1
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Maday SDM, Kingsbury JM, Weaver L, Pantos O, Wallbank JA, Doake F, Masterton H, Hopkins M, Dunlop R, Gaw S, Theobald B, Risani R, Abbel R, Smith D, Handley KM, Lear G. Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant. Appl Environ Microbiol 2024:e0071524. [PMID: 39329490 DOI: 10.1128/aem.00715-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.
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Affiliation(s)
- Stefan D M Maday
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanne M Kingsbury
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Olga Pantos
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Jessica A Wallbank
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Fraser Doake
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Hayden Masterton
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Maisie Hopkins
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rosa Dunlop
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sally Gaw
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | | | | | | | | | - Kim M Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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2
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Dar MA, Xie R, Zabed HM, Pawar KD, Dhole NP, Sun J. Current paradigms and future challenges in harnessing gut bacterial symbionts of insects for biodegradation of plastic wastes. INSECT SCIENCE 2024. [PMID: 38990171 DOI: 10.1111/1744-7917.13417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024]
Abstract
The ubiquitous incorporation of plastics into daily life, coupled with inefficient recycling practices, has resulted in the accumulation of millions of metric tons of plastic waste, that poses a serious threat to the Earth's sustainability. Plastic pollution, a global problem, disrupts the ecological balance and endangers various life forms. Efforts to combat plastic pollution are underway, with a promising avenue being biological degradation facilitated by certain insects and their symbiotic gut microorganisms, particularly bacteria. This review consolidates existing knowledge on plastic degradation by insects and their influence on gut microbiota. Additionally, it delves into the potential mechanisms employed by insects in symbiosis with gut bacteria, exploring the bioconversion of waste plastics into value-added biodegradable polymers through mineralization. These insights hold significant promise for the bio-upcycling of plastic waste, opening new horizons for future biomanufacturing of high-value chemicals from plastic-derived compounds. Finally, we weigh the pros and cons of future research endeavors related to the bioprospection of plastic-degrading bacteria from underexplored insect species. We also underscore the importance of bioengineering depolymerases with novel characteristics, aiming for their application in the remediation and valorization of waste plastics.
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Affiliation(s)
- Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, India
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Hossain M Zabed
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Kiran D Pawar
- School of Nanoscience and Biotechnology, Shivaji University, Vidyanagar, Kolhapur, Maharashtra, India
| | - Neeraja P Dhole
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, India
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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3
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Klauer RR, Hansen DA, Wu D, Monteiro LMO, Solomon KV, Blenner MA. Biological Upcycling of Plastics Waste. Annu Rev Chem Biomol Eng 2024; 15:315-342. [PMID: 38621232 DOI: 10.1146/annurev-chembioeng-100522-115850] [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] [Indexed: 04/17/2024]
Abstract
Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non-polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.
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Affiliation(s)
- Ross R Klauer
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - D Alex Hansen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Derek Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | | | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Mark A Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
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4
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Yu H, Liu X, Qiu X, Sun T, Cao J, Lv M, Sui Z, Wang Z, Jiao S, Xu Y, Wang F. Discrepant soil microbial community and C cycling function responses to conventional and biodegradable microplastics. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134176. [PMID: 38569347 DOI: 10.1016/j.jhazmat.2024.134176] [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: 01/10/2024] [Revised: 03/14/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Biodegradable microplastics (MPs) are promising alternatives to conventional MPs and are of high global concern. However, their discrepant effects on soil microorganisms and functions are poorly understood. In this study, polyethylene (PE) and polylactic acid (PLA) MPs were selected to investigate the different effects on soil microbiome and C-cycling genes using high-throughput sequencing and real-time quantitative PCR, as well as the morphology and functional group changes of MPs, using scanning electron microscopy and Fourier transform infrared spectroscopy, and the driving factors were identified. The results showed that distinct taxa with potential for MP degradation and nitrogen cycling were enriched in soils with PLA and PE, respectively. PLA, smaller size (150-180 µm), and 5% (w/w) of MPs enhanced the network complexity compared with PE, larger size (250-300 µm), and 1% (w/w) of MPs, respectively. PLA increased β-glucosidase by up to 2.53 times, while PE (150-180 µm) reduced by 38.26-44.01% and PE (250-300 µm) increased by 19.00-22.51% at 30 days. Amylase was increased by up to 5.83 times by PLA (150-180 µm) but reduced by 40.26-62.96% by PLA (250-300 µm) and 16.11-43.92% by PE. The genes cbbL, cbhI, abfA, and Lac were enhanced by 37.16%- 1.99 times, 46.35%- 26.46 times, 8.41%- 69.04%, and 90.81%- 5.85 times by PLA except for PLA1B/5B at 30 days. These effects were associated with soil pH, NO3--N, and MP biodegradability. These findings systematically provide an understanding of the impact of biodegradable MPs on the potential for global climate change.
