1
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Fernandes GFS, Kim SH, Castagnolo D. Harnessing biocatalysis as a green tool in antibiotic synthesis and discovery. RSC Adv 2024; 14:30396-30410. [PMID: 39318457 PMCID: PMC11420778 DOI: 10.1039/d4ra04824e] [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: 07/03/2024] [Accepted: 09/16/2024] [Indexed: 09/26/2024] Open
Abstract
Biocatalysis offers a sustainable approach to drug synthesis, leveraging the high selectivity and efficiency of enzymes. This review explores the application of biocatalysis in the early-stage synthesis of antimicrobial compounds, emphasizing its advantages over traditional chemical methods. We discuss various biocatalysts, including enzymes and whole-cell systems, and their role in the selective functionalization and preparation of antimicrobials and antibacterial building blocks. The review underscores the potential of biocatalysis to advance the development of new antibiotics and suggests directions and potential applications of enzymes in drug development.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Seong-Heun Kim
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London 150 Stamford Street London SE1 9NH UK
| | - Daniele Castagnolo
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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2
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Ji T, Liaqat F, Khazi MI, Liaqat N, Nawaz MZ, Zhu D. Lignin biotransformation: Advances in enzymatic valorization and bioproduction strategies. INDUSTRIAL CROPS AND PRODUCTS 2024; 216:118759. [DOI: 10.1016/j.indcrop.2024.118759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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3
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Hussain A, Parveen F, Saxena A, Ashfaque M. A review of nanotechnology in enzyme cascade to address challenges in pre-treating biomass. Int J Biol Macromol 2024; 270:132466. [PMID: 38761904 DOI: 10.1016/j.ijbiomac.2024.132466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
Nanotechnology has become a revolutionary technique for improving the preliminary treatment of lignocellulosic biomass in the production of biofuels. Traditional methods of pre-treatment have encountered difficulties in effectively degrading the intricate lignocellulosic composition, thereby impeding the conversion of biomass into fermentable sugars. Nanotechnology has enabled the development of enzyme cascade processes that present a potential solution for addressing the limitations. The focus of this review article is to delve into the utilization of nanotechnology in the pretreatment of lignocellulosic biomass through enzyme cascade processes. The review commences with an analysis of the composition and structure of lignocellulosic biomass, followed by a discussion on the drawbacks associated with conventional pre-treatment techniques. The subsequent analysis explores the importance of efficient pre-treatment methods in the context of biofuel production. We thoroughly investigate the utilization of nanotechnology in the pre-treatment of enzyme cascades across three distinct sections. Nanomaterials for enzyme immobilization, enhanced enzyme stability and activity through nanotechnology, and nanocarriers for controlled enzyme delivery. Moreover, the techniques used to analyse nanomaterials and the interactions between enzymes and nanomaterials are introduced. This review emphasizes the significance of comprehending the mechanisms underlying the synergy between nanotechnology and enzymes establishing sustainable and environmentally friendly nanotechnology applications.
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Affiliation(s)
- Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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4
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Gama Cavalcante AL, Dari DN, Izaias da Silva Aires F, Carlos de Castro E, Moreira Dos Santos K, Sousa Dos Santos JC. Advancements in enzyme immobilization on magnetic nanomaterials: toward sustainable industrial applications. RSC Adv 2024; 14:17946-17988. [PMID: 38841394 PMCID: PMC11151160 DOI: 10.1039/d4ra02939a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
Enzymes are widely used in biofuels, food, and pharmaceuticals. The immobilization of enzymes on solid supports, particularly magnetic nanomaterials, enhances their stability and catalytic activity. Magnetic nanomaterials are chosen for their versatility, large surface area, and superparamagnetic properties, which allow for easy separation and reuse in industrial processes. Researchers focus on the synthesis of appropriate nanomaterials tailored for specific purposes. Immobilization protocols are predefined and adapted to both enzymes and support requirements for optimal efficiency. This review provides a detailed exploration of the application of magnetic nanomaterials in enzyme immobilization protocols. It covers methods, challenges, advantages, and future perspectives, starting with general aspects of magnetic nanomaterials, their synthesis, and applications as matrices for solid enzyme stabilization. The discussion then delves into existing enzymatic immobilization methods on magnetic nanomaterials, highlighting advantages, challenges, and potential applications. Further sections explore the industrial use of various enzymes immobilized on these materials, the development of enzyme-based bioreactors, and prospects for these biocatalysts. In summary, this review provides a concise comparison of the use of magnetic nanomaterials for enzyme stabilization, highlighting potential industrial applications and contributing to manufacturing optimization.
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Affiliation(s)
- Antônio Luthierre Gama Cavalcante
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
| | - Dayana Nascimento Dari
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - Francisco Izaias da Silva Aires
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - Erico Carlos de Castro
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
| | - Kaiany Moreira Dos Santos
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
| | - José Cleiton Sousa Dos Santos
- Departamento de Química Orgânica e Inorgânica, Centro de Ciências, Universidade Federal do Ceará Campus Pici Fortaleza CEP 60455760 CE Brazil
- Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira Campus das Auroras Redenção CEP 62790970 CE Brazil
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará Campus do Pici, Bloco 940 Fortaleza CEP 60455760 CE Brazil
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5
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Li Y, Yin D, Lee SY, Lv Y. Engineered polymer nanoparticles as artificial chaperones facilitating the selective refolding of denatured enzymes. Proc Natl Acad Sci U S A 2024; 121:e2403049121. [PMID: 38691587 PMCID: PMC11087784 DOI: 10.1073/pnas.2403049121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/28/2024] [Indexed: 05/03/2024] Open
Abstract
Molecular chaperones assist in protein refolding by selectively binding to proteins in their nonnative states. Despite progress in creating artificial chaperones, these designs often have a limited range of substrates they can work with. In this paper, we present molecularly imprinted flexible polymer nanoparticles (nanoMIPs) designed as customizable biomimetic chaperones. We used model proteins such as cytochrome c, laccase, and lipase to screen polymeric monomers and identify the most effective formulations, offering tunable charge and hydrophobic properties. Utilizing a dispersed phase imprinting approach, we employed magnetic beads modified with destabilized whole-protein as solid-phase templates. This process involves medium exchange facilitated by magnetic pulldowns, resulting in the synthesis of nanoMIPs featuring imprinted sites that effectively mimic chaperone cavities. These nanoMIPs were able to selectively refold denatured enzymes, achieving up to 86.7% recovery of their activity, significantly outperforming control samples. Mechanistic studies confirmed that nanoMIPs preferentially bind denatured rather than native enzymes, mimicking natural chaperone interactions. Multifaceted analyses support the functionality of nanoMIPs, which emulate the protective roles of chaperones by selectively engaging with denatured proteins to inhibit aggregation and facilitate refolding. This approach shows promise for widespread use in protein recovery within biocatalysis and biomedicine.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Deping Yin
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
- KAIST Institute for the BioCentury, KAIST Institute for AI, BioProcess Engineering Research Center, BioInformatics Research Center, and Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Yongqin Lv
- State Key Laboratory of Organic-Inorganic Composites, National Energy Research and Development Center for Biorefinery, International Joint Bioenergy Laboratory of Ministry of Education, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing100029, China
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6
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Preethi PS, Hariharan NM, Kumar SD, Rameshpathy M, Subbaiya R, Karmegam N. Actinobacterial peroxidase-mediated biodeterioration of hazardous explosive, 2, 4, 6, trinitrophenol by in silico and in vitro approaches. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:102. [PMID: 38433158 DOI: 10.1007/s10653-024-01903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Explosives are perilous and noxious to aquatic biota disrupting their endocrinal systems. Supplementarily, they exhibit carcinogenic, teratogenic and mutagenic effects on humans and animals. Henceforth, the current study has been targeted to biotransform the explosive, 2, 4, 6 trinitrophenol (TNP) by wetland peroxidase from Streptomyces coelicolor. A total peroxidase yield of 20,779 mg/l with 51.6 folds of purification was observed. In silico molecular docking cum in vitro appraisals were accomplished to assess binding energy and interacting binding site residues of peroxidase and TNP complex. TNP required a minimal binding energy of-6.91 kJ/mol and was subjected to biodeterioration (89.73%) by peroxidase in purified form, with 45 kDa and a similarity score of 34 by MASCOT protein analysis. Moreover, the peroxidase activity was confirmed with Zymogram analysis. Characterization of peroxidase revealed that optimum values of pH and temperature as 6 and 40 °C, respectively, with their corresponding stability varying from 3.5 to 7. Interestingly, the kinetic parameters such as Km and Vmax on 2,2'-azino-bis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and H2O2 were 19.27 µm and 0.41 µm/min; 21.4 µm and 0.1 µm/min, respectively. Among the diverse substrates, chemicals and trace elements, ABTS (40 mM), citric acid (5 mM) and Fe2+ (5 mM) displayed the highest peroxidase activity. Computational docking and in vitro results were corroborative and UV-Vis spectroscopy, HPLC, FTIR and GC-MS indicated the presence of simple metabolites of TNP such as nitrophenols and benzoquinone, showcasing the efficacy of S. coelicolor peroxidase to biotransform TNP. Henceforth, the current study offers a promising channel for biological treatment of explosive munitions, establishing a sustainable green earth.
