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Metz F, Olsen AM, Lu F, Myers KS, Allemann MN, Michener JK, Noguera DR, Donohue TJ. Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans. mBio 2024; 15:e0171824. [PMID: 39012147 PMCID: PMC11323797 DOI: 10.1128/mbio.01718-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 07/17/2024] Open
Abstract
Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome-wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidate genes elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers vanillin and 5-formylferulate (5-FF). We also showed that the aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in the β-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans. A comparative genomic analysis predicted that the newly discovered β-5 aromatic catabolic pathway is common within the order Sphingomonadales. IMPORTANCE In the transition to a circular bioeconomy, the plant polymer lignin holds promise as a renewable source of industrially important aromatic chemicals. However, since lignin contains aromatic subunits joined by various chemical linkages, producing single chemical products from this polymer can be challenging. One strategy to overcome this challenge is using microbes to funnel a mixture of lignin-derived aromatics into target chemical products. This approach requires strategies to cleave the major inter-unit linkages of lignin to release monomers for funneling into valuable products. In this study, we report newly discovered aspects of a pathway by which the Novosphingobium aromaticivorans DSM12444 catabolizes aromatics joined by the second most common inter-unit linkage in lignin, the β-5 linkage. This work advances our knowledge of aromatic catabolic pathways, laying the groundwork for future metabolic engineering of this and other microbes for optimized conversion of lignin into products.
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Affiliation(s)
- Fletcher Metz
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Abigail M. Olsen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Fachuang Lu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Kevin S. Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Marco N. Allemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joshua K. Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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Romero-Soto IC, Rodríguez JA, Armenta-Pérez VP, Martínez-Pérez RB, Camacho-Ruiz RM, Alencar Menezes LR, Sassaki GL, Santana-Filho A, Camacho-Ruiz MA. Development of a rapid assay for β-etherase activity using a novel chromogenic substrate. Talanta 2024; 270:125501. [PMID: 38091749 DOI: 10.1016/j.talanta.2023.125501] [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: 07/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/27/2024]
Abstract
Biocatalytic processes play a crucial role in the valorization of lignin; therefore, methods enabling the monitoring of enzymes such as β-etherases, capable of breaking β-O-4 aryl-ether bonds, are of significant biotechnological interest. A novel method for quantifying β-etherase activity was developed based on the β-ester bond formation between a chromophore and acetovainillone. The chromogenic substrate β-(ρ-nitrophenoxy)-α-acetovanillone (PNPAV), was chemically synthesized. Kintetic monitoring of ρ-nitrophenolate release at 410 nm over 10 min, using recombinant LigF from Sphingobium sp SYK-6, LigF-AB and LigE-AB from Althererytrobacter sp B11, yielded enzimatic activities of 404. 3 mU/mg, 72 mU/mg, and 50 mU/mg, respectively. This method is applicable in a pH range of 7.0-9.0, with a sensitivity of up to 50 ng of enzyme, exhibiting no interference with lipolytic, glycolytic, proteolytic, and oxidoreductase enzymes.
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Affiliation(s)
- Itzel Celeste Romero-Soto
- Laboratorio de Investigación en Biotecnología, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, 46200, Jalisco, Mexico
| | - Jorge A Rodríguez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - Vicente Paúl Armenta-Pérez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - Raúl Balam Martínez-Pérez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - Rosa María Camacho-Ruiz
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - Leociley Rocha Alencar Menezes
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Av. Cel. Francisco H. dos Santos, 100, Curitiba, Parana, Brazil
| | - Guilherme Lanzi Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Av. Cel. Francisco H. dos Santos, 100, Curitiba, Parana, Brazil
| | - Arquimedes Santana-Filho
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Av. Cel. Francisco H. dos Santos, 100, Curitiba, Parana, Brazil
| | - María Angeles Camacho-Ruiz
- Laboratorio de Investigación en Biotecnología, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, 46200, Jalisco, Mexico.
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Gu J, Qiu Q, Yu Y, Sun X, Tian K, Chang M, Wang Y, Zhang F, Huo H. Bacterial transformation of lignin: key enzymes and high-value products. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:2. [PMID: 38172947 PMCID: PMC10765951 DOI: 10.1186/s13068-023-02447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.
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Affiliation(s)
- Jinming Gu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yibing Wang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Fenglin Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China.
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, Changchun, 130117, China.
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Changchun, 130117, China.
