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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024; 17:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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2
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Sánchez-Ruiz MI, Santillana E, Linde D, Romero A, Martínez AT, Ruiz-Dueñas FJ. Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:74. [PMID: 38824538 PMCID: PMC11144326 DOI: 10.1186/s13068-024-02517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure-function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule. RESULTS Two MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD-referred to as Ape-MnP1 and Cst-MnP1, respectively-were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation. CONCLUSIONS Understanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure-function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.
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Affiliation(s)
- María Isabel Sánchez-Ruiz
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Elena Santillana
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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3
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Spasojević D, Prodanović O, Mutavdžić D, Sekuljica N, Jovanović J, Maksimović V, Radotić K. Two-way reaction of versatile peroxidase with artificial lignin enhances low-molecular weight fractions. Biotechnol J 2023; 18:e2300312. [PMID: 37688491 DOI: 10.1002/biot.202300312] [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: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
In recent years, versatile peroxidase (VP) has emerged as a promising enzyme for biotechnological applications, as it can oxidize lignin without the external mediators. To gain insights into the breakdown process of artificial lignin by VP, reaction between the two was studied. Degradation products were fractionated using ultrafiltration and analyzed by RP- high performance liquid chromatography with mass detection (HPLC-MS) chromatography. Four fractions were obtained based on their molecular sizes: >10, 3-10, 1-3, and <1 kDa. Interestingly, while VP did not significantly alter the yields of these fractions, the chromatograms revealed the presence of oligomers with different molecular weights (MWs) resulting from the enzymatic activity. The VP exhibits a dual role in its enzymatic activity: both degrading and synthesizing these oligomers. This was confirmed by principal component analysis (PCA). The positive correlations were found between certain oligomers (D1 and D2, D5 and D6, as well as between D7, D10, T2, and T4), suggesting their simultaneous degradation. On the other hand, a negative correlation was found between the monomer and some oligomers (D7, D10, T2, and T4), indicating the decomposition of these oligomers into monomers. These findings shed light on the intricate interplay between VP and artificial lignin, offering valuable insights for potential applications in lignin valorization.
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Affiliation(s)
- Dragica Spasojević
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Olivera Prodanović
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Dragosav Mutavdžić
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Nataša Sekuljica
- Innovation Center of Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | - Jelena Jovanović
- Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | - Vuk Maksimović
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Ksenija Radotić
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
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4
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Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds. Int J Mol Sci 2023; 24:13115. [PMID: 37685920 PMCID: PMC10487439 DOI: 10.3390/ijms241713115] [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: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.
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Affiliation(s)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (K.V.M.); (O.S.S.); (T.V.F.)
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5
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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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6
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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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7
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Viriato V, Mäkelä MR, Kowalczyk JE, Ballarin CS, Loiola PP, Andrade MCN. Organic residues from agricultural and forest companies in Brazil as useful substrates for cultivation of the edible mushroom Pleurotus ostreatus. Lett Appl Microbiol 2021; 74:44-52. [PMID: 34614248 DOI: 10.1111/lam.13580] [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: 08/19/2021] [Revised: 09/16/2021] [Accepted: 10/02/2021] [Indexed: 11/28/2022]
Abstract
We investigated whether highly available organic residues in Brazil can be used as substrates for the production of the oyster mushroom Pleurotus ostreatus, instead of the conventional cultivation using the eucalyptus sawdust substrate. We assessed the mushroom yield on 13 substrates, of which 12 were formulated with different concentrations of organic residues and one with pure eucalyptus sawdust, and verified whether the raw material used in the substrate formula and the concentration of such alternative residues influenced their biological efficiencies. Substrates containing eucalyptus bark resulted in higher mushroom yield than those containing eucalyptus sawdust, which generally resulted in similar mushroom yield to the remaining formulas. Moreover, the raw material and the concentration of each residue affected the biological efficiency of the substrates. We show that the conventional substrate for P. ostreatus can be replaced by substrates easily accessible to producers without loss in productivity. Furthermore, that the concentration of these mixtures affects the mushroom productivity and should be considered when formulating the growth medium.