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Affiliation(s)
- Prasath Sai Preethi
- Department of Biotechnology, Sree Sastha Institute of Engineering and Technology, Chennai, Tamil Nadu, 600123, India
| | - N M Hariharan
- Department of Biotechnology, Sree Sastha Institute of Engineering and Technology, Chennai, Tamil Nadu, 600123, India
| | - Shanmugam Dilip Kumar
- Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, 600 119, India
| | - Manian Rameshpathy
- School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
| | - Ramasamy Subbaiya
- Department of Biological Sciences, School of Mathematics and Natural Sciences, The Copperbelt University, Riverside, Jambo Drive, P O Box 21692, Kitwe, Zambia
| | - Natchimuthu Karmegam
- PG and Research Department of Botany, Government Arts College (Autonomous), Salem, Tamil Nadu, 636 007, India.
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7
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Tedesco P, Balzano S, Coppola D, Esposito FP, de Pascale D, Denaro R. Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth. MARINE POLLUTION BULLETIN 2024; 200:116157. [PMID: 38364643 DOI: 10.1016/j.marpolbul.2024.116157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.
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Affiliation(s)
- Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Sergio Balzano
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; Institute of Biochemistry and Cellular Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Renata Denaro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti Rome, Italy.
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Han X, Chen F, Li H, Ge R, Shen Q, Duan P, Sheng X, Zhang W. Reaction engineering blocks ether cleavage for synthesizing chiral cyclic hemiacetals catalyzed by unspecific peroxygenase. Nat Commun 2024; 15:1235. [PMID: 38336996 PMCID: PMC10858125 DOI: 10.1038/s41467-024-45545-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Hemiacetal compounds are valuable building blocks in synthetic chemistry, but their enzymatic synthesis is limited and often hindered by the instability of hemiacetals in aqueous environments. Here, we show that this challenge can be addressed through reaction engineering by using immobilized peroxygenase from Agrocybe aegerita (AaeUPO) under neat reaction conditions, which allows for the selective C-H bond oxyfunctionalization of environmentally significant cyclic ethers to cyclic hemiacetals. A wide range of chiral cyclic hemiacetal products are prepared in >99% enantiomeric excess and 95170 turnover numbers of AaeUPO. Furthermore, by changing the reaction medium from pure organic solvent to alkaline aqueous conditions, cyclic hemiacetals are in situ transformed into lactones. Lactams are obtained under the applied conditions, albeit with low enzyme activity. These findings showcase the synthetic potential of AaeUPO and offer a practical enzymatic approach to produce chiral cyclic hemiacetals through C-H oxyfunctionalization under mild conditions.
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Affiliation(s)
- Xiaofeng Han
- College of Chemistry and Materials Science, Inner Mongolia Minzu University, Tongliao, 028000, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Fuqiang Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Huanhuan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ran Ge
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Qianqian Shen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Peigao Duan
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, 32 West 7th Avenue, Tianjin, 300308, China.
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, 32 West 7th Avenue, Tianjin, 300308, China.
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9
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Baratto MC, Pogni R. Special Issue on Biotechnological Applications of Oxidoreductases. Int J Mol Sci 2024; 25:1758. [PMID: 38339033 PMCID: PMC10855645 DOI: 10.3390/ijms25031758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
This Special Issue was launched in conjunction with the 10th edition of the OxiZymes meeting in Siena (Italy) in 2022 [...].
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Affiliation(s)
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
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Meng Z, Tan Y, Duan YL, Li M. Monaspin B, a Novel Cyclohexyl-furan from Cocultivation of Monascus purpureus and Aspergillus oryzae, Exhibits Potent Antileukemic Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1114-1123. [PMID: 38166364 DOI: 10.1021/acs.jafc.3c08187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Natural products are a rich resource for the discovery of innovative drugs. Microbial cocultivation enables discovery of novel natural products through tandem enzymatic catalysis between different fungi. In this study, Monascus purpureus, as a food fermentation strain capable of producing abundant natural products, was chosen as an example of a cocultivation pair strain. Cocultivation screening revealed that M. purpureus and Aspergillus oryzae led to the production of two novel cyclohexyl-furans, Monaspins A and B. Optimization of the cocultivation mode and media enhanced the production of Monaspins A and B to 1.2 and 0.8 mg/L, respectively. Monaspins A and B were structurally elucidated by HR-ESI-MS and NMR. Furthermore, Monaspin B displayed potent antiproliferative activity against the leukemic HL-60 cell line by inducing apoptosis, with a half-maximal inhibitory concentration (IC50) of 160 nM. Moreover, in a mouse leukemia model, Monaspin B exhibited a promising in vivo antileukemic effect by reducing white blood cell, lymphocyte, and neutrophil counts. Collectively, these results indicate that Monaspin B is a promising candidate agent for leukemia therapy.
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Affiliation(s)
- Zitong Meng
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, Tongji Medical College, Huazhong University of Science and Technology, Hangkong Road 13, Wuhan 430030, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Ya-Li Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
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11
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Chandel N, Singh BB, Dureja C, Yang YH, Bhatia SK. Indigo production goes green: a review on opportunities and challenges of fermentative production. World J Microbiol Biotechnol 2024; 40:62. [PMID: 38182914 DOI: 10.1007/s11274-023-03871-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Indigo is a widely used dye in various industries, such as textile, cosmetics, and food. However, traditional methods of indigo extraction and processing are associated with environmental and economic challenges. Fermentative production of indigo using microbial strains has emerged as a promising alternative that offers sustainability and cost-effectiveness. This review article provides a critical overview of microbial diversity, metabolic pathways, fermentation strategies, and genetic engineering approaches for fermentative indigo production. The advantages and limitations of different indigo production systems and a critique of the current understanding of indigo biosynthesis are discussed. Finally, the potential application of indigo in other sectors is also discussed. Overall, fermentative production of indigo offers a sustainable and bio-based alternative to synthetic methods and has the potential to contribute to the development of sustainable and circular biomanufacturing.
