1
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Singh AK, Iqbal HMN, Cardullo N, Muccilli V, Fern'andez-Lucas J, Schmidt JE, Jesionowski T, Bilal M. Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review. Int J Biol Macromol 2023:124968. [PMID: 37217044 DOI: 10.1016/j.ijbiomac.2023.124968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.
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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
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Jesús Fern'andez-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanizaci'on El Bosque, 28670 Villaviciosa de Od'on, Spain; Grupo de Investigaci'on en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jens Ejbye Schmidt
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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2
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Gye H, Baek H, Han S, Kwon H, Nguyen TVT, Pham LTM, Kang S, Nho YH, Lee DW, Kim YH. Recombinant Lignin Peroxidase with Superior Thermal Stability and Melanin Decolorization Efficiency in a Typical Human Skin-Mimicking Environment. Biomacromolecules 2023. [PMID: 37075205 DOI: 10.1021/acs.biomac.3c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Recently, the desire for a safe and effective method for skin whitening has been growing in the cosmetics industry. Commonly used tyrosinase-inhibiting chemical reagents exhibit side effects. Thus, recent studies have focused on performing melanin decolorization with enzymes as an alternative due to the low toxicity of enzymes and their ability to decolorize melanin selectively. Herein, 10 different isozymes were expressed as recombinant lignin peroxidases (LiPs) from Phanerochaete chrysosporium (PcLiPs), and PcLiP isozyme 4 (PcLiP04) was selected due to its high stability and activity at pH 5.5 and 37 °C, which is close to human skin conditions. In vitro melanin decolorization results indicated that PcLiP04 exhibited at least 2.9-fold higher efficiency than that of well-known lignin peroxidase (PcLiP01) in a typical human skin-mimicking environment. The interaction force between melanin films measured by a surface forces apparatus (SFA) revealed that the decolorization of melanin by PcLiP04 harbors a disrupted structure, possibly interrupting π-π stacking and/or hydrogen bonds. In addition, a 3D reconstructed human pigmented epidermis skin model showed a decrease in melanin area to 59.8% using PcLiP04, which suggests that PcLiP04 exhibits a strong potential for skin whitening.
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Affiliation(s)
- Hyeryeong Gye
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Heeyeon Baek
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Seunghyun Han
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Haeun Kwon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Trang Vu Thien Nguyen
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Le Thanh Mai Pham
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Seunghyun Kang
- Bio Technology Lab, COSMAX BTI R&I Center, Seongnam 13486, Republic of Korea
| | - Youn Hwa Nho
- Bio Technology Lab, COSMAX BTI R&I Center, Seongnam 13486, Republic of Korea
| | - Dong Woog Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50, UNIST-gil, Ulsan 44919, Republic of Korea
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3
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Jian T, Zhou Y, Wang P, Yang W, Mu P, Zhang X, Zhang X, Chen CL. Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities. Nat Commun 2022; 13:3025. [PMID: 35641490 PMCID: PMC9156750 DOI: 10.1038/s41467-022-30285-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/25/2022] [Indexed: 02/05/2023] Open
Abstract
Developing tunable and stable peroxidase mimetics with high catalytic efficiency provides a promising opportunity to improve and expand enzymatic catalysis in lignin depolymerization. A class of peptoid-based peroxidase mimetics with tunable catalytic activity and high stability is developed by constructing peptoids and hemins into self-assembled crystalline nanomaterials. By varying peptoid side chain chemistry to tailor the microenvironment of active sites, these self-assembled peptoid/hemin nanomaterials (Pep/hemin) exhibit highly modulable catalytic activities toward two lignin model substrates 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 3,3’,5,5’-tetramethylbenzidine. Among them, a Pep/hemin complex containing the pyridyl side chain showed the best catalytic efficiency (Vmax/Km = 5.81 × 10−3 s−1). These Pep/hemin catalysts are highly stable; kinetics studies suggest that they follow a peroxidase-like mechanism. Moreover, they exhibit a high efficacy on depolymerization of a biorefinery lignin. Because Pep/hemin catalysts are highly robust and tunable, we expect that they offer tremendous opportunities for lignin valorization to high value products. Peroxidase mimics are currently being investigated as catalysts for lignin depolymerisation. In this article, the authors investigate a class of self-assembled and highly stable peptoid/hemin nanomaterials as peroxidase mimics that are highly stable and tuneable for the depolymerisation of a biorefinery lignin.
