-life. Mixed plastic fractions are currently difficult to recycle, but microbial metabolism might open new pathways. With new technologies for degradation of plastics to oligo- and monomers, these carbon sources can be used in biotechnology for the upcycling of plastic waste to valuable products, such as bioplastics and biosurfactants. We briefly summarize well-known monomer degradation pathways and computed their theoretical yields for industrially interesting products. With this information in hand, we calculated replacement scenarios of existing fossil-based synthesis routes for the same products. Thereby, we highlight fossil-based products for which plastic monomers might be attractive alternative carbon sources. Notably, not the highest yield of product on substrate of the biochemical route, but rather the (in-)efficiency of the petrochemical routes (i.e., carbon, energy use) determines the potential of biochemical plastic upcycling. Our results might serve as a guide for future metabolic engineering efforts towards a sustainable plastic economy.
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Affiliation(s)
- Till Tiso
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Benedikt Winter
- Energy & Process Systems Engineering, ETH Zurich, Zurich, Switzerland; Institute of Technical Thermodynamics, RWTH Aachen University, Germany
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Johann Hee
- Unit of Technology of Fuels, RWTH Aachen University, Aachen, Germany
| | - Jan de Witt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Peter Quicker
- Unit of Technology of Fuels, RWTH Aachen University, Aachen, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - André Bardow
- Energy & Process Systems Engineering, ETH Zurich, Zurich, Switzerland; Institute of Technical Thermodynamics, RWTH Aachen University, Germany; Institute of Energy and Climate Research (IEK 10), Research Center Jülich GmbH, Germany
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany.
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16
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Marjanovic A, Rozeboom HJ, de Vries MS, Mayer C, Otzen M, Wijma HJ, Janssen DB. Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. Proteins 2021; 89:1079-1098. [PMID: 33826169 PMCID: PMC8453981 DOI: 10.1002/prot.26082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0 '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αβ)2 tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.
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Affiliation(s)
- Antonija Marjanovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Meintje S. de Vries
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Clemens Mayer
- Biomolecular Chemistry and Catalysis, Stratingh Institute for ChemistryUniversity of GroningenGroningenThe Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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17
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Zhao S, Chen X, Sun Q, Wang F, Hu C, Guo L, Bai J, Yu H. Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1. Front Microbiol 2021; 12:694874. [PMID: 34447357 PMCID: PMC8383072 DOI: 10.3389/fmicb.2021.694874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.
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Affiliation(s)
- Shuxue Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xi Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qianshu Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fei Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Hu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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18
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Mindubaev AZ, Babynin EV, Bedeeva EK, Minzanova ST, Mironova LG, Akosah YA. Biological Degradation of Yellow (White) Phosphorus, a Compound of First Class Hazard. RUSS J INORG CHEM+ 2021. [DOI: 10.1134/s0036023621080155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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García-Depraect O, Bordel S, Lebrero R, Santos-Beneit F, Börner RA, Börner T, Muñoz R. Inspired by nature: Microbial production, degradation and valorization of biodegradable bioplastics for life-cycle-engineered products. Biotechnol Adv 2021; 53:107772. [PMID: 34015389 DOI: 10.1016/j.biotechadv.2021.107772] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/01/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
The global environmental pollution by micro- and macro-plastics reveals the consequences of an extensive use of recalcitrant plastic products together with inappropriate waste management practices that fail to sufficiently recycle the broad types of conventional plastic waste. Biobased and biodegradable plastics are experiencing an uprising as their properties offer alternative waste management solutions for a more circular material economy. However, although the production of such bioplastics has advanced on scale, the end-of-life (EOL) (bio)technologies to promote circularity are lacking behind. While composting and biogas plants are the only managed EOL options today, advanced biotechnological recycling technologies for biodegradable bioplastics are still in an embryonic stage. Thus, developing efficient biotechnologies capable of transforming bioplastic waste into high-value chemical building blocks or into the constituents of the original polymer offers promising routes towards life-cycle-engineered products. This review aims at providing a comprehensive state-of-the-art overview of microbial-based processes involved in the complete lifecycle of bioplastics. The current trends in the bioplastic market, the beginning and EOL scenarios of bioplastics, and a critical discussion on the key factors and mechanisms governing microbial degradation are systematically presented. Also, a critical evaluation of terminology and international standards to quantify polymer biodegradability is provided together with the latest biotechnological recycling strategies, including the use of different pre-treatments for (bio)plastic waste. Finally, the challenges and future perspectives for the development of life-cycle-engineered biobased and biodegradable plastic products are discussed.
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Affiliation(s)
- Octavio García-Depraect
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Sergio Bordel
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Raquel Lebrero
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Fernando Santos-Beneit
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Rosa Aragão Börner
- Nestlé Research, Société des Produits Nestlé S.A, Route du Jorat 57, 1000 Lausanne, Switzerland
| | - Tim Börner
- Nestlé Research, Société des Produits Nestlé S.A, Route du Jorat 57, 1000 Lausanne, Switzerland.
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain.