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Affiliation(s)
- Neha Chandel
- School of Medical and Allied Sciences, GD Goenka University, Gurugram, Haryana, 122103, India
| | - Bharat Bhushan Singh
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chetna Dureja
- Center for Inflammatory and Infectious Diseases, Texas A&M Health Science Center, Institute of Bioscience and Technology, Houston, TX, USA
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
- Institute for Ubiquitous Information Technology and Applications, Seoul, 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
- Institute for Ubiquitous Information Technology and Applications, Seoul, 05029, Republic of Korea.
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12
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Chadha A, Padhi SK, Stella S, Venkataraman S, Saravanan T. Microbial alcohol dehydrogenases: recent developments and applications in asymmetric synthesis. Org Biomol Chem 2024; 22:228-251. [PMID: 38050738 DOI: 10.1039/d3ob01447a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Alcohol dehydrogenases are a well-known group of enzymes in the class of oxidoreductases that use electron transfer cofactors such as NAD(P)+/NAD(P)H for oxidation or reduction reactions of alcohols or carbonyl compounds respectively. These enzymes are utilized mainly as purified enzymes and offer some advantages in terms of green chemistry. They are environmentally friendly and a sustainable alternative to traditional chemical synthesis of bulk and fine chemicals. Industry has implemented several whole-cell biocatalytic processes to synthesize pharmaceutically active ingredients by exploring the high selectivity of enzymes. Unlike the whole cell system where cofactor regeneration is well conserved within the cellular environment, purified enzymes require additional cofactors or a cofactor recycling system in the reaction, even though cleaner reactions can be carried out with fewer downstream work-up problems. The challenge of producing purified enzymes in large quantities has been solved in large part by the use of recombinant enzymes. Most importantly, recombinant enzymes find applications in many cascade biotransformations to produce several important chiral precursors. Inevitably, several dehydrogenases were engineered as mere recombinant enzymes could not meet the industrial requirements for substrate and stereoselectivity. In recent years, a significant number of engineered alcohol dehydrogenases have been employed in asymmetric synthesis in industry. In a parallel development, several enzymatic and non-enzymatic methods have been established for regenerating expensive cofactors (NAD+/NADP+) to make the overall enzymatic process more efficient and economically viable. In this review article, recent developments and applications of microbial alcohol dehydrogenases are summarized by emphasizing notable examples.
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Affiliation(s)
- Anju Chadha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, Tamil Nadu, India.
| | - Santosh Kumar Padhi
- Biocatalysis and Enzyme Engineering Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
| | - Selvaraj Stella
- Department of Chemistry, Sarah Tucker College (Affiliated to Manonmaniam Sundaranar University), Tirunelveli-627007, Tamil Nadu, India.
| | - Sowmyalakshmi Venkataraman
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education & Research, Chennai, 600116, Tamil Nadu, India.
| | - Thangavelu Saravanan
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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13
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Psurtseva NV, Kiyashko AA, Senik SV, Shakhova NV, Belova NV. The Conservation and Study of Macromycetes in the Komarov Botanical Institute Basidiomycetes Culture Collection-Their Taxonomical Diversity and Biotechnological Prospects. J Fungi (Basel) 2023; 9:1196. [PMID: 38132796 PMCID: PMC10744906 DOI: 10.3390/jof9121196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Culture collections (CCs) play an important role in the ex situ conservation of biological material and maintaining species and strains, which can be used for scientific and practical purposes. The Komarov Botanical Institute Basidiomycetes Culture Collection (LE-BIN) preserves a large number of original dikaryon strains of various taxonomical and ecological groups of fungi from different geographical regions. Started in the late 1950s for the investigation of Basidiomycetes' biological activity, today, in Russia, it has become a unique specialized macromycetes collection, preserving 3680 strains from 776 species of fungi. The Collection's development is aimed at ex situ conservation of fungal diversity, with an emphasis on preserving rare and endangered species, ectomycorrhizal fungi, and strains useful for biotechnology and medicine. The main methods applied in the collection for maintaining and working with cultures are described, and the results are presented. Some problems for the isolation and cultivation of species are discussed. The taxonomical structure and variety of the strains in the collection fund are analyzed, and they show that the taxonomical diversity of fungi in the LE-BIN is commensurable with the largest CCs in the world. The achievements from the ex situ conservation of the diversity of macromycetes and the main results from the screening and investigation of the collection's strains demonstrate that a number of strains can be prospective producers of enzymes (oxidoreductases and proteases), lipids, and biologically active compounds (terpenoids, phthalides, etc.) for biotechnology and medicine.
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Affiliation(s)
- Nadezhda V. Psurtseva
- Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.A.K.); (S.V.S.); (N.V.S.); (N.V.B.)
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14
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Zhang L, Zhou R, Fu X, Zhang G, Zhang L, Zhou SF, Jiang W. Specific coenzyme preference switching for an aldo-keto reductase that synthesizes the chiral intermediate of duloxetine. Enzyme Microb Technol 2023; 171:110326. [PMID: 37717530 DOI: 10.1016/j.enzmictec.2023.110326] [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: 07/02/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The synthesis of chiral intermediates for the traditional antidepressant duloxetine has gained significant attention as the number of depressed patients continues to grow. S-N, N-Dimethyl-3-hydroxy-3-(2-thienyl)-1-propanamide (S-DHTP) is a critical intermediate in the synthesis of duloxetine, and the chemical synthesis process is complex and environmentally unfriendly. Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a major cost driver in the biocatalytic production of S-DHTP from N, N-Dimethyl-3-keto-3-(2-thienyl)-1-propanamide (DKTP). Here, we successfully modified the coenzyme preference of an aldo-keto reductase (AKR7-2-1) to use the cheaper reduced nicotinamide adenine dinucleotide (NADH) through a coenzyme preference modification approach. We utilized protein engineering to create a superior mutant, Y53F, which increased the coenzyme specificity of AKR7-2-1 by 875-fold and improved its thermal stability, enhancing its potential for industrial applications. Molecular dynamics simulations were performed to demonstrate the effect of mutations at key sites on the protein, revealing the altered coenzyme preference and increased thermal stability from structural and energetic changes. This study validates the viability of the coenzyme preference modification strategy for aldo-keto reductase, offering valuable insights for fellow researchers and guiding future investigations.
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Affiliation(s)
- Lingzhi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Rui Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Xiaoli Fu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guangya Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Lijuan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
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15
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Dirks T, Yayci A, Klopsch S, Krewing M, Zhang W, Hollmann F, Bandow JE. Immobilization protects enzymes from plasma-mediated inactivation. J R Soc Interface 2023; 20:20230299. [PMID: 37876274 PMCID: PMC10598437 DOI: 10.1098/rsif.2023.0299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Non-thermal plasmas are used in various applications to inactivate biological agents or biomolecules. A complex cocktail of reactive species, (vacuum) UV radiation and in some cases exposure to an electric field together cause the detrimental effects. In contrast to this disruptive property of technical plasmas, we have shown previously that it is possible to use non-thermal plasma-generated species such as H2O2 as cosubstrates in biocatalytic reactions. One of the main limitations in plasma-driven biocatalysis is the relatively short enzyme lifetime under plasma-operating conditions. This challenge could be overcome by immobilizing the enzymes on inert carrier materials. Here, we tested whether immobilization is suited to protect proteins from inactivation by plasma. To this end, using a dielectric barrier discharge device (PlasmaDerm), plasma stability was tested for five enzymes immobilized on ten different carrier materials. A comparative analysis of the treatment times needed to reduce enzyme activity of immobilized and free enzyme by 30% showed a maximum increase by a factor of 44. Covalent immobilization on a partly hydrophobic carrier surface proved most effective. We conclude from the study, that immobilization universally protects enzymes under plasma-operating conditions, paving the way for new emerging applications.