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Affiliation(s)
- Hui Yu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Xin Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Xiaoguo Qiu
- Shandong Provincial Eco-Environment Monitoring Center, Jinan 250101, China
| | - Tao Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Jianfeng Cao
- Taian Ecological Environment Monitoring Center of Shandong Province, Taian 271000, China
| | - Ming Lv
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Zhiyuan Sui
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Zhizheng Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Shuying Jiao
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yuxin Xu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China.
| | - Fenghua Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian 271018, Shandong, China.
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5
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Tournier V, Duquesne S, Guillamot F, Cramail H, Taton D, Marty A, André I. Enzymes' Power for Plastics Degradation. Chem Rev 2023; 123:5612-5701. [PMID: 36916764 DOI: 10.1021/acs.chemrev.2c00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.
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Affiliation(s)
- Vincent Tournier
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Sophie Duquesne
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Frédérique Guillamot
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Henri Cramail
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Daniel Taton
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Alain Marty
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
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6
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Negoro S, Shibata N, Kato DI, Tanaka Y, Yasuhira K, Nagai K, Oshima S, Furuno Y, Yokoyama R, Miyazaki K, Takeo M, Hengphasatporn K, Shigeta Y, Lee YH, Higuchi Y. X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase. FEBS J 2023. [PMID: 36799721 DOI: 10.1111/febs.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/18/2023]
Abstract
Nylon hydrolase (NylC), a member of the N-terminal nucleophile (Ntn) hydrolase superfamily, is responsible for the degradation of various aliphatic nylons, including nylon-6 and nylon-66. NylC is initially expressed as an inactive precursor (36 kDa), but the precursor is autocatalytically cleaved at Asn266/Thr267 to generate an active enzyme composed of 27 and 9 kDa subunits. We isolated various mutants with amino acid changes at the catalytic centre. X-ray crystallographic analysis revealed that the NylC precursor forms a doughnut-shaped quaternary structure composed of four monomers (molecules A-D) with D2 symmetry. Catalytic residues in the precursor are covered by loop regions at the A/B interface (equivalent to the C/D interface). However, the catalytic residues are exposed to the solvent environment through autocleavage followed by movements of the loop regions. T267A, D306A and D308A mutations resulted in a complete loss of autocleavage. By contrast, in the T267S mutant, autocleavage proceeded slowly at a constant reaction rate (k = 2.8 × 10-5 s-1 ) until complete conversion, but the reaction was inhibited by K189A and N219A mutations. Based on the crystallographic and molecular dynamic simulation analyses, we concluded that the Asp308-Asp306-Thr267 triad, resembling the Glu-Ser-Ser triad conserved in Ntn-hydrolase family enzymes, is responsible for autocleavage and that hydrogen-bonding networks connecting Thr267 with Lys189 and Asn219 are required for increasing the nucleophilicity of Thr267-OH in both the water accessible and water inaccessible systems. Furthermore, we determined that NylC employs the Asp308-Asp306-Thr267 triad as catalytic residues for substrate hydrolysis, but the reaction requires Lys189 and Tyr146 as additional catalytic/substrate-binding residues specific for nylon hydrolysis.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yusuke Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Shohei Oshima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yoko Furuno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Risa Yokoyama
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kaito Miyazaki
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | | | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Suita, Japan.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju-si, South Korea.,Bio-Analytical Science, University of Science and Technology, Daejeon, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
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7
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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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8
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Rapid biodegradation of high molecular weight semi-crystalline polylactic acid at ambient temperature via enzymatic and alkaline hydrolysis by a defined bacterial consortium. Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
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10
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Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A. Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus
Agromyces
. The type strain with the highest pairwise similarity was
Agromyces marinus
H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus
Agromyces
, and only
Agromyces atrinae
P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus
Agromyces
indicated that G127ATT represented a previously undescribed species of the genus
Agromyces
. Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus
Agromyces
. The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus
Agromyces
, for which we propose the name Agromyces archimandritae sp. nov.