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Affiliation(s)
- V Viriato
- Graduate Program in Agriculture - Energy in Agriculture, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo State, Brazil
| | - M R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - J E Kowalczyk
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - C S Ballarin
- Graduate Program in Biological Sciences (Botany), Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo State, Brazil
| | - P P Loiola
- Department of Biodiversity, Laboratory of Phenology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo State, Brazil
| | - M C N Andrade
- Graduate Program in Agriculture - Energy in Agriculture, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo State, Brazil
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8
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Lim HJ, Kim DM. Cell-free synthesis of industrial chemicals and biofuels from carbon feedstocks. Curr Opin Biotechnol 2021; 73:158-163. [PMID: 34450473 DOI: 10.1016/j.copbio.2021.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2021] [Accepted: 08/01/2021] [Indexed: 12/26/2022]
Abstract
The power of biological systems can be harnessed with higher efficiency when biosynthetic reactions are decoupled from cellular physiology. This can be achieved by cell-free synthesis, which relies on the in vitro use of cellular machinery under optimized reaction conditions. As exemplified by the recent development of mRNA vaccines and therapeutics, the cell-free synthesis of biomolecules is fast, efficient and flexible. Cell-free synthesis of industrial chemicals and biofuels is drawing considerable attention as a promising alternative to microbial fermentation processes, which currently show low conversion yields and toxicity to host cells. Here, we provide a brief overview of the history of cell-free synthesis systems and the state-of-the-art cell-free technologies used to produce diverse chemicals and biofuels. We also discuss the future directions of cell-free synthesis that can fully harness the synthetic power of biological systems.
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Affiliation(s)
- Hye Jin Lim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
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9
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Kour D, Kaur T, Devi R, Yadav A, Singh M, Joshi D, Singh J, Suyal DC, Kumar A, Rajput VD, Yadav AN, Singh K, Singh J, Sayyed RZ, Arora NK, Saxena AK. Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:24917-24939. [PMID: 33768457 DOI: 10.1007/s11356-021-13252-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/28/2021] [Indexed: 05/21/2023]
Abstract
Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.
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Affiliation(s)
- Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India
| | - Ashok Yadav
- Department of Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Manali Singh
- Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, Uttar Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Dehradun, Uttarakhand, India
| | - Jyoti Singh
- Department of Microbiology, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, 173101, India
| | - Ajay Kumar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | | | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, Sirmour, India.
| | - Karan Singh
- Department of Chemistry, Indira Gandhi University, Haryana, 122502, Meerpur, Rewari, India
| | - Joginder Singh
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Riyaz Z Sayyed
- Department of Microbiology, PSGVP Mandal's Arts, Science and Commerce College, Shahada, Maharashtra, India
| | - Naveen Kumar Arora
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central University), Rae Bareli Road, Uttar Pradesh, 226025, Lucknow, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kusmaur, Mau, 275103, India
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10
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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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11
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Fungal Secondary Metabolites for Bioremediation of Hazardous Heavy Metals. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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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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13
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Biological Pretreatment by Solid-State Fermentation of Oat Straw to Enhance Physical Quality of Pellets. J CHEM-NY 2020. [DOI: 10.1155/2020/3060475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pelleting can increase the efficiency of handling and transportation of biomass. Pretreatment obtains lignin fragments by disrupting the lignocellulosic structure of biomass and ensures the high-quality compressed pellets. In this study, solid-state fermentation (SSF) is used as a biological method to improve the quality of pellets of oat straw. SSF of oat straw using Trametes versicolor 52J (TV52J) and Phanerochaete chrysosporium (PC) was conducted. Response surface methodology (RSM) was employed by using a four-factor, three-level Box–Behnken design with fermentation time (days), moisture content (%), particle size (mm), and fermentation temperature (°C) as independent parameters. Pellet density, dimensional stability, and tensile strength were the response variables. The optimization options of fermentation time (33.96 and 35 days), moisture content (70%), particle size (150 and 50 mm), and fermentation temperature (22°C) of oat straw pretreated with these two fungal strains were obtained. The microscopic structural changes of oat straw caused by biological pretreatment were investigated by scanning electron microscopy (SEM). Observation results of SEM showed that the connection between single fibers became relatively loose, and this was beneficial to improve the physical quality of the pellets.