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Affiliation(s)
- Tim Dirks
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Abdulkadir Yayci
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sabrina Klopsch
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Marco Krewing
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Wuyuan Zhang
- National Innovation Center for Synthetic Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People's Republic of China
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Julia E. Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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16
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Wang Q, Hu Z, Li Z, Liu T, Bian G. Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305828. [PMID: 37677048 DOI: 10.1002/adma.202305828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Indexed: 09/09/2023]
Abstract
At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.
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Affiliation(s)
- Qiwen Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhehui Hu
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, 430071, China
| | - Zhixuan Li
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tiangang Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Guangkai Bian
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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17
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Kyomuhimbo HD, Feleni U, Haneklaus NH, Brink H. Recent Advances in Applications of Oxidases and Peroxidases Polymer-Based Enzyme Biocatalysts in Sensing and Wastewater Treatment: A Review. Polymers (Basel) 2023; 15:3492. [PMID: 37631549 PMCID: PMC10460086 DOI: 10.3390/polym15163492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Oxidase and peroxidase enzymes have attracted attention in various biotechnological industries due to their ease of synthesis, wide range of applications, and operation under mild conditions. Their applicability, however, is limited by their poor stability in harsher conditions and their non-reusability. As a result, several approaches such as enzyme engineering, medium engineering, and enzyme immobilization have been used to improve the enzyme properties. Several materials have been used as supports for these enzymes to increase their stability and reusability. This review focusses on the immobilization of oxidase and peroxidase enzymes on metal and metal oxide nanoparticle-polymer composite supports and the different methods used to achieve the immobilization. The application of the enzyme-metal/metal oxide-polymer biocatalysts in biosensing of hydrogen peroxide, glucose, pesticides, and herbicides as well as blood components such as cholesterol, urea, dopamine, and xanthine have been extensively reviewed. The application of the biocatalysts in wastewater treatment through degradation of dyes, pesticides, and other organic compounds has also been discussed.
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Affiliation(s)
- Hilda Dinah Kyomuhimbo
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
| | - Usisipho Feleni
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, Johannesburg 1710, South Africa;
| | - Nils H. Haneklaus
- Transdisciplinarity Laboratory Sustainable Mineral Resources, University for Continuing Education Krems, 3500 Krems, Austria;
| | - Hendrik Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
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18
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Al-Shameri A, Siebert DL, Sutiono S, Lauterbach L, Sieber V. Hydrogenase-based oxidative biocatalysis without oxygen. Nat Commun 2023; 14:2693. [PMID: 37258512 DOI: 10.1038/s41467-023-38227-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
Biocatalysis-based synthesis can provide a sustainable and clean platform for producing chemicals. Many oxidative biocatalytic routes require the cofactor NAD+ as an electron acceptor. To date, NADH oxidase (NOX) remains the most widely applied system for NAD+ regeneration. However, its dependence on O2 implies various technical challenges in terms of O2 supply, solubility, and mass transfer. Here, we present the suitability of a NAD+ regeneration system in vitro based on H2 evolution. The efficiency of the hydrogenase-based system is demonstrated by integrating it into a multi-enzymatic cascade to produce ketoacids from sugars. The total NAD+ recycled using the hydrogenase system outperforms NOX in all different setups reaching up to 44,000 mol per mol enzyme. This system proves to be scalable and superior to NOX in terms of technical simplicity, flexibility, and total output. Furthermore, the system produces only green H2 as a by-product even in the presence of O2.
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Affiliation(s)
- Ammar Al-Shameri
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Dominik L Siebert
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Lars Lauterbach
- RWTH Universität Aachen, Institute of Applied Microbiology, Worringerweg 1, 52074, Aachen, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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19
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Berhe MH, Song X, Yao L. Improving the Enzymatic Activity and Stability of a Lytic Polysaccharide Monooxygenase. Int J Mol Sci 2023; 24:ijms24108963. [PMID: 37240310 DOI: 10.3390/ijms24108963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Lytic Polysaccharide Monooxygenases (LPMOs) are copper-dependent enzymes that play a pivotal role in the enzymatic conversion of the most recalcitrant polysaccharides, such as cellulose and chitin. Hence, protein engineering is highly required to enhance their catalytic efficiencies. To this effect, we optimized the protein sequence encoding for an LPMO from Bacillus amyloliquefaciens (BaLPMO10A) using the sequence consensus method. Enzyme activity was determined using the chromogenic substrate 2,6-Dimethoxyphenol (2,6-DMP). Compared with the wild type (WT), the variants exhibit up to a 93.7% increase in activity against 2,6-DMP. We also showed that BaLPMO10A can hydrolyze p-nitrophenyl-β-D-cellobioside (PNPC), carboxymethylcellulose (CMC), and phosphoric acid-swollen cellulose (PASC). In addition to this, we investigated the degradation potential of BaLPMO10A against various substrates such as PASC, filter paper (FP), and Avicel, in synergy with the commercial cellulase, and it showed up to 2.7-, 2.0- and 1.9-fold increases in production with the substrates PASC, FP, and Avicel, respectively, compared to cellulase alone. Moreover, we examined the thermostability of BaLPMO10A. The mutants exhibited enhanced thermostability with an apparent melting temperature increase of up to 7.5 °C compared to the WT. The engineered BaLPMO10A with higher activity and thermal stability provides a better tool for cellulose depolymerization.
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Affiliation(s)
- Miesho Hadush Berhe
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Biotechnology, College of Natural and Computational Sciences, Aksum University, Axum 1010, Ethiopia
| | - Xiangfei Song
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Lishan Yao
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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20
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Kappen J, Manurung J, Fuchs T, Vemulapalli SPB, Schmitz LM, Frolov A, Agusta A, Muellner-Riehl AN, Griesinger C, Franke K, Wessjohann LA. Challenging Structure Elucidation of Lumnitzeralactone, an Ellagic Acid Derivative from the Mangrove Lumnitzera racemosa. Mar Drugs 2023; 21:md21040242. [PMID: 37103381 PMCID: PMC10144801 DOI: 10.3390/md21040242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
The previously undescribed natural product lumnitzeralactone (1), which represents a derivative of ellagic acid, was isolated from the anti-bacterial extract of the Indonesian mangrove species Lumnitzera racemosa Willd. The structure of lumnitzeralactone (1), a proton-deficient and highly challenging condensed aromatic ring system, was unambiguously elucidated by extensive spectroscopic analyses involving high-resolution mass spectrometry (HRMS), 1D 1H and 13C nuclear magnetic resonance spectroscopy (NMR), and 2D NMR (including 1,1-ADEQUATE and 1,n-ADEQUATE). Determination of the structure was supported by computer-assisted structure elucidation (CASE system applying ACD-SE), density functional theory (DFT) calculations, and a two-step chemical synthesis. Possible biosynthetic pathways involving mangrove-associated fungi have been suggested.
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Affiliation(s)
- Jonas Kappen
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
| | - Jeprianto Manurung
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Tristan Fuchs
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
| | - Sahithya Phani Babu Vemulapalli
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Lea M Schmitz
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
| | - Andria Agusta
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Jl. M.H. Thamrin No. 8, Jakarta 10340, Indonesia
| | - Alexandra N Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Katrin Franke
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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21
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Benítez-Mateos AI, Paradisi F. Halomonas elongata: a microbial source of highly stable enzymes for applied biotechnology. Appl Microbiol Biotechnol 2023; 107:3183-3190. [PMID: 37052635 PMCID: PMC10160191 DOI: 10.1007/s00253-023-12510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Extremophilic microorganisms, which are resistant to extreme levels of temperature, salinity, pH, etc., have become popular tools for biotechnological applications. Due to their availability and cost-efficacy, enzymes from extremophiles are getting the attention of researchers and industries in the field of biocatalysis to catalyze diverse chemical reactions in a selective and sustainable manner. In this mini-review, we discuss the advantages of Halomonas elongata as moderate halophilic bacteria to provide suitable enzymes for biotechnology. While enzymes from H. elongata are more resistant to the presence of salt compared to their mesophilic counterparts, they are also easier to produce in heterologous hosts compared with more extremophilic microorganisms. Herein, a set of different enzymes (hydrolases, transferases, and oxidoreductases) from H. elongata are showcased, highlighting their interesting properties as more efficient and sustainable biocatalysts. With this, we aim to improve the visibility of halotolerant enzymes and their uncommon properties to integrate biocatalysis in industrial set-ups. KEYPOINTS: • Production and use of halotolerant enzymes can be easier than strong halophilic ones. • Enzymes from halotolerant organisms are robust catalysts under harsh conditions. • Halomonas elongata has shown a broad enzyme toolbox with biotechnology applications.