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Maite Ortúzar
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Martha E. Trujillo
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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11
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Bhatt P, Pathak VM, Bagheri AR, Bilal M. Microplastic contaminants in the aqueous environment, fate, toxicity consequences, and remediation strategies. ENVIRONMENTAL RESEARCH 2021; 200:111762. [PMID: 34310963 DOI: 10.1016/j.envres.2021.111762] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Microplastic is a fragmented plastic part that emerges as a potential marine and terrestrial contaminant. The microplastic wastes in marine and soil environments cause severe problems in living systems. Microplastic wastes have been linked to various health problems, including reproductive harm and obesity, plus issues such as organ problems and developmental delays in children. Recycling plastic/microplastics from the environment is very low, so remediating these polymers after their utilization is of paramount concern. The microplastic causes severe toxic effects and contaminates the environment. Microplastic affects marine life, microorganism in soil, soil enzymes, plants system, and physicochemical properties. Ecotoxicology of the microplastic raised many questions about its use and development from the environment. Various physicochemical and microbial technologies have been developed for their remediation from the environment. The microplastic effects are linked with its concentration, size, and shape in contaminated environments. Microplastic is able to sorb the inorganic and organic contaminants and affect their fate into the contaminated sites. Microbial technology is considered safer for the remediation of the microplastics via its unique metabolic machinery. Bioplastic is regarded as safer and eco-friendly as compared to plastics. The review article explored an in-depth understanding of the microplastic, its fate, toxicity to the environment, and robust remediation strategies.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingman Modern Agriculture, Guangzhou, 510642, China.
| | - Vinay Mohan Pathak
- Department of Microbiology, University of Delhi, South Campus, New Delhi, 110021, India; Department of Botany and Microbiology, Gurukul Kangri (Deemed to University), Haridwar, Uttarakhand, 249404, India
| | | | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
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Amobonye A, Bhagwat P, Singh S, Pillai S. Plastic biodegradation: Frontline microbes and their enzymes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143536. [PMID: 33190901 DOI: 10.1016/j.scitotenv.2020.143536] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 05/07/2023]
Abstract
Plastic polymers with different properties have been developed in the last 150 years to replace materials such as wood, glass and metals across various applications. Nevertheless, the distinct properties which make plastic desirable for our daily use also threaten our planet's sustainability. Plastics are resilient, non-reactive and most importantly, non-biodegradable. Hence, there has been an exponential increase in plastic waste generation, which has since been recognised as a global environmental threat. Plastic wastes have adversely affected life on earth, primarily through their undesirable accumulation in landfills, leaching into the soil, increased greenhouse gas emission, etc. Even more damaging is their impact on the aquatic ecosystems as they cause entanglement, ingestion and intestinal blockage in aquatic animals. Furthermore, plastics, especially in the microplastic form, have also been found to interfere with chemical interaction between marine organisms, to cause intrinsic toxicity by leaching, and by absorbing persistent organic contaminants as well as pathogens. The current methods for eliminating these wastes (incineration, landfilling, and recycling) come at massive costs, are unsustainable, and put more burden on our environment. Thus, recent focus has been placed more on the potential of biological systems to degrade synthetic plastics. In this regard, some insects, bacteria and fungi have been shown to ingest these polymers and convert them into environmentally friendly carbon compounds. Hence, in the light of recent literature, this review emphasises the multifaceted roles played by microorganisms in this process. The current understanding of the roles played by actinomycetes, algae, bacteria, fungi and their enzymes in enhancing the degradation of synthetic plastics are reviewed, with special focus on their modes of action and probable enzymatic mechanisms. Besides, key areas for further exploration, such as the manipulation of microorganisms through molecular cloning, modification of enzymatic characteristics and metabolic pathway design, are also highlighted.