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20
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Asymmetric Synthesis of Optically Pure Aliphatic Amines with an Engineered Robust ω-Transaminase. Catalysts 2020. [DOI: 10.3390/catal10111310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The production of chiral amines by transaminase-catalyzed amination of ketones is an important application of biocatalysis in synthetic chemistry. It requires transaminases that show high enantioselectivity in asymmetric conversion of the ketone precursors. A robust derivative of ω-transaminase from Pseudomonasjessenii (PjTA-R6) that naturally acts on aliphatic substrates was constructed previously by our group. Here, we explore the catalytic potential of this thermostable enzyme for the synthesis of optically pure aliphatic amines and compare it to the well-studied transaminases from Vibrio fluvialis (VfTA) and Chromobacterium violaceum (CvTA). The product yields indicated improved performance of PjTA-R6 over the other transaminases, and in most cases, the optical purity of the produced amine was above 99% enantiomeric excess (e.e.). Structural analysis revealed that the substrate binding poses were influenced and restricted by the switching arginine and that this accounted for differences in substrate specificities. Rosetta docking calculations with external aldimine structures showed a correlation between docking scores and synthetic yields. The results show that PjTA-R6 is a promising biocatalyst for the asymmetric synthesis of aliphatic amines with a product spectrum that can be explained by its structural features.
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21
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Thompson MG, Pearson AN, Barajas JF, Cruz-Morales P, Sedaghatian N, Costello Z, Garber ME, Incha MR, Valencia LE, Baidoo EEK, Martin HG, Mukhopadhyay A, Keasling JD. Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida. ACS Synth Biol 2020; 9:53-62. [PMID: 31841635 DOI: 10.1021/acssynbio.9b00292] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Caprolactam is an important polymer precursor to nylon traditionally derived from petroleum and produced on a scale of 5 million tons per year. Current biological pathways for the production of caprolactam are inefficient with titers not exceeding 2 mg/L, necessitating novel pathways for its production. As development of novel metabolic routes often require thousands of designs and result in low product titers, a highly sensitive biosensor for the final product has the potential to rapidly speed up development times. Here we report a highly sensitive biosensor for valerolactam and caprolactam from Pseudomonas putida KT2440 which is >1000× more sensitive to an exogenous ligand than previously reported sensors. Manipulating the expression of the sensor oplR (PP_3516) substantially altered the sensing parameters, with various vectors showing Kd values ranging from 700 nM (79.1 μg/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detect in vivo production of caprolactam above background at ∼6 μg/L. The high sensitivity and range of OplR is a powerful tool toward the development of novel routes to the biological synthesis of caprolactam.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jesus F. Barajas
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios superiores de Monterrey, Monterrey, 64849, Mexico
| | - Nima Sedaghatian
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Megan E. Garber
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Comparative Biochemistry Graduate Group, University of California, Berkeley, California United States
| | - Matthew R. Incha
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Luis E. Valencia
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Comparative Biochemistry Graduate Group, University of California, Berkeley, California United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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22
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Thompson MG, Valencia LE, Blake-Hedges JM, Cruz-Morales P, Velasquez AE, Pearson AN, Sermeno LN, Sharpless WA, Benites VT, Chen Y, Baidoo EE, Petzold CJ, Deutschbauer AM, Keasling JD. Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer. Metab Eng Commun 2019; 9:e00098. [PMID: 31720214 PMCID: PMC6838509 DOI: 10.1016/j.mec.2019.e00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/13/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas putida is a promising bacterial chassis for metabolic engineering given its ability to metabolize a wide array of carbon sources, especially aromatic compounds derived from lignin. However, this omnivorous metabolism can also be a hindrance when it can naturally metabolize products produced from engineered pathways. Herein we show that P. putida is able to use valerolactam as a sole carbon source, as well as degrade caprolactam. Lactams represent important nylon precursors, and are produced in quantities exceeding one million tons per year (Zhang et al., 2017). To better understand this metabolism we use a combination of Random Barcode Transposon Sequencing (RB-TnSeq) and shotgun proteomics to identify the oplBA locus as the likely responsible amide hydrolase that initiates valerolactam catabolism. Deletion of the oplBA genes prevented P. putida from growing on valerolactam, prevented the degradation of valerolactam in rich media, and dramatically reduced caprolactam degradation under the same conditions. Deletion of oplBA, as well as pathways that compete for precursors L-lysine or 5-aminovalerate, increased the titer of valerolactam from undetectable after 48 h of production to ~90 mg/L. This work may serve as a template to rapidly eliminate undesirable metabolism in non-model hosts in future metabolic engineering efforts.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Luis E. Valencia
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, CA, 94720, USA
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios Superiores de Monterrey, Mexico
| | - Alexandria E. Velasquez
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lauren N. Sermeno
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William A. Sharpless
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Veronica T. Benites
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E.K. Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam M. Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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23