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Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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22
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Rovaletti A, De Gioia L, Fantucci P, Greco C, Vertemara J, Zampella G, Arrigoni F, Bertini L. Recent Theoretical Insights into the Oxidative Degradation of Biopolymers and Plastics by Metalloenzymes. Int J Mol Sci 2023; 24:6368. [PMID: 37047341 PMCID: PMC10094197 DOI: 10.3390/ijms24076368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.
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Affiliation(s)
- Anna Rovaletti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giuseppe Zampella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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23
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Zhang H, Zhou H, Zhao Y, Li T, Yin H. Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis. PeerJ 2023; 11:e14670. [PMID: 36684673 PMCID: PMC9851047 DOI: 10.7717/peerj.14670] [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: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023] Open
Abstract
Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B.
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Affiliation(s)
- Huiyan Zhang
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Zhao
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tang Li
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Decoding whole genome of Anoxybacillus rupiensis TPH1 isolated from Tatapani hot spring, India and giving insight into bioremediation ability of TPH1 via heavy metals and azo dyes. Res Microbiol 2023; 174:104027. [PMID: 36646262 DOI: 10.1016/j.resmic.2023.104027] [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: 05/09/2022] [Revised: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
A moderately thermophilic, gram-positive genomospecies Anoxybacillus rupiensis TPH1 was isolated from Tatapani hot spring, Chhattisgarh, India. Genome of 3.70 Mb with 42.3% GC subsumed 4131 CDSs, 65 tRNA, 5 rRNA, 35 AMR and 19 drug target genes. Further, comparative genomics of 19 Anoxybacillus spp. exhibited an open pan genome of 13102 genes along with core (10.62%), unique (43.5%) and accessory (45.9%) genes. Moreover, phylogenomic tree displayed clustering of Anoxybacillus spp. into two distinct clades where clade A species harbored larger genomes, more unique genes, CDS and hypothetical proteins than clade B species. Further, distribution of azoreductases showed FMN-binding NADPH azoreductase (AzoRed1) presence in clade A species only and FMN-binding NADH azoreductase (AzoRed2) harboring by species of both clades. Heavy metal resistance genes distribution showed omnipresence of znuA, copZ and arsC in both clades, dispersed presence of cbiM, czcD, merA and feoB over both clades and harboring of nikA and acr3 by few species of clade A only. Additionally, molecular docking of AzoRed1, AzoRed2, ZnuA, CopZ, Acr3, CbiM, CzcD, MerA and NikA with their respective ligands indicated high affinity and stable binding. Conclusively, present study provided insight into gene repertoire of genus Anoxybacillus and a basis for the potential application of this thermophile in bioremediation of azo dyes and heavy metals.
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25
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Biko OD, Viljoen-Bloom M, van Zyl WH. Medium optimization for enhanced production of recombinant lignin peroxidase in Pichia pastoris. Biotechnol Lett 2023; 45:105-113. [PMID: 36400875 DOI: 10.1007/s10529-022-03321-3] [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: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Different cultivation conditions and parameters were evaluated to improve the production and secretion of a recombinant Phanerochaete chrysosporium lipH8 gene in Komagataella phaffii (Pichia pastoris). RESULTS The recombinant lipH8 gene with its native secretion signal was successfully cloned and expressed in Komagataella phaffii (Pichia pastoris) under the control of the alcohol oxidase 1 promoter (PAOX1). The results revealed that co-feeding with sorbitol and methanol increased rLiP secretion by 5.9-fold compared to the control conditions. The addition of 1 mM FeSO4 increased LiP activity a further 6.0-fold during the induction phase. Moreover, the combination of several optimal conditions and parameters yielded an extracellular rLiP activity of 20.05 U l-1, which is more than ten-fold higher relative to standard growth conditions (BMM10 medium, pH 6 and 30 °C). CONCLUSION Extracellular activity of a recombinant LiP expressed in P. pastoris increased more than ten-fold when co-feeding sorbitol and methanol as carbon sources, together with urea as nitrogen source, FeSO4 supplementation, lower pH and lower cultivation temperature.
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Affiliation(s)
- Odwa D Biko
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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26
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Lzaod S, Dutta T. Recent Advances in the Development of Oxidoreductase-Based Biosensors for Detection of Phenolic Antioxidants in Food and Beverages. ACS OMEGA 2022; 7:47434-47448. [PMID: 36591143 PMCID: PMC9798740 DOI: 10.1021/acsomega.2c05604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/28/2022] [Indexed: 05/31/2023]
Abstract
Antioxidants are known to exhibit a protective effect against reactive oxygen species (ROS)-related oxidative damage. As a result, inclusion of exogenous antioxidants in the diet has greatly increased. In this sense, detection and quantification of such antioxidants in various food and beverage items are of eminent importance. Monophenols and polyphenols are among the most prominent natural antioxidants. In this regard, biosensors have emerged as a simple, fast, and economical method for determination of such antioxidants. Owing to the fact that majority of the phenolic antioxidants are electroactive, oxidoreductase enzymes are the most extensively availed bioreceptors for their detection. Herein, the different types of oxidoreductases that have been utilized in biosensors for the biorecognition and quantification of natural phenolic compounds commonly present in foods and beverages are discussed. Apart from the most accustomed electrochemical biosensors, this review sheds light on the alternative transduction systems for the detection of phenolic antioxidants. Recent advances in the strategies involved in enzyme immobilization and surface modification of the biosensing platform are analyzed. This review aims to provide a brief overview of the latest developments in biosensor technology for phenolic antioxidant analysis in foodstuffs and future directions in this field.
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27
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Valotta A, Malihan-Yap L, Hinteregger K, Kourist R, Gruber-Woelfler H. Design and Investigation of a Photocatalytic Setup for Efficient Biotransformations Within Recombinant Cyanobacteria in Continuous Flow. CHEMSUSCHEM 2022; 15:e202201468. [PMID: 36069133 PMCID: PMC9828554 DOI: 10.1002/cssc.202201468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Photo- and biocatalysis show many advantages as more sustainable solutions for the production of fine chemicals. In an effort to combine the benefits and the knowledge of both these areas, a continuous photobiocatalytic setup was designed and optimized to carry out whole-cell biotransformations within cells of the cyanobacterium Synechocystis sp. PCC 6803 expressing the gene of the ene-reductase YqjM from B. subtilis. The effect of the light intensity and flow rate on the specific activity in the stereoselective reduction of 2-methyl maleimide was investigated via a design-of-experiments approach. The cell density in the setup was further increased at the optimal operating conditions without loss in specific activity, demonstrating that the higher surface area/volume ratio in the coil reactor improved the illumination efficiency of the process. Furthermore, different reactor designs were compared, proving that the presented approach was the most cost- and time-effective solution for intensifying photobiotransformations within cyanobacterial cells.