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14
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Stevens JC, Shi J. Biocatalysis in ionic liquids for lignin valorization: Opportunities and recent developments. Biotechnol Adv 2019; 37:107418. [DOI: 10.1016/j.biotechadv.2019.107418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/13/2019] [Accepted: 07/15/2019] [Indexed: 01/11/2023]
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15
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Nakazawa T, Morimoto R, Wu H, Kodera R, Sakamoto M, Honda Y. Dominant effects of gat1 mutations on the ligninolytic activity of the white-rot fungus Pleurotus ostreatus. Fungal Biol 2018; 123:209-217. [PMID: 30798876 DOI: 10.1016/j.funbio.2018.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
In nature, white-rot fungi efficiently degrade lignin present in wood biomass. Elucidation of molecular mechanisms underlying wood lignin biodegradation by white-rot fungi would contribute to the development of efficient and ecofriendly methods of producing valuable chemical products from wood biomass. Here, using forward genetics approach, we demonstrate that the mutant of a putative transcription factor gene, gat1-1, significantly decreases the ligninolytic activity of the white-rot fungus Pleurotus ostreatus, when grown on beech wood sawdust medium. We also show that this phenotype is dominant. In Schizophyllum commune, Gat1 was previously shown to be involved in fruiting body development. In this study, we reveal that the mutations in gat1 gene cause defects in fruiting body development in P. ostreatus. Unlike the previously reported recessive gene mutations that decrease the ligninolytic activity of P. ostreatus, the gat1-1 mutation and Δgat1 are dominant and would thus be useful for future studies on the functional role of the orthologs in other white-rot fungi.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Ryota Morimoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hongli Wu
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Rina Kodera
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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16
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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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17
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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18
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Bronikowski A, Koschorreck K, Urlacher VB. Redesign of a New Manganese Peroxidase Highly Expressed in
Pichia pastoris
towards a Lignin‐Degrading Versatile Peroxidase. Chembiochem 2018; 19:2481-2489. [DOI: 10.1002/cbic.201800500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Agathe Bronikowski
- Institute of Biochemistry and Bioeconomy Science Center (BioSc)Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Katja Koschorreck
- Institute of Biochemistry and Bioeconomy Science Center (BioSc)Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry and Bioeconomy Science Center (BioSc)Heinrich Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
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19
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Ceci A, Pinzari F, Russo F, Persiani AM, Gadd GM. Roles of saprotrophic fungi in biodegradation or transformation of organic and inorganic pollutants in co-contaminated sites. Appl Microbiol Biotechnol 2018; 103:53-68. [PMID: 30362074 DOI: 10.1007/s00253-018-9451-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/14/2023]
Abstract
For decades, human activities, industrialization, and agriculture have contaminated soils and water with several compounds, including potentially toxic metals and organic persistent xenobiotics. The co-occurrence of those toxicants poses challenging environmental problems, as complicated chemical interactions and synergies can arise and lead to severe and toxic effects on organisms. The use of fungi, alone or with bacteria, for bioremediation purposes is a growing biotechnology with high potential in terms of cost-effectiveness, an environmental-friendly perspective and feasibility, and often representing a sustainable nature-based solution. This paper reviews different ecological, metabolic, and physiological aspects involved in fungal bioremediation of co-contaminated soils and water systems, not only addressing best methods and approaches to assess the simultaneous presence of metals and organic toxic compounds and their consequences on provided ecosystem services but also the interactions between fungi and bacteria, in order to suggest further study directions in this field.