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Baxi NN, Patel S, Hansoti D. An Arthrobacter citreus strain suitable for degrading ε-caprolactam in polyamide waste and accumulation of glutamic acid. AMB Express 2019; 9:161. [PMID: 31605246 PMCID: PMC6789059 DOI: 10.1186/s13568-019-0887-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022] Open
Abstract
ε-Caprolactam-a toxic xenobiotic compound present in industrial polyamide waste was found to be degraded by caprolactam-degrading bacteria. Arthrobacter citreus was able to utilize up to 20 g ε-caprolactam/l as the sole source of carbon more efficiently as compared to the other Gram positive caprolactam-degrading bacteria Rhodococcus rhodochrous and Bacillus sphaericus. The cells of A. citreus remained viable in medium up to 40 g caprolactam/l. The degradation of 10 g caprolactam/l by A. citreus, when supplied as the sole source of carbon and nitrogen lead to the formation of 6-aminocaproic acid which was detected in broth and there was also an increase in the ammonium content. One of the other metabolites found to consistently accumulate in extracellular medium during the utilization of caprolactam by A. citreus was glutamic acid, though not reported in case of other caprolactam-degrading bacteria. A. citreus could metabolise caprolactam to form non toxic products such as 6-aminocaproic acid and glutamic acid which are amino acids of physiological and commercial importance. In the presence of 6-aminocaproic acid, the rate of caprolactam utilization by A. citreus was decreased but not inhibited and the viable count of cells was found to increase using both the substrates simultaneously. A. citreus was also suitable for degradation of caprolactam in presence of low phosphate as prevalent in soil, and in sterile soil without the supplementation of any other carbon or nitrogen, as well as in native non sterile soil where other microorganisms are present.
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24
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Samson R, Shah M, Yadav R, Sarode P, Rajput V, Dastager SG, Dharne MS, Khairnar K. Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:288-299. [PMID: 31005831 DOI: 10.1016/j.scitotenv.2019.04.166] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Manan Shah
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Priyanka Sarode
- Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Syed G Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India.
| | - Krishna Khairnar
- Academy of Scientific and Industrial Research (AcSIR), New Delhi, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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25
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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26
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Zhang D, Ji X, Meng Z, Qi W, Qiao K. Effects of fumigation with 1,3-dichloropropene on soil enzyme activities and microbial communities in continuous-cropping soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:730-736. [PMID: 30502523 DOI: 10.1016/j.ecoenv.2018.11.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
The compound 1,3-D (1,3-dichloropropene) is a potential candidate soil fumigant due to the restrictions on methyl bromide (MB). To date, little is known about the soil microbial community changes induced by 1,3-D fumigation. Therefore, soil properties, related soil enzymes, genes encoding the key enzymes of ammonia oxidation in both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and bacterial diversity were investigated to assess the effects of 1,3-D fumigation on the soil microbial community. The results exhibited that fumigation with 1,3-D caused accumulation of NH4+-N, but it led to decrease in the rate of NO3--N, and the concentration of NO3--N gradually recovered. At 12 weeks after transplant (WAT) of tomato seedlings, the concentration of NH4+-N and NO3--N were not statistically significant between the 1,3-D treatment groups and the untreated control group. A similar tendency was found for organic matter, soil pH, urease and protease activities. Moreover, quantitative real-time PCR (qPCR) showed that 1,3-D decreased total bacterial abundance, AOA-amoA and AOB-amoA genes. In addition, Illumina MiSeq sequencing analysis revealed that soil bacterial community diversities were significantly reduced at earlier sampling time points, and at later sampling time points, soil bacterial diversity gradually recovered, there was no significant difference compared to the control group. The present study provides useful information to evaluate the environmental safety of 1,3-D.
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Affiliation(s)
- Dianli Zhang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Xiaoxue Ji
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Zhen Meng
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Wenzhe Qi
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China
| | - Kang Qiao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong 271018, People's Republic of China.
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27
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Detheridge AP, Griffith GW, Hopper DJ. Genome Sequence Analysis of Two Pseudomonas putida Strains to Identify a 17-Hydroxylase Putatively Involved in Sparteine Degradation. Curr Microbiol 2018; 75:1649-1654. [PMID: 30267141 PMCID: PMC6208669 DOI: 10.1007/s00284-018-1573-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/29/2018] [Indexed: 11/28/2022]
Abstract
Two strains of Pseudomonas putida, Psp-LUP and Psp-SPAR, capable of growth on the quinolizidine alkaloids, lupanine and sparteine respectively, were studied here. We report the isolation of Psp-SPAR and the complete genome sequencing of both bacteria. Both were confirmed to belong to P. putida, Psp-LUP close to the type isolate of the species (NBRC14164T) and Psp-SPAR close to strains KT2440 and F1. Psp-SPAR did not grow on lupanine but did contain a gene encoding a putative quinolizidine-17-hydroxylase peptide which exhibited high similarity (76%identity) to the lupanine-17-hydroxylase characterised from Psp-LUP.
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Affiliation(s)
- Andrew P Detheridge
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK
| | - Gareth W Griffith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK.
| | - David J Hopper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK
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