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Li B, Ruffoni A, Leonori D. A Photochemical Strategy for ortho-Aminophenol Synthesis via Dearomative-Rearomative Coupling Between Aryl Azides and Alcohols. Angew Chem Int Ed Engl 2023; 62:e202310540. [PMID: 37926921 DOI: 10.1002/anie.202310540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
ortho-Aminophenols are aromatic derivatives featuring vicinal N- and O-based functionalities commonly found in the structures of many high-value materials. These molecules are generally prepared using multistep strategies that follow the rules of electrophilic aromatic substitution (SE Ar) chemistry. Despite their high fidelity, such approaches cannot target substrates featuring a "contra-SE Ar" arrangement of N- and O-groups. Here we report an alternative strategy for the preparation of such ortho-aminophenols using aryl azides as the precursors. The process utilizes low-energy photoexcitation to trigger the decomposition of aryl azides into singlet nitrenes that undergo a dearomative-rearomative sequence. This allows the incorporation of alcoholic nucleophiles into a seven-membered ring azepine intermediate via temporary disruption of aromaticity, followed by electrophile-induced re-aromatization. The net retrosynthetic logic is that the alcohol displaces the azide, which, in turn, moves to its ortho position and furthermore is converted into an amide. The synthetic value and complementarity of this strategy has been demonstrated by the coupling of aryl azides with complex, drug-like alcohols and phenols as well as amines, thiols and thiophenols, which provides a general platform for the fast and selective heterofunctionalization of aromatics.
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Affiliation(s)
- Bo Li
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Alessandro Ruffoni
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Daniele Leonori
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
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Robles-Machuca M, Aviles-Mejía L, Romero-Soto IC, Rodríguez JA, Armenta-Pérez VP, Camacho-Ruiz MA. Cloning, expression, and biochemical characterization of β-etherase LigF from Altererythrobacter sp. B11. Heliyon 2023; 9:e21006. [PMID: 37916079 PMCID: PMC10616338 DOI: 10.1016/j.heliyon.2023.e21006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
Lignin, a complex heteropolymer present in plant cell walls, is now recognized as a valuable renewable resource with potential applications in various industries. The lignin biorefinery concept, which aims to convert lignin into value-added products, has gained significant attention in recent years. β-etherases, enzymes that selectively cleave β-O-4 aryl ether bonds in lignin, have shown promise in lignin depolymerization. In this study, the β-etherase LigF from Altererythrobacter sp. B11 was cloned, expressed, purified, and biochemically characterized. The LigF-AB11 enzyme exhibited optimal activity at 32 °C and pH 8.5 when catalyzing the substrate PNP-AV. The enzyme displayed mesophilic behavior and demonstrated higher activity at moderate temperatures. Stability analysis revealed that LigF-AB11 was not thermostable, with a complete loss of activity at 60 °C within an hour. Moreover, LigF-AB11 exhibited excellent pH stability, retaining over 50 % of its activity after 1 h under pH conditions ranging from 3.0 to 11.0. Metal ions and surface impregnation agents were found to affect the enzyme's activity, highlighting the importance of considering these factors in enzymatic processes for lignin depolymerization. This study provides valuable insights into the biochemical properties of LigF-AB11 and contributes to the development of efficient enzymatic processes for lignin biorefineries. Further optimization and understanding of β-etherases will facilitate their practical application in the valorization of lignin.
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Affiliation(s)
- Marcela Robles-Machuca
- Tecnología de Alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Tepic, 63000, Nayarit, Mexico
| | - Lucero Aviles-Mejía
- Laboratorio de Investigación en Biotecnología, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, 46200, Jalisco, Mexico
| | - Itzel Celeste Romero-Soto
- Laboratorio de Investigación en Biotecnología, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, 46200, Jalisco, Mexico
| | - Jorge A. Rodríguez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - Vicente Paúl Armenta-Pérez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Zapopan, 45019, Jalisco, Mexico
| | - María Angeles Camacho-Ruiz
- Laboratorio de Investigación en Biotecnología, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, 46200, Jalisco, Mexico
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6
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Kumagawa E, Katsumata M, Ohta Y. Catalytic and molecular properties of alkaliphilic and thermotolerant β-etherase from Altererythrobacter sp. B11. Biosci Biotechnol Biochem 2023; 87:1183-1192. [PMID: 37403406 DOI: 10.1093/bbb/zbad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Phenylpropanone monomers, including guaiacyl hydroxypropanone, are important precursors for the synthesis of various chemicals. The monomers are obtained in a three-step cascade reaction catalyzed by a group of enzymes in the β-etherase system that cleaves the β-O-4 bond, the major bond in lignin. In this study, one of the β-etherase of the glutathione-S-transferase superfamily, AbLigF2, was discovered in genus Altererythrobacter, and the recombinant etherase was characterized. The enzyme showed maximal activity at 45 °C, maintained 30% of its activity after 2 h at 50 °C, and was the most thermostable among the previously reported enzymes. Moreover, N13, S14, and S115, located near the thiol group of glutathione, had a significant effect on the maximum reaction rate of enzyme activity. This study suggests that AbLigF2 has the potential to serve as a thermostable enzyme for lignin utilization and provides insights into its catalytic mechanism.