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Affiliation(s)
- Andrea Ceci
- Laboratorio di Biodiversità dei Funghi, Dipartimento di Biologia Ambientale, Sapienza Università di Roma, 00185, Rome, Italy
| | - Flavia Pinzari
- Centro di Ricerca Agricoltura e Ambiente, Consiglio per la Ricerca in agricoltura e l'analisi dell'Economia Agraria (CREA-AA), 00184, Rome, Italy.,Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Fabiana Russo
- Laboratorio di Biodiversità dei Funghi, Dipartimento di Biologia Ambientale, Sapienza Università di Roma, 00185, Rome, Italy
| | - Anna Maria Persiani
- Laboratorio di Biodiversità dei Funghi, Dipartimento di Biologia Ambientale, Sapienza Università di Roma, 00185, Rome, Italy.
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
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20
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Kohler AC, Simmons BA, Sale KL. Structure-based Engineering of a Plant-Fungal Hybrid Peroxidase for Enhanced Temperature and pH Tolerance. Cell Chem Biol 2018; 25:974-983.e3. [DOI: 10.1016/j.chembiol.2018.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/07/2018] [Accepted: 04/13/2018] [Indexed: 11/24/2022]
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21
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Bilal M, Iqbal HMN, Guo S, Hu H, Wang W, Zhang X. State-of-the-art protein engineering approaches using biological macromolecules: A review from immobilization to implementation view point. Int J Biol Macromol 2018; 108:893-901. [PMID: 29102791 DOI: 10.1016/j.ijbiomac.2017.10.182] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023]
Abstract
Over the past years, technological and scientific advances have proven biocatalysis as a sustainable alternative than traditional chemical catalysis including organo- or metallocatalysis. In this context, immobilization based approaches represent simple but effective routes for engineering enzyme catalysts with higher activities than wild-type derivatives. Many enzymes including oxidoreductases have been engineered by rational and directed evolution, to realize the catalytic activity, enantioselectivity, and stability attributes which are essential for their biotechnological exploitation. Induce yet stable activity in enzyme catalysis offer new insights and motivation to engineer efficient catalysts for practical and commercial purposes. It has now become possible to envisage substrate accessibility to the catalytic site of the enzyme by current computational capabilities that reduce the experimental work related to the enzyme selection, screening, and engineering. Herein, state-of-the-art protein engineering approaches for improving enzymatic activities including chemical modification, directed evolution, and rational design or their combination methods are discussed. The emphasis is also given to the applications of the resulting tailored catalysts ranging from fine chemicals to novel pharmaceutical compounds that use biocatalysts as a vital step.
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Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico
| | - Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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22
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Ho JCH, Pawar SV, Hallam SJ, Yadav VG. An Improved Whole-Cell Biosensor for the Discovery of Lignin-Transforming Enzymes in Functional Metagenomic Screens. ACS Synth Biol 2018; 7:392-398. [PMID: 29182267 DOI: 10.1021/acssynbio.7b00412] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery and utilization of biocatalysts that selectively valorize lignocellulose is critical to the profitability of next-generation biorefineries. Here, we report the development of a refactored, whole-cell, GFP-based biosensor for high-throughput identification of biocatalysts that transform lignin into specialty chemicals from environmental DNA of uncultivable archaea and bacteria. The biosensor comprises the transcriptional regulator and promoter of the emrRAB operon of E. coli, and the configuration of the biosensor was tuned with the aid of mathematical model. The biosensor sensitively and selectively detects vanillin and syringaldehyde, and responds linearly over a wide detection range. We employed the biosensor to screen 42 520 fosmid clones comprising environmental DNA isolated from two coal beds and successfully identified 147 clones that transform hardwood kraft lignin to vanillin and syringaldehyde.