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Affiliation(s)
- Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Peipei Wang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, NY, 13902, USA
| | - Xin Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xiao Zhang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA.
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. .,Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
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4
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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5
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Pham LTM, Deng K, Northen TR, Singer SW, Adams PD, Simmons BA, Sale KL. Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:108. [PMID: 33926536 PMCID: PMC8082889 DOI: 10.1186/s13068-021-01953-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/11/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4' ether bonds and C-C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4' ether bonds and of C-C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. RESULTS Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4' ether bond cleavage, 27.0% Cα-C1 carbon bond cleavage, and 3.6% Cα-oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4' bonds. CONCLUSION These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.
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Affiliation(s)
- Le Thanh Mai Pham
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94550 USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94550 USA
| | - Trent R. Northen
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Steven W. Singer
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- University of California, Berkeley, CA 94720 USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94550 USA
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6
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Son H, Seo H, Han S, Kim SM, Pham LTM, Khan MF, Sung HJ, Kang SH, Kim KJ, Kim YH. Extra disulfide and ionic salt bridge improves the thermostability of lignin peroxidase H8 under acidic condition. Enzyme Microb Technol 2021; 148:109803. [PMID: 34116764 DOI: 10.1016/j.enzmictec.2021.109803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022]
Abstract
The development of a lignin peroxidase (LiP) that is thermostable even under acidic pH conditions is a main issue for efficient enzymatic lignin degradation due to reduced repolymerization of free phenolic products at acidic pH (< 3). Native LiP under mild conditions (half-life (t1/2) of 8.2 days at pH 6) exhibits a marked decline in thermostability under acidic conditions (t1/2 of only 14 min at pH 2.5). Thus, improving the thermostability of LiP in acidic environments is required for effective lignin depolymerization in practical applications. Here, we show the improved thermostability of a synthetic LiPH8 variant (S49C/A67C/H239E, PDB: 6ISS) capable of strengthening the helix-loop interactions under acidic conditions. This variant retained excellent thermostability at pH 2.5 with a 10-fold increase in t1/2 (2.52 h at 25 °C) compared with that of the native enzyme. X-ray crystallography analysis showed that the recombinant LiPH8 variant is the only unique lignin peroxidase containing five disulfide bridges, and the helix-loop interactions of the synthetic disulfide bridge and ionic salt bridge in its structure are responsible for stabilizing the Ca2+-binding region and heme environment, resulting in an increase in overall structural resistance against acidic conditions. Our work will allow the design of biocatalysts for ligninolytic enzyme engineering and for efficient biocatalytic degradation of plant biomass in lignocellulose biorefineries.
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Affiliation(s)
- Haewon Son
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Seunghyun Han
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Suk Min Kim
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Le Thanh Mai Pham
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Mohd Faheem Khan
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Ho Joon Sung
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Sung-Heuck Kang
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea.
| | - Yong Hwan Kim
- Department of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea.
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7