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Affiliation(s)
- Alessia Valotta
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
| | - Lenny Malihan-Yap
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Kerstin Hinteregger
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- ACIB GmbH, Krenngasse 37, 8010, Graz, Austria
| | - Heidrun Gruber-Woelfler
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13, 8010, Graz, Austria
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28
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Kinner A, Lütz S, Rosenthal K. Agar Plate‐Based Screening Approach for the Identification of Enzyme‐Catalyzed Oxidations. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alina Kinner
- TU Dortmund University Chair for Bioprocess Engineering Department of Biochemical and Chemical Engineering Emil-Figge-Straße 66 44227 Dortmund Germany
| | - Stephan Lütz
- TU Dortmund University Chair for Bioprocess Engineering Department of Biochemical and Chemical Engineering Emil-Figge-Straße 66 44227 Dortmund Germany
| | - Katrin Rosenthal
- TU Dortmund University Chair for Bioprocess Engineering Department of Biochemical and Chemical Engineering Emil-Figge-Straße 66 44227 Dortmund Germany
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30
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Zhao J, Ma T, Chang B, Fang J. Recent Progress on NIR Fluorescent Probes for Enzymes. Molecules 2022; 27:molecules27185922. [PMID: 36144654 PMCID: PMC9503431 DOI: 10.3390/molecules27185922] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
The majority of diseases’ biomarkers are enzymes, and the regulation of enzymes is fundamental but crucial. Biological system disorders and diseases can result from abnormal enzymatic activity. Given the biological significance of enzymes, researchers have devised a plethora of tools to map the activity of particular enzymes in order to gain insight regarding their function and distribution. Near-infrared (NIR) fluorescence imaging studies on enzymes may help to better understand their roles in living systems due to their natural imaging advantages. We review the NIR fluorescent probe design strategies that have been attempted by researchers to develop NIR fluorescent sensors of enzymes, and these works have provided deep and intuitive insights into the study of enzymes in biological systems. The recent enzyme-activated NIR fluorescent probes and their applications in imaging are summarized, and the prospects and challenges of developing enzyme-activated NIR fluorescent probes are discussed.
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31
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [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: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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32
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Niu Q, Li K, Yang H, Zhu P, Huang Y, Wang Y, Li X, Li Q. Exploring the effects of heavy metal passivation under Fenton-like reaction on the removal of antibiotic resistance genes during composting. BIORESOURCE TECHNOLOGY 2022; 359:127476. [PMID: 35714777 DOI: 10.1016/j.biortech.2022.127476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
This study aims to explore the succession of microbes carrying antibiotic resistance genes (ARGs), the relationship between heavy metal speciation and ARGs via Fenton-like reaction during composting. The results indicated that the passivation of Cu and Ni was more prominent, and the Fenton-like reaction promoted exceptionally the passivation of Zn, Ni and Mn. The removals of macrolides-lincosamids-streptogramins (MLS), aminoglycoside and tetracycline resistance genes were induced with the composting process, but the relative abundance of bacitracin resistance genes increased. Additionally, Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were main carriers and disseminators of ARGs, and the Fenton-like reaction improved the contribution degree of Proteobacteria to bacitracin, tetracycline and aminoglycoside resistance genes. Redundancy analysis revealed the passivation of heavy metal contributed to the removal of tetracycline, MLS and aminoglycoside resistance genes. Conclusively, the Fenton-like reaction promoted the passivation of Zn, Ni and Mn, and controlled the abundance of bacitracin resistance genes in composting.
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Affiliation(s)
- Qiuqi Niu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hongxiang Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Pengfei Zhu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yite Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaolan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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33
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Mathieu Y, Cleveland ME, Brumer H. Active-Site Engineering Switches Carbohydrate Regiospecificity in a Fungal Copper Radical Oxidase. ACS Catal 2022; 12:10264-10275. [PMID: 36033369 PMCID: PMC9397409 DOI: 10.1021/acscatal.2c01956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/15/2022] [Indexed: 11/30/2022]
Abstract
Copper radical oxidases (CROs) from Auxiliary Activity Family 5, Subfamily 2 (AA5_2), are organic cofactor-free biocatalysts for the selective oxidation of alcohols to the corresponding aldehydes. AA5_2 CROs comprise canonical galactose-6-oxidases as well as the more recently discovered general alcohol oxidases and aryl alcohol oxidases. Guided by primary and tertiary protein structural analyses, we targeted a distinct extended loop in the active site of a Colletotrichum graminicola aryl alcohol oxidase (CgrAAO) to explore its effect on catalysis in the broader context of AA5_2. Deletion of this loop, which is bracketed by a conserved disulfide bridge, significantly reduced the inherent activity of the enzyme toward extended galacto-oligosaccharides, as anticipated from molecular modeling. Unexpectedly, kinetic and product analysis on a range of monosaccharides and disaccharides revealed that an altered carbohydrate specificity in CgrAAO-Δloop was accompanied by a complete change in regiospecificity from C-6 to C-1 oxidation, thereby generating aldonic acids. C-1 regiospecificity is unprecedented in AA5 enzymes and is classically associated with flavin-dependent carbohydrate oxidases of Auxiliary Activity Family 3. Thus, this work further highlights the catalytic adaptability of the unique mononuclear copper radical active site and provides a basis for the design of improved biocatalysts for diverse potential applications.
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Affiliation(s)
- Yann Mathieu
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- BioProducts
Institute, University of British Columbia, 2385 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Maria E. Cleveland
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- BioProducts
Institute, University of British Columbia, 2385 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Harry Brumer
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- BioProducts
Institute, University of British Columbia, 2385 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Biochemistry and Molecular Biology, University
of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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34
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Long L, Hu Y, Sun F, Gao W, Hao Z, Yin H. Advances in lytic polysaccharide monooxygenases with the cellulose-degrading auxiliary activity family 9 to facilitate cellulose degradation for biorefinery. Int J Biol Macromol 2022; 219:68-83. [PMID: 35931294 DOI: 10.1016/j.ijbiomac.2022.07.240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/18/2022]
Abstract
One crucial step in processing the recalcitrant lignocellulosic biomass is the fast hydrolysis of natural cellulose to fermentable sugars that can be subsequently converted to biofuels and bio-based chemicals. Recent studies have shown that lytic polysaccharide monooxygenase (LPMOs) with auxiliary activity family 9 (AA9) are capable of efficiently depolymerizing the crystalline cellulose via regioselective oxidation reaction. Intriguingly, the catalysis by AA9 LPMOs requires reductant to provide electrons, and lignin and its phenolic derivatives can be oxidized, releasing reductant to activate the reaction. The activity of AA9 LPMOs can be enhanced by in-situ generation of H2O2 in the presence of O2. Although scientific understanding of these enzymes remains somewhat unknown or controversial, structure modifications on AA9 LPMOs through protein engineering have emerged in recent years, which are prerequisite for their extensive applications in the development of cellulase-mediated lignocellulosic biorefinery processes. In this review, we critically comment on advances in studies for AA9 LPMOs, i.e., characteristic of AA9 LPMOs catalysis, external electron donors to AA9 LPMOs, especially the role of the oxidization of lignin and its derivatives, and AA9 LPMOs protein engineering as well as their extensive applications in the bioprocessing of lignocellulosic biomass. Perspectives are also highlighted for addressing the challenges.