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Affiliation(s)
- Joe C. H. Ho
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sandip V. Pawar
- Department of Chemical & Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Steven J. Hallam
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Vikramaditya G. Yadav
- Department of Chemical & Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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23
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Martínez AT, Ruiz-Dueñas FJ, Camarero S, Serrano A, Linde D, Lund H, Vind J, Tovborg M, Herold-Majumdar OM, Hofrichter M, Liers C, Ullrich R, Scheibner K, Sannia G, Piscitelli A, Pezzella C, Sener ME, Kılıç S, van Berkel WJ, Guallar V, Lucas MF, Zuhse R, Ludwig R, Hollmann F, Fernández-Fueyo E, Record E, Faulds CB, Tortajada M, Winckelmann I, Rasmussen JA, Gelo-Pujic M, Gutiérrez A, del Río JC, Rencoret J, Alcalde M. Oxidoreductases on their way to industrial biotransformations. Biotechnol Adv 2017. [DOI: 10.1016/j.biotechadv.2017.06.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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24
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Busse N, Kraume M, Czermak P. Modeling the design and operational mode of a continuous membrane reactor for enzymatic lignin modification. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Borin GP, Sanchez CC, de Santana ES, Zanini GK, Dos Santos RAC, de Oliveira Pontes A, de Souza AT, Dal'Mas RMMTS, Riaño-Pachón DM, Goldman GH, Oliveira JVDC. Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei. BMC Genomics 2017; 18:501. [PMID: 28666414 PMCID: PMC5493111 DOI: 10.1186/s12864-017-3857-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. Results Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. Conclusions This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Camila Cristina Sanchez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Eliane Silva de Santana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Guilherme Keppe Zanini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Angélica de Oliveira Pontes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Aline Tieppo de Souza
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Roberta Maria Menegaldo Tavares Soares Dal'Mas
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.,Current address: Laboratório de Biologia de Sistemas Regulatórios, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748 - Butantã - São Paulo - SP, São Paulo, CEP 05508-000, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, Ribeirão Preto, CEP, São Paulo, 14040-903, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.
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26
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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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27
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Vasina DV, Moiseenko KV, Fedorova TV, Tyazhelova TV. Lignin-degrading peroxidases in white-rot fungus Trametes hirsuta 072. Absolute expression quantification of full multigene family. PLoS One 2017; 12:e0173813. [PMID: 28301519 PMCID: PMC5354401 DOI: 10.1371/journal.pone.0173813] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Ligninolytic heme peroxidases comprise an extensive family of enzymes, which production is characteristic for white-rot Basidiomycota. The majority of fungal heme peroxidases are encoded by multigene families that differentially express closely related proteins. Currently, there were very few attempts to characterize the complete multigene family of heme peroxidases in a single fungus. Here we are focusing on identification and characterization of peroxidase genes, which are transcribed and secreted by basidiomycete Trametes hirsuta 072, an efficient lignin degrader. The T. hirsuta genome contains 18 ligninolytic peroxidase genes encoding 9 putative lignin peroxidases (LiP), 7 putative short manganese peroxidases (MnP) and 2 putative versatile peroxidases (VP). Using ddPCR method we have quantified the absolute expression of the 18 peroxidase genes under different culture conditions and on different growth stages of basidiomycete. It was shown that only two genes (one MnP and one VP) were prevalently expressed as well as secreted into cultural broth under all conditions investigated. However their transcriptome and protein profiles differed in time depending on the effector used. The expression of other peroxidase genes revealed a significant variability, so one can propose the specific roles of these enzymes in fungal development and lifestyle.
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Affiliation(s)
- Daria V. Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
| | - Konstantin V. Moiseenko
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
- * E-mail:
| | - Tatiana V. Fedorova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
| | - Tatiana V. Tyazhelova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
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28
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Duwe A, Tippkötter N, Ulber R. Lignocellulose-Biorefinery: Ethanol-Focused. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:177-215. [PMID: 29071401 DOI: 10.1007/10_2016_72] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development prospects of the world markets for petroleum and other liquid fuels are diverse and partly contradictory. However, comprehensive changes for the energy supply of the future are essential. Notwithstanding the fact that there are still very large deposits of energy resources from a geological point of view, the finite nature of conventional oil reserves is indisputable. To reduce our dependence on oil, the EU, the USA, and other major economic zones rely on energy diversification. For this purpose, alternative materials and technologies are being sought, and is most obvious in the transport sector. The objective is to progressively replace fossil fuels with renewable and more sustainable fuels. In this respect, biofuels have a pre-eminent position in terms of their capability of blending with fossil fuels and being usable in existing cars without substantial modification. Ethanol can be considered as the primary renewable liquid fuel. In this chapter enzymes, micro-organisms, and processes for ethanol production based on renewable resources are described.