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Singh AK, Katari SK, Umamaheswari A, Raj A. In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. RSC Adv 2021; 11:14632-14653. [PMID: 35423962 PMCID: PMC8697836 DOI: 10.1039/d0ra10840e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Lignin peroxidase is a heme-containing biocatalyst, well-known for its diverse applications in the fields from environmental chemistry to biotechnology. LiP-mediated oxidative catalysis is H2O2-dependent, and can oxidize phenolic, and non-phenolic substrates by oxidative cleavage of the C-C and C-O bonds of lignin. In contrast to fungi-derived LiP, the binding affinity of bacterial-derived LiP to lignin at the molecular level is poorly known to date. Tremendous wet-lab studies have been unveiled that provide degradation and biotransformation information on kraft lignin, whilst studies on the completely transformed compounds and the degradation of each transformed compounds simultaneously during degradation are scarce. To gain an understanding of the degradation process using docking, and MDS based studies, we assessed the binding affinity of selected lignin model compounds with bacterial origin LiP and validated such docked complexes exploiting 30 ns molecular dynamics simulations. We selected and picked a total of 12 lignin model compounds for molecular modeling analysis, namely two chlorinated lignin model compounds (monomer) (2-chlorosyringaldehyde and 5-chlorovanillin), eight standard lignin model compounds (veratryl alcohol, syringyl alcohol, sinapyl alcohol, methyl hydroquinone, guaiacol, coniferyl alcohol, catechol, and 4-methoxy phenol), while, two 4-O-5, and β-O-4 linkage-based multimeric model compounds (dimer: 2-methoxy-6-(2-methoxy-4-methylphenoxy)-4-methylphenol; trimer: syringyl β-O-4 syringyl β-O-4 sinapyl alcohol). Far more specific binding residues were observed from XP-Glide docking, as TYR, HIP (protonated histidine), PHE, VAL, ASP, THR, LYS and GLN. The binding affinity was confirmed by the Gibbs free energy or binding energy (ΔG) score; furthermore, it is found that the maximum binding energy seems to be observed for 4-methoxyphenol with a Glide score of -3.438 with Pi-Pi stacking and H-bond type bonding interactions, whilst the lowest XP Gscore as -8.136 with Pi-Pi stacking and H-bond (side chain) type bonding interactions were found for the trimer model compound. The docked complexes were further evaluated for deep rigorous structural and functional fluctuation analyses through high-performance molecular dynamics simulations-DESMOND, after a post simulation run of 30 ns. The RMSD trajectory analyses of the protein-ligands were found to be in the equilibrium state at the end of simulation run for multimeric lignin model compounds. In addition, ionic ligand-protein interaction occurs among chlorinated compounds, while hydrophobic and H-bond contacts have frequently been observed in all lignin-model compounds. The findings herein demonstrate that bacterial LiP can effectively catalyze multiple lignin model compounds, and it might further be used as an effective tool for sustainable mitigation of diverse environmental contaminants.
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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
| | - Sudheer Kumar Katari
- Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences (SVIMS) University Tirupati 517507 Andhra Pradesh India
| | - Amineni Umamaheswari
- Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences (SVIMS) University Tirupati 517507 Andhra Pradesh India
| | - Abhay Raj
- 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
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8
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Microbial lignin peroxidases: Applications, production challenges and future perspectives. Enzyme Microb Technol 2020; 141:109669. [DOI: 10.1016/j.enzmictec.2020.109669] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
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9
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Wang L, Wang D, Zhang Z, Cheng S, Liu B, Wang C, Li R, Guo S. Comparative Glucose and Xylose Coutilization Efficiencies of Soil-Isolated Yeast Strains Identify Cutaneotrichosporon dermatis as a Potential Producer of Lipid. ACS OMEGA 2020; 5:23596-23603. [PMID: 32984679 PMCID: PMC7512434 DOI: 10.1021/acsomega.0c02089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Glucose and xylose are the major hydrolysates of lignocellulose, and therefore, it is of great implication to identify the microbes involved in simultaneous utilization of glucose and xylose. In this study, the strain ZZ-46 isolated from the soil of Nanyang, China, could simultaneously assimilate glucose and xylose efficiently to produce lipid. Upon cultivation with a 2:1 glucose/xylose mixture as the carbon source for 144 h, the cell biomass, lipid concentration, lipid content, and lipid yield of ZZ-46 reached 19.85 ± 0.39 g/L, 9.53 ± 0.60 g/L, 48.05 ± 3.51%, and 0.142 ± 0.003 g/g sugar, respectively. Moreover, C16 and C18 fatty acids were the main constituents of lipid produced by ZZ-46. In addition, ZZ-46 was identified as Cutaneotrichosporon dermatis by the morphology features and phylogenetic analyses. The strain ZZ-46 would have good perspective in practical application for converting lignocellulose into microbial lipid.