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Affiliation(s)
- Ayodeji Amobonye
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
| | - Prashant Bhagwat
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
| | - Suren Singh
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
| | - Santhosh Pillai
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
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Lear G, Kingsbury JM, Franchini S, Gambarini V, Maday SDM, Wallbank JA, Weaver L, Pantos O. Plastics and the microbiome: impacts and solutions. ENVIRONMENTAL MICROBIOME 2021; 16:2. [PMID: 33902756 PMCID: PMC8066485 DOI: 10.1186/s40793-020-00371-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/28/2020] [Indexed: 05/12/2023]
Abstract
Global plastic production has increased exponentially since manufacturing commenced in the 1950's, including polymer types infused with diverse additives and fillers. While the negative impacts of plastics are widely reported, particularly on marine vertebrates, impacts on microbial life remain poorly understood. Plastics impact microbiomes directly, exerting toxic effects, providing supplemental carbon sources and acting as rafts for microbial colonisation and dispersal. Indirect consequences include increased environmental shading, altered compositions of host communities and disruption of host organism or community health, hormone balances and immune responses. The isolation and application of plastic-degrading microbes are of substantial interest yet little evidence supports the microbial biodegradation of most high molecular weight synthetic polymers. Over 400 microbial species have been presumptively identified as capable of plastic degradation, but evidence for the degradation of highly prevalent polymers including polypropylene, nylon, polystyrene and polyvinyl chloride must be treated with caution; most studies fail to differentiate losses caused by the leaching or degradation of polymer monomers, additives or fillers. Even where polymer degradation is demonstrated, such as for polyethylene terephthalate, the ability of microorganisms to degrade more highly crystalline forms of the polymer used in commercial plastics appears limited. Microbiomes frequently work in conjunction with abiotic factors such as heat and light to impact the structural integrity of polymers and accessibility to enzymatic attack. Consequently, there remains much scope for extremophile microbiomes to be explored as a source of plastic-degrading enzymes and microorganisms. We propose a best-practice workflow for isolating and reporting plastic-degrading taxa from diverse environmental microbiomes, which should include multiple lines of evidence supporting changes in polymer structure, mass loss, and detection of presumed degradation products, along with confirmation of microbial strains and enzymes (and their associated genes) responsible for high molecular weight plastic polymer degradation. Such approaches are necessary for enzymatic degraders of high molecular weight plastic polymers to be differentiated from organisms only capable of degrading the more labile carbon within predominantly amorphous plastics, plastic monomers, additives or fillers.
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Affiliation(s)
- G Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand.
| | - J M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
| | - S Franchini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - V Gambarini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - S D M Maday
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - J A Wallbank
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - L Weaver
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
| | - O Pantos
- Institute of Environmental Science and Research, 27 Creyke Rd, Ilam, Christchurch, 8041, New Zealand
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Gatz-Schrupp J, Deckard P, Hufford B, Ly S, Tupa P, Masuda H. Isolation and genomic analysis of 11-aminoundecanoic acid-degrading bacterium Pseudomonas sp. JG-B from nylon 11 enrichment culture. J Genomics 2020; 8:16-20. [PMID: 32064005 PMCID: PMC7019077 DOI: 10.7150/jgen.42095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/02/2020] [Indexed: 11/05/2022] Open
Abstract
Nylon 11 is a polymer synthesized from 11-aminoundecanoic acid, and widely used in commercial manufacturing. In this study, we describe the isolation of the first organism capable of metabolizing 11-aminoundecanoic acid from nylon 11 enrichment culture. The strain shows rapid growth on 11-aminoundecanoic acid as a sole source of carbon, nitrogen, and energy. Furthermore, the genome sequence of strain JG-B was deciphered and shown to belong to genus Pseudomonas. Many genes encoding putative extracellular hydrolases, as well as homologues of nylon 6 hydrolases (NylB and NylA) were identified, suggesting the metabolic versatility and possibility that this organism could also depolymerase nylon 11 polymers.
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15
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Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase. Sci Rep 2018; 8:9725. [PMID: 29950566 PMCID: PMC6021441 DOI: 10.1038/s41598-018-27860-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nylon hydrolase (NylC) is initially expressed as an inactive precursor (36 kDa). The precursor is cleaved autocatalytically at Asn266/Thr267 to generate an active enzyme composed of an α subunit (27 kDa) and a β subunit (9 kDa). Four αβ heterodimers (molecules A-D) form a doughnut-shaped quaternary structure. In this study, the thermostability of the parental NylC was altered by amino acid substitutions located at the A/D interface (D122G/H130Y/D36A/L137A) or the A/B interface (E263Q) and spanned a range of 47 °C. Considering structural, biophysical, and biochemical analyses, we discuss the structural basis of the stability of nylon hydrolase. From the analytical centrifugation data obtained regarding the various mutant enzymes, we conclude that the assembly of the monomeric units is dynamically altered by the mutations. Finally, we propose a model that can predict whether the fate of the nascent polypeptide will be correct subunit assembly, inappropriate protein-protein interactions causing aggregation, or intracellular degradation of the polypeptide.