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Affiliation(s)
- A Duwe
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany.
| | - N Tippkötter
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
| | - R Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
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29
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Deshmukh R, Khardenavis AA, Purohit HJ. Diverse Metabolic Capacities of Fungi for Bioremediation. Indian J Microbiol 2016; 56:247-64. [PMID: 27407289 PMCID: PMC4920763 DOI: 10.1007/s12088-016-0584-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 04/12/2016] [Indexed: 11/30/2022] Open
Abstract
Bioremediation refers to cost-effective and environment-friendly method for converting the toxic, recalcitrant pollutants into environmentally benign products through the action of various biological treatments. Fungi play a major role in bioremediation owing to their robust morphology and diverse metabolic capacity. The review focuses on different fungal groups from a variety of habitats with their role in bioremediation of different toxic and recalcitrant compounds; persistent organic pollutants, textile dyes, effluents from textile, bleached kraft pulp, leather tanning industries, petroleum, polyaromatic hydrocarbons, pharmaceuticals and personal care products, and pesticides. Bioremediation of toxic organics by fungi is the most sustainable and green route for cleanup of contaminated sites and we discuss the multiple modes employed by fungi for detoxification of different toxic and recalcitrant compounds including prominent fungal enzymes viz., catalases, laccases, peroxidases and cyrochrome P450 monooxygeneses. We have also discussed the recent advances in enzyme engineering and genomics and research being carried out to trace the less understood bioremediation pathways.
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Affiliation(s)
- Radhika Deshmukh
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Anshuman A. Khardenavis
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Hemant J. Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
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30
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Lambertz C, Ece S, Fischer R, Commandeur U. Progress and obstacles in the production and application of recombinant lignin-degrading peroxidases. Bioengineered 2016; 7:145-54. [PMID: 27295524 DOI: 10.1080/21655979.2016.1191705] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Lignin is 1 of the 3 major components of lignocellulose. Its polymeric structure includes aromatic subunits that can be converted into high-value-added products, but this potential cannot yet been fully exploited because lignin is highly recalcitrant to degradation. Different approaches for the depolymerization of lignin have been tested, including pyrolysis, chemical oxidation, and hydrolysis under supercritical conditions. An additional strategy is the use of lignin-degrading enzymes, which imitates the natural degradation process. A versatile set of enzymes for lignin degradation has been identified, and research has focused on the production of recombinant enzymes in sufficient amounts to characterize their structure and reaction mechanisms. Enzymes have been analyzed individually and in combinations using artificial substrates, lignin model compounds, lignin and lignocellulose. Here we consider progress in the production of recombinant lignin-degrading peroxidases, the advantages and disadvantages of different expression hosts, and obstacles that must be overcome before such enzymes can be characterized and used for the industrial processing of lignin.