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Affiliation(s)
- Laiyou Wang
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
- State
Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473004, China
| | - Dongmei Wang
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
| | - Zhili Zhang
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
| | - Shuang Cheng
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
| | - Bingbing Liu
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
| | - Chunyan Wang
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
| | - Ruige Li
- School
of Mathematics and Statistics, Nanyang Institute
of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
| | - Shuxian Guo
- School
of Biological and Chemical Engineering, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng
District, Nanyang 473004, Henan, China
- Henan
Key Laboratory of Industrial Microbial Resources and Fermentation
Technology, Nanyang Institute of Technology, No. 80 Changjiang Road, Wancheng District, Nanyang 473004, Henan, China
- State
Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473004, China
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10
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Unassisted solar lignin valorisation using a compartmented photo-electro-biochemical cell. Nat Commun 2019; 10:5123. [PMID: 31719532 PMCID: PMC6851146 DOI: 10.1038/s41467-019-13022-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/10/2019] [Indexed: 11/08/2022] Open
Abstract
Lignin is a major component of lignocellulosic biomass. Although it is highly recalcitrant to break down, it is a very abundant natural source of valuable aromatic carbons. Thus, the effective valorisation of lignin is crucial for realising a sustainable biorefinery chain. Here, we report a compartmented photo-electro-biochemical system for unassisted, selective, and stable lignin valorisation, in which a TiO2 photocatalyst, an atomically dispersed Co-based electrocatalyst, and a biocatalyst (lignin peroxidase isozyme H8, horseradish peroxidase) are integrated, such that each system is separated using Nafion and cellulose membranes. This cell design enables lignin valorisation upon irradiation with sunlight without the need for any additional bias or sacrificial agent and allows the protection of the biocatalyst from enzyme-damaging elements, such as reactive radicals, gas bubbles, and light. The photo-electro-biochemical system is able to catalyse lignin depolymerisation with a 98.7% selectivity and polymerisation with a 73.3% yield using coniferyl alcohol, a lignin monomer.
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Min K, Park GW, Yoo YJ, Lee JS. A perspective on the biotechnological applications of the versatile tyrosinase. BIORESOURCE TECHNOLOGY 2019; 289:121730. [PMID: 31279520 DOI: 10.1016/j.biortech.2019.121730] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Tyrosinase (E.C. 1.14.18. 1) is a type of Cu-containing oxidoreductase which has bifunctional activity for various phenolic substrates: ortho-hydroxylation of monophenols to diphenols (a cresolase activity) and oxidation of diphenols to quinones (a catecholase activity). Based on the broad substrate spectrum, tyrosinase has been used in bioremediation of phenolic pollutants, constructing biosensors for identifying phenolic compounds, and L-DOPA synthesis. Furthermore, not only tyrosinase has been used to produce useful polyphenol derivatives, but also it is recently revealed that the promiscuous activity of tyrosinase is closely related with delignification in the biorefinery. Accordingly, tyrosinase might be a potential biocatalyst for industrial applications (e.g., electroenzymatic L-DOPA production, but its long-term stability and reusability should be further explored. In this review, we emphasize the versatility of tyrosinase, which includes conventional applications, and suggest new perspectives as an industrial biocatalyst (e.g., electroenzymatic L-DOPA production). Especially, this review focuses on and comprehensively discusses recent innovative studies.
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Affiliation(s)
- Kyoungseon Min
- Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Young Je Yoo
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Suk Lee
- Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
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Pham LTM, Seo H, Kim KJ, Kim YH. In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:325. [PMID: 30555531 PMCID: PMC6287364 DOI: 10.1186/s13068-018-1324-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/29/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND The lignin peroxidase isozyme H8 from the white-rot fungus Phanerochaete chrysosporium (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin. RESULTS The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from Phanerochaete chrysosporium and acid-stable manganese peroxidase isozyme 6 (MnP6) from Ceriporiopsis subvermispora. Effective salt bridges were probed by molecular dynamics simulation and changes to Gibbs free energy following mutagenesis were predicted, suggesting promising variants with higher stability under extremely acidic conditions. The rationally designed variant, A55R/N156E-H239E, demonstrated a 12.5-fold increased half-life under extremely acidic conditions, 9.9-fold increased catalytic efficiency toward veratryl alcohol, and a 7.8-fold enhanced lignin model dimer conversion efficiency compared to those of native LiPH8. Furthermore, the two constructed salt bridges in the variant A55R/N156E-H239E were experimentally confirmed to be identical to the intentionally designed LiPH8 variant using X-ray crystallography (PDB ID: 6A6Q). CONCLUSION Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.