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Affiliation(s)
- Lingfeng Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
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35
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Monterrey DT, Ayuso-Fernández I, Oroz-Guinea I, García-Junceda E. Design and biocatalytic applications of genetically fused multifunctional enzymes. Biotechnol Adv 2022; 60:108016. [PMID: 35781046 DOI: 10.1016/j.biotechadv.2022.108016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
Fusion proteins, understood as those created by joining two or more genes that originally encoded independent proteins, have numerous applications in biotechnology, from analytical methods to metabolic engineering. The use of fusion enzymes in biocatalysis may be even more interesting due to the physical connection of enzymes catalyzing successive reactions into covalently linked complexes. The proximity of the active sites of two enzymes in multi-enzyme complexes can make a significant contribution to the catalytic efficiency of the reaction. However, the physical proximity of the active sites does not guarantee this result. Other aspects, such as the nature and length of the linker used for the fusion or the order in which the enzymes are fused, must be considered and optimized to achieve the expected increase in catalytic efficiency. In this review, we will relate the new advances in the design, creation, and use of fused enzymes with those achieved in biocatalysis over the past 20 years. Thus, we will discuss some examples of genetically fused enzymes and their application in carbon‑carbon bond formation and oxidative reactions, generation of chiral amines, synthesis of carbohydrates, biodegradation of plant biomass and plastics, and in the preparation of other high-value products.
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Affiliation(s)
- Dianelis T Monterrey
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Iván Ayuso-Fernández
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Isabel Oroz-Guinea
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Eduardo García-Junceda
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
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Singh AK, Bilal M, Barceló D, Iqbal HMN. A predictive toolset for the identification of degradation pattern and toxic hazard estimation of multimeric hazardous compounds persists in water bodies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153979. [PMID: 35181354 DOI: 10.1016/j.scitotenv.2022.153979] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
An array of industrial processing units generates many multimeric hazardous compounds, such as complex technical lignin and its toxic derivatives, thereby persist in expelled water bodies. The inclusion of some group of motifs in the complex technical lignin structure helps it resist degrade biologically, most often even recalcitrant. Relatively small concentrations of lignin are harmful to aquatic organisms and can trigger environmental hazards. Sadly, the entire biotransformation pathway and insightful information about these toxic derivatives are incomplete and missing in the literature. This is mainly because the current conventional treatments often fail to identify all transformed compounds and their environmental fate. Thus, a robust toolset is much needed to cover this literature gap. Inadequate performance of conventional remediation processes and biological degradation patterns can be maximally optimized with the aid of predictive toolset methods that could offer better degradability and complete transformed compound information. A predictive toolset-assisted biodegradation pattern determination is a multifaceted and reliable analytical technique that can help to overcome existing shortcomings by providing an entire transformation pathway. Considering the above critiques, this work reports on the degradation pattern, and toxicological endpoints of five hazardous compounds, i.e., 2-chlorosyringaldehyde, 5-chlorovanillin, catechol, guaiacyl 4-O-5 guaiacyl, and syringyl β-O-4 syringyl β-O-4 sinapyl alcohol, that persists in water matrices. The predictive transformation pattern was revealed notably less complex end-products of catechol as; succinate, and 2-Oxo-4-pentenoate. The gastrointestinal (GI) absorption rate was found high for all tested compounds, excluding trimer compound, i.e., syringyl β-O-4 syringyl β-O-4 sinapyl alcohol. The toxicity and persistence profile tested via Toxtree showed that the Cramer Rules, Verhaar Scheme, and Structural Alerts for Reactivity, (START) biodegradation ability as positive, and all five target compounds were found as class-II persistent compounds. Furthermore, the Ecological Structure-Activity Relationships (ECOSAR)assisted testing specifies that all tested derivatives have multiple aquatic toxic levels. In summary, the current findings endorse the hazardous compounds and undertake prescreening of the deprivation policy to protect the environment.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18-26, 08034 Barcelona, Spain; Catalan Institute of Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, c/Emili Grahit, 101, Edifici H2O, 17003 Girona, Spain; Sustainability Cluster, School of Engineering, UPES, Dehradun, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
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37
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The identification of biotransformation pathways for removing fishy malodor from Bangia fusco-purpurea using fermentation with Saccharomyces cerevisiae. Food Chem 2022; 380:132103. [DOI: 10.1016/j.foodchem.2022.132103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/26/2021] [Accepted: 01/05/2022] [Indexed: 01/15/2023]
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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Screening of fungi from the phylum Basidiomycota for degradation of boar taint aroma compounds. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-04045-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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van Eerde A, Várnai A, Wang Y, Paruch L, Jameson JK, Qiao F, Eiken HG, Su H, Eijsink VGH, Clarke JL. Successful Production and Ligninolytic Activity of a Bacterial Laccase, Lac51, Made in Nicotiana benthamiana via Transient Expression. FRONTIERS IN PLANT SCIENCE 2022; 13:912293. [PMID: 35646038 PMCID: PMC9141054 DOI: 10.3389/fpls.2022.912293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Giant panda could have bamboo as their exclusive diet for about 2 million years because of the contribution of numerous enzymes produced by their gut bacteria, for instance laccases. Laccases are blue multi-copper oxidases that catalyze the oxidation of a broad spectrum of phenolic and aromatic compounds with water as the only byproduct. As a "green enzyme," laccases have potential in industrial applications, for example, when dealing with degradation of recalcitrant biopolymers, such as lignin. In the current study, a bacterial laccase, Lac51, originating from Pseudomonas putida and identified in the gut microbiome of the giant panda's gut was transiently expressed in the non-food plant Nicotiana benthamiana and characterized. Our results show that recombinant Lac51 exhibits bacterial laccase properties, with optimal pH and temperature at 7-8 and 40°C, respectively, when using syringaldazine as substrate. Moreover, we demonstrate the functional capability of the plant expressed Lac51 to oxidize lignin using selected lignin monomers that serve as substrates of Lac51. In summary, our study demonstrates the potential of green and non-food plants as a viable enzyme production platform for bacterial laccases. This result enriches our understanding of plant-made enzymes, as, to our knowledge, Lac51 is the first functional recombinant laccase produced in plants.
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Affiliation(s)
- André van Eerde
- NIBIO - Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Yanliang Wang
- NIBIO - Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Lisa Paruch
- NIBIO - Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - John-Kristian Jameson
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Fen Qiao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Haidian, China
| | - Hans Geir Eiken
- NIBIO - Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Hang Su
- NIBIO - Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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41
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Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements. Antioxidants (Basel) 2022; 11:antiox11050891. [PMID: 35624755 PMCID: PMC9137552 DOI: 10.3390/antiox11050891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are extracellular fungal enzymes of biotechnological interest as self-sufficient (and more stable) counterparts of cytochrome P450 monooxygenases, the latter being present in most living cells. Expression hosts and structural information are crucial for exploiting UPO diversity (over eight thousand UPO-type genes were identified in sequenced genomes) in target reactions of industrial interest. However, while many thousands of entries in the Protein Data Bank include molecular coordinates of P450 enzymes, only 19 entries correspond to UPO enzymes, and UPO structures from only two species (Agrocybe aegerita and Hypoxylon sp.) have been published to date. In the present study, two UPOs from the basidiomycete Marasmius rotula (rMroUPO) and the ascomycete Collariella virescens (rCviUPO) were crystallized after sequence optimization and Escherichia coli expression as active soluble enzymes. Crystals of rMroUPO and rCviUPO were obtained at sufficiently high resolution (1.45 and 1.95 Å, respectively) and the corresponding structures were solved by molecular replacement. The crystal structures of the two enzymes (and two mutated variants) showed dimeric proteins. Complementary biophysical and molecular biology studies unveiled the diverse structural bases of the dimeric nature of the two enzymes. Intermolecular disulfide bridge and parallel association between two α-helices, among other interactions, were identified at the dimer interfaces. Interestingly, one of the rCviUPO variants incorporated the ability to produce fatty acid diepoxides—reactive compounds with valuable cross-linking capabilities—due to removal of the enzyme C-terminal tail located near the entrance of the heme access channel. In conclusion, different dimeric arrangements could be described in (short) UPO crystal structures.
