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Qiu J, Chen Y, Zhang L, Wu J, Zeng X, Shi X, Liu L, Chen J. A comprehensive review on enzymatic biodegradation of polyethylene terephthalate. ENVIRONMENTAL RESEARCH 2024; 240:117427. [PMID: 37865324 DOI: 10.1016/j.envres.2023.117427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023]
Abstract
Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.
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Affiliation(s)
- Jiarong Qiu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China; Development Center of Science and Education Park of Fuzhou University, Jinjiang, 362251, China
| | - Yuxin Chen
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Liangqing Zhang
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China; Development Center of Science and Education Park of Fuzhou University, Jinjiang, 362251, China.
| | - Jinzhi Wu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Xianhai Zeng
- College of Energy, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Lemian Liu
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
| | - Jianfeng Chen
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362251, China
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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Sobat M, Asad S, Kabiri M, Mehrshad M. Metagenomic discovery and functional validation of L-asparaginases with anti-leukemic effect from the Caspian Sea. iScience 2021; 24:101973. [PMID: 33458619 PMCID: PMC7797908 DOI: 10.1016/j.isci.2020.101973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/21/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022] Open
Abstract
By screening 27,000 publicly available prokaryotic genomes, we recovered ca. 6300 type I and ca. 5200 type II putative L-asparaginase highlighting the vast potential of prokaryotes. Caspian water with similar salt composition to the human serum was targeted for in silico L-asparaginase screening. We screened ca. three million predicted genes of its assembled metagenomes that resulted in annotation of 87 putative L-asparaginase genes. The L-asparagine hydrolysis was experimentally confirmed by synthesizing and cloning three selected genes in E. coli. Catalytic parameters of the purified enzymes were determined to be among the most desirable reported values. Two recombinant enzymes represented remarkable anti-proliferative activity (IC50 <1IU/ml) against leukemia cell line Jurkat while no cytotoxic effect on human erythrocytes or human umbilical vein endothelial cells was detected. Similar salinity and ionic concentration of the Caspian water to the human serum highlights the potential of secretory L-asparaginases recovered from these metagenomes as potential treatment agents.
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Affiliation(s)
- Motahareh Sobat
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sedigheh Asad
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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de Moura WAF, Schultz L, Breyer CA, de Oliveira ALP, Tairum CA, Fernandes GC, Toyama MH, Pessoa-Jr A, Monteiro G, de Oliveira MA. Functional and structural evaluation of the antileukaemic enzyme L-asparaginase II expressed at low temperature by different Escherichia coli strains. Biotechnol Lett 2020; 42:2333-2344. [PMID: 32638188 DOI: 10.1007/s10529-020-02955-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) affects lymphoblastic cells and is the most common neoplasm during childhood. Among the pharmaceuticals used in the treatment protocols for ALL, Asparaginase (ASNase) from Escherichia coli (EcAII) is an essential biodrug. Meanwhile, the use of EcAII in neoplastic treatments causes several side effects, such as immunological reactions, hepatotoxicity, neurotoxicity, depression, and coagulation abnormalities. Commercial EcAII is expressed as a recombinant protein, similar to novel enzymes from different organisms; in fact, EcAII is a tetrameric enzyme with high molecular weight (140 kDa), and its overexpression in recombinant systems often results in bacterial cell death or the production of aggregated or inactive EcAII protein, which is related to the formation of inclusion bodies. On the other hand, several commercial expression strains have been developed to overcome these expression issues, but no studies on a systematic evaluation of the E. coli strains aiming to express recombinant asparaginases have been performed to date. In this study, we evaluated eleven expression strains at a low temperature (16 °C) with different characteristics to determine which is the most appropriate for asparaginase expression; recombinant wild-type EcAII (rEcAII) was used as a prototype enzyme and the secondary structure content, oligomeric state, aggregation and specific activity of the enzymes were assessed. Structural analysis suggested that a correctly folded tetrameric rEcAII was obtained using ArcticExpress (DE3), a strain that co-express chaperonins, while all other strains produced poorly folded proteins. Additionally, the enzymatic assays showed high specific activity of proteins expressed by ArcticExpress (DE3) when compared to the other strains used in this work.
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Affiliation(s)
- Werner Alfinito Feio de Moura
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Leonardo Schultz
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Carlos Alexandre Breyer
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Ana Laura Pires de Oliveira
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Carlos Abrunhosa Tairum
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Gabriella Costa Fernandes
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Marcos Hikari Toyama
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil
| | - Adalberto Pessoa-Jr
- Biochemical-Pharmaceutical Technology Department, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, 05508-000, Brazil
| | - Gisele Monteiro
- Biochemical-Pharmaceutical Technology Department, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, 05508-000, Brazil
| | - Marcos Antonio de Oliveira
- Institute of Biosciences, São Paulo State University (UNESP), Coastal Campus, São Vicente, São Paulo, 11330-900, Brazil.
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Gavin DP, Murphy EJ, Foley AM, Castilla IA, Reen FJ, Woods DF, Collins SG, O'Gara F, Maguire AR. Identification of an Esterase Isolated Using Metagenomic Technology which Displays an Unusual Substrate Scope and its Characterisation as an Enantioselective Biocatalyst. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Declan P. Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Edel J. Murphy
- School of Chemistry; Analytical and Biological Chemistry Research Facility; University College Cork; T12 K8AF Cork Ireland
| | - Aoife M. Foley
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Ignacio Abreu Castilla
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - F. Jerry Reen
- School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - David F. Woods
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - Stuart G. Collins
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute; Curtin University; Perth WA 6102 Australia
- Telethon Kids Institute; Perth WA 6008 Australia
| | - Anita R. Maguire
- School of Chemistry; School of Pharmacy; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
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Anticancer Activity of Bacterial Proteins and Peptides. Pharmaceutics 2018; 10:pharmaceutics10020054. [PMID: 29710857 PMCID: PMC6027124 DOI: 10.3390/pharmaceutics10020054] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Despite much progress in the diagnosis and treatment of cancer, tumour diseases constitute one of the main reasons of deaths worldwide. The side effects of chemotherapy and drug resistance of some cancer types belong to the significant current therapeutic problems. Hence, searching for new anticancer substances and medicines are very important. Among them, bacterial proteins and peptides are a promising group of bioactive compounds and potential anticancer drugs. Some of them, including anticancer antibiotics (actinomycin D, bleomycin, doxorubicin, mitomycin C) and diphtheria toxin, are already used in the cancer treatment, while other substances are in clinical trials (e.g., p28, arginine deiminase ADI) or tested in in vitro research. This review shows the current literature data regarding the anticancer activity of proteins and peptides originated from bacteria: antibiotics, bacteriocins, enzymes, nonribosomal peptides (NRPs), toxins and others such as azurin, p28, Entap and Pep27anal2. The special attention was paid to the still poorly understood active substances obtained from the marine sediment bacteria. In total, 37 chemical compounds or groups of compounds with antitumor properties have been described in the present article.
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