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Affiliation(s)
- Le Thanh Mai Pham
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
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Sakai K, Kojiya S, Kamijo J, Tanaka Y, Tanaka K, Maebayashi M, Oh JS, Ito M, Hori M, Shimizu M, Kato M. Oxygen-radical pretreatment promotes cellulose degradation by cellulolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:290. [PMID: 29213329 PMCID: PMC5713004 DOI: 10.1186/s13068-017-0979-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The efficiency of cellulolytic enzymes is important in industrial biorefinery processes, including biofuel production. Chemical methods, such as alkali pretreatment, have been extensively studied and demonstrated as effective for breaking recalcitrant lignocellulose structures. However, these methods have a detrimental effect on the environment. In addition, utilization of these chemicals requires alkali- or acid-resistant equipment and a neutralization step. RESULTS Here, a radical generator based on non-thermal atmospheric pressure plasma technology was developed and tested to determine whether oxygen-radical pretreatment enhances cellulolytic activity. Our results showed that the viscosity of carboxymethyl cellulose (CMC) solutions was reduced in a time-dependent manner by oxygen-radical pretreatment using the radical generator. Compared with non-pretreated CMC, oxygen-radical pretreatment of CMC significantly increased the production of reducing sugars in culture supernatant containing various cellulases from Phanerochaete chrysosporium. The production of reducing sugar from oxygen-radical-pretreated CMC by commercially available cellobiohydrolases I and II was 1.7- and 1.6-fold higher, respectively, than those from non-pretreated and oxygen-gas-pretreated CMC. Moreover, the amount of reducing sugar from oxygen-radical-pretreated wheat straw was 1.8-fold larger than those from non-pretreated and oxygen-gas-pretreated wheat straw. CONCLUSIONS Oxygen-radical pretreatment of CMC and wheat straw enhanced the degradation of cellulose by reducing- and non-reducing-end cellulases in the supernatant of a culture of the white-rot fungus P. chrysosporium. These findings indicated that oxygen-radical pretreatment of plant biomass offers great promise for improvements in lignocellulose-deconstruction processes.
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Affiliation(s)
- Kiyota Sakai
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Saki Kojiya
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Junya Kamijo
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Yuta Tanaka
- Faculty of Science and Technology, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Kenta Tanaka
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
| | | | - Jun-Seok Oh
- Faculty of Science and Technology, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Masafumi Ito
- Faculty of Science and Technology, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Masaru Hori
- Institute of Innovation for Future Society, Nagoya University, Nagoya, Aichi 464-8603 Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
| | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502 Japan
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Acebes S, Ruiz-Dueñas FJ, Toubes M, Sáez-Jiménez V, Pérez-Boada M, Lucas MF, Martínez AT, Guallar V. Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases. J Phys Chem B 2017; 121:3946-3954. [PMID: 28375014 DOI: 10.1021/acs.jpcb.7b00835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.
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Affiliation(s)
- Sandra Acebes
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Program in Computational Biology , Jordi Girona 29, E-08034 Barcelona, Spain
| | | | - Mario Toubes
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Veronica Sáez-Jiménez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Marta Pérez-Boada
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - M Fátima Lucas
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Program in Computational Biology , Jordi Girona 29, E-08034 Barcelona, Spain.,Anaxomics Biotech , Balmes 89, 08008 Barcelona, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Program in Computational Biology , Jordi Girona 29, E-08034 Barcelona, Spain.,ICREA , Passeig Lluís Companys 23, E-08010 Barcelona, Spain
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Albarrán-Velo J, López-Iglesias M, Gotor V, Gotor-Fernández V, Lavandera I. Synthesis of nitrogenated lignin-derived compounds and reactivity with laccases. Study of their application in mild chemoenzymatic oxidative processes. RSC Adv 2017. [DOI: 10.1039/c7ra10497a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The chemical synthesis of a series of nitrogenated lignin-derived compounds, their reactivity with laccases and further application in mild oxidative processes are here disclosed.
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Affiliation(s)
- Jesús Albarrán-Velo
- Organic and Inorganic Chemistry Department
- Biotechnology Institute of Asturias (IUBA)
- University of Oviedo
- 33006 Oviedo
- Spain
| | - María López-Iglesias
- Organic and Inorganic Chemistry Department
- Biotechnology Institute of Asturias (IUBA)
- University of Oviedo
- 33006 Oviedo
- Spain
| | - Vicente Gotor
- Organic and Inorganic Chemistry Department
- Biotechnology Institute of Asturias (IUBA)
- University of Oviedo
- 33006 Oviedo
- Spain
| | - Vicente Gotor-Fernández
- Organic and Inorganic Chemistry Department
- Biotechnology Institute of Asturias (IUBA)
- University of Oviedo
- 33006 Oviedo
- Spain
| | - Iván Lavandera
- Organic and Inorganic Chemistry Department
- Biotechnology Institute of Asturias (IUBA)
- University of Oviedo
- 33006 Oviedo
- Spain
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