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Arteaga-Castrejón AA, Trejo-Hernández MR, Mekmouche Y, Amouric A, Rousselot-Pailley P, Robert V, Tron T, Martínez-Morales F. Relevance of Surface-Exposed Lysine Residues Designed for Functionalization of Laccase. Mol Biol 2022. [DOI: 10.1134/s0026893322040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kinner A, Nerke P, Siedentop R, Steinmetz T, Classen T, Rosenthal K, Nett M, Pietruszka J, Lütz S. Recent Advances in Biocatalysis for Drug Synthesis. Biomedicines 2022; 10:964. [PMID: 35625702 PMCID: PMC9138302 DOI: 10.3390/biomedicines10050964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 02/01/2023] Open
Abstract
Biocatalysis is constantly providing novel options for the synthesis of active pharmaceutical ingredients (APIs). In addition to drug development and manufacturing, biocatalysis also plays a role in drug discovery and can support many active ingredient syntheses at an early stage to build up entire scaffolds in a targeted and preparative manner. Recent progress in recruiting new enzymes by genome mining and screening or adapting their substrate, as well as product scope, by protein engineering has made biocatalysts a competitive tool applied in academic and industrial spheres. This is especially true for the advances in the field of nonribosomal peptide synthesis and enzyme cascades that are expanding the capabilities for the discovery and synthesis of new bioactive compounds via biotransformation. Here we highlight some of the most recent developments to add to the portfolio of biocatalysis with special relevance for the synthesis and late-stage functionalization of APIs, in order to bypass pure chemical processes.
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Affiliation(s)
- Alina Kinner
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Philipp Nerke
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Regine Siedentop
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Till Steinmetz
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Thomas Classen
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Markus Nett
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Jörg Pietruszka
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf Located at Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
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44
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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Sharma A, Vázquez LAB, Hernández EOM, Becerril MYM, Oza G, Ahmed SSSJ, Ramalingam S, Iqbal HMN. Green remediation potential of immobilized oxidoreductases to treat halo-organic pollutants persist in wastewater and soil matrices - A way forward. CHEMOSPHERE 2022; 290:133305. [PMID: 34929272 DOI: 10.1016/j.chemosphere.2021.133305] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
The alarming presence of hazardous halo-organic pollutants in wastewater and soils generated by industrial growth, pharmaceutical and agricultural activities is a major environmental concern that has drawn the attention of scientists. Unfortunately, the application of conventional technologies within hazardous materials remediation processes has radically failed due to their high cost and ineffectiveness. Consequently, the design of innovative and sustainable techniques to remove halo-organic contaminants from wastewater and soils is crucial. Altogether, these aspects have led to the search for safe and efficient alternatives for the treatment of contaminated matrices. In fact, over the last decades, the efficacy of immobilized oxidoreductases has been explored to achieve the removal of halo-organic pollutants from diverse tainted media. Several reports have indicated that these enzymatic constructs possess unique properties, such as high removal rates, improved stability, and excellent reusability, making them promising candidates for green remediation processes. Hence, in this current review, we present an insight of green remediation approaches based on the use of immobilized constructs of phenoloxidases (e.g., laccase and tyrosinase) and peroxidases (e.g., horseradish peroxidase, chloroperoxidase, and manganese peroxidase) for sustainable decontamination of wastewater and soil matrices from halo-organic pollutants, including 2,4-dichlorophenol, 4-chlorophenol, diclofenac, 2-chlorophenol, 2,4,6-trichlorophenol, among others.
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Affiliation(s)
- Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Centre of Bioengineering, Campus Queretaro, 76130, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Centre of Bioengineering, Campus Queretaro, 76130, Mexico
| | | | | | - Goldie Oza
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Parque Tecnológico Querétaro S/n, Sanfandila. Pedro Escobedo, Querétaro, 76703, Mexico
| | - Shiek S S J Ahmed
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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46
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Morgan T, Tavares MP, Ladeira-Ázar RI, de Oliveira Mendes TA, Guimarães VM. The lytic polysaccharide monooxigenases secreted by the fungus Chrysoporthe cubensis: Genomic analysis and impact on sugarcane bagasse saccharification. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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47
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Lin Z, Cheng S, Li H, Li L. A novel, rapidly preparable and easily maintainable biocathode electrochemical biosensor for the continuous and stable detection of nitrite in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150945. [PMID: 34655619 DOI: 10.1016/j.scitotenv.2021.150945] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/17/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Nitrite is a highly toxic and pathogenic pollutant that is widely distributed in various nitrogenous wastewaters. Therefore, there is an urgent need for fast and stable nitrite detection to avoid water pollution and protect human health. In this study, we developed a novel rapidly preparable and easily maintainable biocathode electrochemical biosensor (BEB) using nitrite-reducing bacteria as the detectors to realize continuous nitrite monitoring in wastewater. The preparation of the biocathode was shortened by the polarity inversion method to less than 6 d. The BEB could detect nitrite solution samples in the range of 0.1- 16.0 mg NO2--N L-1 within 1.7 min. The BEB was also successfully used to detect nitrite in real wastewater with a relative error < 4.0% and a relative standard deviation < 5.8%. In addition, the BEB could be easily maintained by an operation mode of microbial fuel cells and stably detected nitrite for at least 150 tests. Our study provided a feasible and convenient way to develop electrochemical biosensors based on the biocathode for continuous and stable monitoring of pollutants in wastewater.
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Affiliation(s)
- Zhufan Lin
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Shaoan Cheng
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China.
| | - Huahua Li
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Longxin Li
- State Key Laboratory of Clean Energy, Department of Energy Engineering, Zhejiang University, Hangzhou 310027, PR China
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48
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Fard PT, Kim K, Lee S, Kim J. Ligand effects in rhodium complexes for chemical
NADH
regeneration. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kayoung Kim
- Department of Chemistry and Nano Science Ewha Womans University Seoul Korea
| | - Sohyun Lee
- Department of Chemistry and Nano Science Ewha Womans University Seoul Korea
| | - Jinheung Kim
- Department of Chemistry and Nano Science Ewha Womans University Seoul Korea
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49
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Broadening the Biocatalytic Toolbox-Screening and Expression of New Unspecific Peroxygenases. Antioxidants (Basel) 2022; 11:antiox11020223. [PMID: 35204106 PMCID: PMC8868357 DOI: 10.3390/antiox11020223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
Unspecific peroxygenases (UPOs) catalyze the selective transfer of single oxygen atoms from peroxides to a broad range of substrates such as un-activated hydrocarbons. Since specific oxyfunctionalizations are among the most-desired reactions in synthetic chemistry, UPOs are of high industrial interest. To broaden the number of available enzymes, computational and experimental methods were combined in this study. After a comparative alignment and homology modelling, the enzymes were expressed directly in P. pastoris. Out of ten initially selected sequences, three enzymes (one from Aspergillus niger and two from Candolleomyces aberdarensis) were actively expressed. Cultivation of respective expression clones in a bioreactor led to production titers of up to 300 mg L−1. Enzymes were purified to near homogeneity and characterized regarding their specific activities and pH-optima for typical UPO substrates. This work demonstrated that directed evolution is not necessarily required to produce UPOs in P. pastoris at respective titers. The heterologous producibility of these three UPOs will expand the toolbox of available enzymes and help to advance their synthetic application.
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50
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Hofrichter M, Kellner H, Herzog R, Karich A, Kiebist J, Scheibner K, Ullrich R. Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases. Antioxidants (Basel) 2022; 11:163. [PMID: 35052667 PMCID: PMC8772875 DOI: 10.3390/antiox11010163] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/03/2022] Open
Abstract
Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.
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Affiliation(s)
- Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Robert Herzog
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Alexander Karich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Jan Kiebist
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Katrin Scheibner
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
| | - René Ullrich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
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