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Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate. Appl Microbiol Biotechnol 2017; 102:801-814. [DOI: 10.1007/s00253-017-8657-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
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17
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Draft Genome Sequence of the Nylon Oligomer-Degrading Bacterium Arthrobacter sp. Strain KI72. GENOME ANNOUNCEMENTS 2017; 5:5/17/e00217-17. [PMID: 28450506 PMCID: PMC5408104 DOI: 10.1128/genomea.00217-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the 4.6-Mb genome sequence of a nylon oligomer-degrading bacterium, Arthrobacter sp. strain KI72. The draft genome sequence of strain KI72 consists of 4,568,574 bp, with a G+C content of 63.47%, 4,372 coding sequences (CDSs), 54 tRNAs, and six rRNAs.
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18
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Negoro S, Kawashima Y, Shibata N, Kobayashi T, Baba T, Lee YH, Kamiya K, Shigeta Y, Nagai K, Takehara I, Kato DI, Takeo M, Higuchi Y. Mutations affecting the internal equilibrium of the reaction catalyzed by 6-aminohexanoate-dimer hydrolase. FEBS Lett 2016; 590:3133-43. [DOI: 10.1002/1873-3468.12354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Yasuyuki Kawashima
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Naoki Shibata
- Department of Life Science; Graduate School of Life Science; University of Hyogo; Himeji Hyogo Japan
| | - Tatsuya Kobayashi
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Takeshi Baba
- Department of Material Engineering Science; Graduate School of Engineering Science; Osaka University; Suita Japan
| | - Young-Ho Lee
- Institute for Protein Research; Osaka University; Suita Japan
| | - Katsumasa Kamiya
- Center for Basic Education and Integrated Learning; Kanagawa Institute of Technology; Atsugi Kanagawa Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences; University of Tsukuba; Ibaraki Japan
| | - Keisuke Nagai
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Ikki Takehara
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Dai-ichiro Kato
- Graduate School of Science and Engineering; Kagoshima University; Japan
| | - Masahiro Takeo
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; Himeji Hyogo Japan
| | - Yoshiki Higuchi
- Department of Life Science; Graduate School of Life Science; University of Hyogo; Himeji Hyogo Japan
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Esikova TZ, Taran SA. A novel strain Gulosibacter sp. BS4 degrading epsilon-caprolactam and Nylon-6 oligomers. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716050052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Krueger MC, Harms H, Schlosser D. Prospects for microbiological solutions to environmental pollution with plastics. Appl Microbiol Biotechnol 2015; 99:8857-74. [DOI: 10.1007/s00253-015-6879-4] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 02/06/2023]
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21
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Pearce SL, Oakeshott JG, Pandey G. Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains. G3 (BETHESDA, MD.) 2015; 5:1081-94. [PMID: 25850427 PMCID: PMC4478539 DOI: 10.1534/g3.114.015933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022]
Abstract
Hexachlorocyclohexane (HCH), a synthetic organochloride, was first used as a broad-acre insecticide in the 1940s, and many HCH-degrading bacterial strains have been isolated from around the globe during the last 20 years. To date, the same degradation pathway (the lin pathway) has been implicated in all strains characterized, although the pathway has only been characterized intensively in two strains and for only a single HCH isomer. To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains. The three new strains each yielded a distinct set of metabolites during their degradation of HCH isomers. Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F). The analysis also confirmed the important role of horizontal transfer mediated by insertion sequence IS6100 in the acquisition of the pathway, with a stronger association of IS6100 to the lin genes in the new strains. In one strain, a linA variant was identified that likely caused a novel degradation phenotype involving a shift in isomer preference. This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.