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Affiliation(s)
- Eri Kumagawa
- Graduate School of Science and Technology, Gunma University, Gunma, Japan
| | - Madoka Katsumata
- Gunma University Center for Food Science and Wellness, Gunma, Japan
| | - Yukari Ohta
- Gunma University Center for Food Science and Wellness, Gunma, Japan
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Hall BW, Bingman CA, Fox BG, Noguera DR, Donohue TJ. A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone. J Biol Chem 2023; 299:102782. [PMID: 36502920 PMCID: PMC9843451 DOI: 10.1016/j.jbc.2022.102782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca2+-dependent enzyme from Rhodopseudomonas palustris (Rpa3624) and showed that it can hydrolyze aliphatic and aromatic lactones and esters, including GVL. Maximum-likelihood phylogenetic analysis of other related lactonases with experimentally determined substrate preferences shows that Rpa3624 separates by sequence motifs into a subclade with preference for hydrophobic substrates. Additionally, we solved crystal structures of this β-propeller enzyme separately with either phosphate, an inhibitor, or a mixture of GVL and products to define an active site where calcium-bound water and calcium-bound aspartic and glutamic acid residues make close contact with substrate and product. Our kinetic characterization of WT and mutant enzymes combined with structural insights inform a reaction mechanism that centers around activation of a calcium-bound water molecule promoted by general base catalysis and close contacts with substrate and a potential intermediate. Similarity of Rpa3624 with other β-propeller lactonases suggests this mechanism may be relevant for other members of this emerging class of versatile catalysts.
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Affiliation(s)
- Benjamin W Hall
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R Noguera
- Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J Donohue
- Department of Energy Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA; Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Periplasmic expression of Pseudomonas fluorescens peroxidase Dyp1B and site-directed mutant Dyp1B enzymes enhances polymeric lignin degradation activity in Pseudomonas putida KT2440. Enzyme Microb Technol 2023; 162:110147. [DOI: 10.1016/j.enzmictec.2022.110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
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Lakey BD, Myers KS, Alberge F, Mettert EL, Kiley PJ, Noguera DR, Donohue TJ. The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis. PLoS Genet 2022; 18:e1010270. [PMID: 35767559 PMCID: PMC9275681 DOI: 10.1371/journal.pgen.1010270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/12/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Bacterial two-component systems (TCSs) often function through the detection of an extracytoplasmic stimulus and the transduction of a signal by a transmembrane sensory histidine kinase. This kinase then initiates a series of reversible phosphorylation modifications to regulate the activity of a cognate, cytoplasmic response regulator as a transcription factor. Several TCSs have been implicated in the regulation of cell cycle dynamics, cell envelope integrity, or cell wall development in Escherichia coli and other well-studied Gram-negative model organisms. However, many α-proteobacteria lack homologs to these regulators, so an understanding of how α-proteobacteria orchestrate extracytoplasmic events is lacking. In this work we identify an essential TCS, CenKR (Cell envelope Kinase and Regulator), in the α-proteobacterium Rhodobacter sphaeroides and show that modulation of its activity results in major morphological changes. Using genetic and biochemical approaches, we dissect the requirements for the phosphotransfer event between CenK and CenR, use this information to manipulate the activity of this TCS in vivo, and identify genes that are directly and indirectly controlled by CenKR in Rb. sphaeroides. Combining ChIP-seq and RNA-seq, we show that the CenKR TCS plays a direct role in maintenance of the cell envelope, regulates the expression of subunits of the Tol-Pal outer membrane division complex, and indirectly modulates the expression of peptidoglycan biosynthetic genes. CenKR represents the first TCS reported to directly control the expression of Tol-Pal machinery genes in Gram-negative bacteria, and we predict that homologs of this TCS serve a similar function in other closely related organisms. We propose that Rb. sphaeroides genes of unknown function that are directly regulated by CenKR play unknown roles in cell envelope biosynthesis, assembly, and/or remodeling in this and other α-proteobacteria. The bacterial cell envelope is home to an array of important functions including energy conservation, motility, influx/efflux of nutrients and toxins, modulation of cell morphology and division, cell-cell interaction, and biofilm formation. Consequently, it is a major target of antibiotics and antimicrobial agents that inhibit these essential processes. Key to the recognition of environmental stressors or stimuli are bacterial TCSs, however systems that monitor or directly regulate cell envelope assembly and homeostasis are not widely conserved amongst bacteria. Here, we use Rhodobacter sphaeroides as a model to investigate the function of the CenKR TCS in this and other α-proteobacteria. We show that this essential TCS plays a key role in maintenance of the cell envelope through the regulation of outer membrane integrity and division, cell wall remodeling and homeostasis, and an alternate sigma factor that controls global cellular stress response. We provide evidence that this TCS and its function is widely conserved in α-proteobacteria and identify genes of unknown function as candidates for the study of cell envelope assembly in this and related bacteria.