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Affiliation(s)
- Camilla Lambertz
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
| | - Selin Ece
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
| | - Rainer Fischer
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany.,b Fraunhofer Institute for Molecular Biology and Applied Ecology , Aachen , Germany
| | - Ulrich Commandeur
- a Institute for Molecular Biotechnology, RWTH Aachen University , Aachen , Germany
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Comparative analysis of lignin peroxidase and manganese peroxidase activity on coniferous and deciduous wood using ToF-SIMS. Appl Microbiol Biotechnol 2016; 100:8013-20. [DOI: 10.1007/s00253-016-7560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/10/2016] [Accepted: 04/16/2016] [Indexed: 11/30/2022]
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32
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Sáez-Jiménez V, Fernández-Fueyo E, Medrano FJ, Romero A, Martínez AT, Ruiz-Dueñas FJ. Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase. PLoS One 2015; 10:e0140984. [PMID: 26496708 PMCID: PMC4619715 DOI: 10.1371/journal.pone.0140984] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/04/2015] [Indexed: 11/18/2022] Open
Abstract
Versatile peroxidase (VP) from the white-rot fungus Pleurotus eryngii is a high redox potential peroxidase of biotechnological interest able to oxidize a wide range of recalcitrant substrates including lignin, phenolic and non-phenolic aromatic compounds and dyes. However, the relatively low stability towards pH of this and other fungal peroxidases is a drawback for their industrial application. A strategy based on the comparative analysis of the crystal structures of VP and the highly pH-stable manganese peroxidase (MnP4) from Pleurotus ostreatus was followed to improve the VP pH stability. Several interactions, including hydrogen bonds and salt bridges, and charged residues exposed to the solvent were identified as putatively contributing to the pH stability of MnP4. The eight amino acid residues responsible for these interactions and seven surface basic residues were introduced into VP by directed mutagenesis. Furthermore, two cysteines were also included to explore the effect of an extra disulfide bond stabilizing the distal Ca2+ region. Three of the four designed variants were crystallized and new interactions were confirmed, being correlated with the observed improvement in pH stability. The extra hydrogen bonds and salt bridges stabilized the heme pocket at acidic and neutral pH as revealed by UV-visible spectroscopy. They led to a VP variant that retained a significant percentage of the initial activity at both pH 3.5 (61% after 24 h) and pH 7 (55% after 120 h) compared with the native enzyme, which was almost completely inactivated. The introduction of extra solvent-exposed basic residues and an additional disulfide bond into the above variant further improved the stability at acidic pH (85% residual activity at pH 3.5 after 24 h when introduced separately, and 64% at pH 3 when introduced together). The analysis of the results provides a rational explanation to the pH stability improvement achieved.
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Affiliation(s)
| | | | - Francisco Javier Medrano
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
| | - Antonio Romero
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
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33
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Fernández-Fueyo E, Linde D, Almendral D, López-Lucendo MF, Ruiz-Dueñas FJ, Martínez AT. Description of the first fungal dye-decolorizing peroxidase oxidizing manganese(II). Appl Microbiol Biotechnol 2015; 99:8927-42. [PMID: 25967658 PMCID: PMC4619462 DOI: 10.1007/s00253-015-6665-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 12/29/2022]
Abstract
Two phylogenetically divergent genes of the new family of dye-decolorizing peroxidases (DyPs) were found during comparison of the four DyP genes identified in the Pleurotus ostreatus genome with over 200 DyP genes from other basidiomycete genomes. The heterologously expressed enzymes (Pleos-DyP1 and Pleos-DyP4, following the genome nomenclature) efficiently oxidize anthraquinoid dyes (such as Reactive Blue 19), which are characteristic DyP substrates, as well as low redox-potential dyes (such as 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)) and substituted phenols. However, only Pleos-DyP4 oxidizes the high redox-potential dye Reactive Black 5, at the same time that it displays high thermal and pH stability. Unexpectedly, both enzymes also oxidize Mn2+ to Mn3+, albeit with very different catalytic efficiencies. Pleos-DyP4 presents a Mn2+ turnover (56 s−1) nearly in the same order of the two other Mn2+-oxidizing peroxidase families identified in the P. ostreatus genome: manganese peroxidases (100 s−1 average turnover) and versatile peroxidases (145 s−1 average turnover), whose genes were also heterologously expressed. Oxidation of Mn2+ has been reported for an Amycolatopsis DyP (24 s−1) and claimed for other bacterial DyPs, albeit with lower activities, but this is the first time that Mn2+ oxidation is reported for a fungal DyP. Interestingly, Pleos-DyP4 (together with ligninolytic peroxidases) is detected in the secretome of P. ostreatus grown on different lignocellulosic substrates. It is suggested that generation of Mn3+ oxidizers plays a role in the P. ostreatus white-rot lifestyle since three different families of Mn2+-oxidizing peroxidase genes are present in its genome being expressed during lignocellulose degradation.
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Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - David Almendral
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - María F López-Lucendo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | | | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain.
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34
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Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J 2015; 466:253-62. [PMID: 25495127 PMCID: PMC4357238 DOI: 10.1042/bj20141211] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.
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