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Affiliation(s)
| | | | - Gunjan Pandey
- CSIRO Ecosystem Sciences, Acton, ACT-2601, Australia
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22
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Esikova TZ, Akatova EV, Taran SA. Bacteria that degrade low-molecular linear epsilon-caprolactam oligomers. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814050044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Nagai K, Yasuhira K, Tanaka Y, Kato DI, Takeo M, Higuchi Y, Negoro S, Shibata N. Crystallization and X-ray diffraction analysis of nylon hydrolase (NylC) from Arthrobacter sp. KI72. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1151-4. [PMID: 24100570 PMCID: PMC3792678 DOI: 10.1107/s1744309113024263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/30/2013] [Indexed: 11/10/2022]
Abstract
Nylon hydrolase (NylC) encoded by Arthrobacter plasmid pOAD2 (NylCp2) was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylCp2 was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl and 25% glycerol. Diffraction data were collected from the native crystal to a resolution of 1.60 Å. The obtained crystal was spindle shaped and belonged to the C-centred orthorhombic space group C2221, with unit-cell parameters a=70.84, b=144.90, c=129.05 Å. A rotation and translation search gave one clear solution containing two molecules per asymmetric unit.
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Affiliation(s)
- Keisuke Nagai
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kengo Yasuhira
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yusuke Tanaka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Dai-ichiro Kato
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
| | - Seiji Negoro
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
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Negoro S, Shibata N, Tanaka Y, Yasuhira K, Shibata H, Hashimoto H, Lee YH, Oshima S, Santa R, Oshima S, Mochiji K, Goto Y, Ikegami T, Nagai K, Kato DI, Takeo M, Higuchi Y. Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis. J Biol Chem 2011; 287:5079-90. [PMID: 22187439 DOI: 10.1074/jbc.m111.321992] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 Å-resolution. This enzyme is a member of the N-terminal nucleophile hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct. We observed four identical heterodimers (27 kDa + 9 kDa), which resulted from the autoprocessing of the precursor protein (36 kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr-267 of the 9-kDa subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked αββα core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130Y/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T(m) = 52 °C, enhanced the protein thermostability by 36 °C (T(m) = 88 °C), whereas a single mutation (G111S or L137A) decreased the stability by ∼10 °C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60 °C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.
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Affiliation(s)
- Seiji Negoro
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671-2280
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Ponamoreva ON, Esikova TZ, Vlasova YA, Baskunov BP, Alferov VA. Transformation of low-molecular linear caprolactam oligomers by the caprolactam-degrading bacterium Pseudomonas putida BS394(pBS268). Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710030070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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27
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Yasuhira K, Shibata N, Mongami G, Uedo Y, Atsumi Y, Kawashima Y, Hibino A, Tanaka Y, Lee YH, Kato DI, Takeo M, Higuchi Y, Negoro S. X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation. J Biol Chem 2009; 285:1239-48. [PMID: 19889645 DOI: 10.1074/jbc.m109.041285] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We performed x-ray crystallographic analyses of the 6-aminohexanoate cyclic dimer (Acd) hydrolase (NylA) from Arthrobacter sp., an enzyme responsible for the degradation of the nylon-6 industry byproduct. The fold adopted by the 472-amino acid polypeptide generated a compact mixed alpha/beta fold, typically found in the amidase signature superfamily; this fold was especially similar to the fold of glutamyl-tRNA(Gln) amidotransferase subunit A (z score, 49.4) and malonamidase E2 (z score, 44.8). Irrespective of the high degree of structural similarity to the typical amidase signature superfamily enzymes, the specific activity of NylA for glutamine, malonamide, and indoleacetamide was found to be lower than 0.5% of that for Acd. However, NylA possessed carboxylesterase activity nearly equivalent to the Acd hydrolytic activity. Structural analysis of the inactive complex between the activity-deficient S174A mutant of NylA and Acd, performed at 1.8 A resolution, suggested the following enzyme/substrate interactions: a Ser(174)-cis-Ser(150)-Lys(72) triad constitutes the catalytic center; the backbone N in Ala(171) and Ala(172) are involved in oxyanion stabilization; Cys(316)-S(gamma) forms a hydrogen bond with nitrogen (Acd-N(7)) at the uncleaved amide bond in two equivalent amide bonds of Acd. A single S174A, S150A, or K72A substitution in NylA by site-directed mutagenesis decreased the Acd hydrolytic and esterolytic activities to undetectable levels, indicating that Ser(174)-cis-Ser(150)-Lys(72) is essential for catalysis. In contrast, substitutions at position 316 specifically affected Acd hydrolytic activity, suggesting that Cys(316) is responsible for Acd binding. On the basis of the structure and functional analysis, we discussed the catalytic mechanisms and evolution of NylA in comparison with other Ser-reactive hydrolases.
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Affiliation(s)
- Kengo Yasuhira
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Hyogo 671-2201, Japan
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