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erin L. Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones. Appl Environ Microbiol 2021; 87:e0174221. [PMID: 34613756 PMCID: PMC8612281 DOI: 10.1128/aem.01742-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lignin is a potential source of valuable chemicals, but its chemical depolymerization results in a heterogeneous mixture of aromatics and other products. Microbes could valorize depolymerized lignin by converting multiple substrates into one or a small number of products. In this study, we describe the ability of Novosphingobium aromaticivorans to metabolize 1-(4-hydroxy-3-methoxyphenyl)propane-1,2-dione (G-diketone), an aromatic Hibbert diketone that is produced during formic acid-catalyzed lignin depolymerization. By assaying genome-wide transcript levels from N. aromaticivorans during growth on G-diketone and other chemically-related aromatics, we hypothesized that the Lig dehydrogenases, previously characterized as oxidizing β-O-4 linkages in aromatic dimers, were involved in G-diketone metabolism by N. aromaticivorans. Using purified N. aromaticivorans Lig dehydrogenases, we found that LigL, LigN, and LigD each reduced the Cα ketone of G-diketone in vitro but with different substrate specificities and rates. Furthermore, LigL, but not LigN or LigD, also reduced the Cα ketone of 2-hydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-1-one (GP-1) in vitro, a derivative of G-diketone with the Cβ ketone reduced, when GP-1 was provided as a substrate. The newly identified activity of these Lig dehydrogenases expands the potential range of substrates utilized by N. aromaticivorans beyond what has been previously recognized. This is beneficial both for metabolizing a wide range of natural and non-native depolymerized lignin substrates and for engineering microbes and enzymes that are active with a broader range of aromatic compounds. IMPORTANCE Lignin is a major plant polymer composed of aromatic units that have value as chemicals. However, the structure and composition of lignin have made it difficult to use this polymer as a renewable source of industrial chemicals. Bacteria like Novosphingobium aromaticivorans have the potential to make chemicals from lignin not only because of their natural ability to metabolize a variety of aromatics but also because there are established protocols to engineer N. aromaticivorans strains to funnel lignin-derived aromatics into valuable products. In this work, we report a newly discovered activity of previously characterized dehydrogenase enzymes with a chemically modified by-product of lignin depolymerization. We propose that the activity of N. aromaticivorans enzymes with both native lignin aromatics and those produced by chemical depolymerization will expand opportunities for producing industrial chemicals from the heterogenous components of this abundant plant polymer.
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Li T, Zhang Q, Zhang X, Wan Q, Wang S, Zhang R, Zhang Z. Transcriptome and microbiome analyses of the mechanisms underlying antibiotic-mediated inhibition of larval development of the saprophagous insect Musca domestica (Diptera: Muscidae). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112602. [PMID: 34385061 DOI: 10.1016/j.ecoenv.2021.112602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/15/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics are designed to treat bacterial infections in humans and animals; however, the overuse of various antibiotics and consequent contamination in the environment can have adverse effects on aquatic, soil, and saprophytic organisms. The house fly, an important decomposer in ecosystems, has been used for bioconversion of human and animal waste. Vermireactors have been used to remove antibiotics from waste for pollution control, but the effects of antibiotics on fly larvae are unclear. In the present work, we aimed to reveal the mechanism underlying the effects of antibiotics on larval growth in house flies at the transcriptome and microbiome levels and the relationships between genes and the microbiota. Observation of house flies after antibiotic exposure showed that gentamicin sulfate and levofloxacin hydrochloride inhibited larval development to a greater extent than amoxicillin. Transcriptome analysis revealed that biological pathways related to protein synthesis and the metabolism of fatty acids, pentose, and glucuronate were significantly enriched in flies exposed to gentamicin sulfate and levofloxacin hydrochloride. Crucial genes in these pathways were identified as candidates for future study. Microbiome analysis revealed three key bacteria that were closely correlated with gentamicin sulfate and levofloxacin hydrochloride exposure. The correlation network between the differentially expressed genes and bacteria identified an important microbic effector, Pseudomonas and its associated genes. This work will improve the knowledge about the mechanism underlying the effects of antibiotics on the larval development of house flies in the environment and provide guidance for improving the application of house fly bioconversion.
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Affiliation(s)
- Ting Li
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China; School of Life Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Qian Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Xinyu Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Qing Wan
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Shumin Wang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Ruiling Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China.
| | - Zhong Zhang
- Collaborative Innovation Center for the Origin and Control of Emerging Infectious Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), No. 619, Changcheng Road, Taian 271016, Shandong, China; School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China.
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12
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Myers KS, Noguera DR, Donohue TJ. Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. mSystems 2021; 6:e0052621. [PMID: 34254822 PMCID: PMC8407463 DOI: 10.1128/msystems.00526-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Much of our knowledge of bacterial transcription initiation has been derived from studying the promoters of Escherichia coli and Bacillus subtilis. Given the expansive diversity across the bacterial phylogeny, it is unclear how much of this knowledge can be applied to other organisms. Here, we report on bioinformatic analyses of promoter sequences of the primary σ factor (σ70) by leveraging publicly available transcription start site (TSS) sequencing data sets for nine bacterial species spanning five phyla. This analysis identifies previously unreported differences in the -35 and -10 elements of σ70-dependent promoters in several groups of bacteria. We found that Actinobacteria and Betaproteobacteria σ70-dependent promoters lack the TTG triad in their -35 element, which is predicted to be conserved across the bacterial phyla. In addition, the majority of the Alphaproteobacteria σ70-dependent promoters analyzed lacked the thymine at position -7 that is highly conserved in other phyla. Bioinformatic examination of the Alphaproteobacteria σ70-dependent promoters identifies a significant overrepresentation of essential genes and ones encoding proteins with common cellular functions downstream of promoters containing an A, C, or G at position -7. We propose that transcription of many σ70-dependent promoters in Alphaproteobacteria depends on the transcription factor CarD, which is an essential protein in several members of this phylum. Our analysis expands the knowledge of promoter architecture across the bacterial phylogeny and provides new information that can be used to engineer bacteria for use in medical, environmental, agricultural, and biotechnological processes. IMPORTANCE Transcription of DNA to RNA by RNA polymerase is essential for cells to grow, develop, and respond to stress. Understanding the process and control of transcription is important for health, disease, the environment, and biotechnology. Decades of research on a few bacteria have identified promoter DNA sequences that are recognized by the σ subunit of RNA polymerase. We used bioinformatic analyses to reveal previously unreported differences in promoter DNA sequences across the bacterial phylogeny. We found that many Actinobacteria and Betaproteobacteria promoters lack a sequence in their -35 DNA recognition element that was previously assumed to be conserved and that Alphaproteobacteria lack a thymine residue at position -7, also previously assumed to be conserved. Our work reports important new information about bacterial transcription, illustrates the benefits of studying bacteria across the phylogenetic tree, and proposes new lines of future investigation.
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Affiliation(s)
- Kevin S. Myers
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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13
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Weng C, Peng X, Han Y. Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:84. [PMID: 33812391 PMCID: PMC8019502 DOI: 10.1186/s13068-021-01934-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/19/2021] [Indexed: 05/23/2023]
Abstract
Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics. Appl Environ Microbiol 2021; 87:AEM.02794-20. [PMID: 33579679 PMCID: PMC8091115 DOI: 10.1128/aem.02794-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lignin is a plant heteropolymer composed of phenolic subunits. Because of its heterogeneity and recalcitrance, the development of efficient methods for its valorization still remains an open challenge. One approach to utilize lignin is its chemical deconstruction into mixtures of monomeric phenolic compounds followed by biological funneling into a single product. Novosphingobium aromaticivorans DSM12444 has been previously engineered to produce 2-pyrone-4,6-dicarboxylic acid (PDC) from depolymerized lignin by simultaneously metabolizing multiple aromatics through convergent routes involving the intermediates 3-methoxygallic acid (3-MGA) and protocatechuic acid (PCA). We investigated enzymes predicted to be responsible for O-demethylation and oxidative aromatic ring opening, two critical reactions involved in the metabolism of phenolics compounds by N. aromaticivorans The results showed the involvement of DesA in O-demethylation of syringic and vanillic acids, LigM in O-demethylation of vanillic acid and 3-MGA, and a new O-demethylase, DmtS, in the conversion of 3-MGA into gallic acid (GA). In addition, we found that LigAB was the main aromatic ring opening dioxygenase involved in 3-MGA, PCA, and GA metabolism, and that a previously uncharacterized dioxygenase, LigAB2, had high activity with GA. Our results indicate a metabolic route not previously identified in N. aromaticivorans that involves O-demethylation of 3-MGA to GA. We predict this pathway channels ∼15% of the carbon flow from syringic acid, with the rest following ring opening of 3-MGA. The new knowledge obtained in this study allowed for the creation of an improved engineered strain for the funneling of aromatic compounds that exhibits stoichiometric conversion of syringic acid into PDC.IMPORTANCE For lignocellulosic biorefineries to effectively contribute to reduction of fossil fuel use, they need to become efficient at producing chemicals from all major components of plant biomass. Making products from lignin will require engineering microorganisms to funnel multiple phenolic compounds to the chemicals of interest, and N. aromaticivorans is a promising chassis for this technology. The ability of N. aromaticivorans to efficiently and simultaneously degrade many phenolic compounds may be linked to having functionally redundant aromatic degradation pathways and enzymes with broad substrate specificity. A detailed knowledge of aromatic degradation pathways is thus essential to identify genetic engineering targets to maximize product yields. Furthermore, knowledge of enzyme substrate specificity is critical to redirect flow of carbon to desired pathways. This study described an uncharacterized pathway in N. aromaticivorans and the enzymes that participate in this pathway, allowing the engineering of an improved strain for production of PDC from lignin.
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dos Santos Melo-Nascimento AO, Mota Moitinho Sant´Anna B, Gonçalves CC, Santos G, Noronha E, Parachin N, de Abreu Roque MR, Bruce T. Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1. PLoS One 2020; 15:e0243739. [PMID: 33351813 PMCID: PMC7755216 DOI: 10.1371/journal.pone.0243739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.
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Affiliation(s)
| | | | - Carolyne Caetano Gonçalves
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Giovanna Santos
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Eliane Noronha
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Nádia Parachin
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Milton Ricardo de Abreu Roque
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Instituto de Ciências da Saúde, Laboratório de Bioprospecção, Universidade Federal da Bahia, Salvador, Brazil
| | - Thiago Bruce
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
- * E-mail:
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16
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Lahive CW, Kamer PCJ, Lancefield CS, Deuss PJ. An Introduction to Model Compounds of Lignin Linking Motifs; Synthesis and Selection Considerations for Reactivity Studies. CHEMSUSCHEM 2020; 13:4238-4265. [PMID: 32510817 PMCID: PMC7540175 DOI: 10.1002/cssc.202000989] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 05/31/2023]
Abstract
The development of fundamentally new valorization strategies for lignin plays a vital role in unlocking the true potential of lignocellulosic biomass as sustainable and economically compatible renewable carbon feedstock. In particular, new catalytic modification and depolymerization strategies are required. Progress in this field, past and future, relies for a large part on the application of synthetic model compounds that reduce the complexity of working with the lignin biopolymer. This aids the development of catalytic methodologies and in-depth mechanistic studies and guides structural characterization studies in the lignin field. However, due to the volume of literature and the piecemeal publication of methodology, the choice of suitable lignin model compounds is far from straight forward, especially for those outside the field and lacking a background in organic synthesis. For example, in catalytic depolymerization studies, a balance between synthetic effort and fidelity compared to the actual lignin of interest needs to be found. In this Review, we provide a broad overview of the model compounds available to study the chemistry of the main native linking motifs typically found in lignins from woody biomass, the synthetic routes and effort required to access them, and discuss to what extent these represent actual lignin structures. This overview can aid researchers in their selection of the most suitable lignin model systems for the development of emerging lignin modification and depolymerization technologies, maximizing their chances of successfully developing novel lignin valorization strategies.
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Affiliation(s)
- Ciaran W. Lahive
- Department of Chemical Engineering (ENTEG)University of GroningenNijenborgh 49747 AGGroningenNetherlands
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
| | - Paul C. J. Kamer
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
- Leibniz-Institut für Katalyse e.V.Albert-Einstein-Straße 29a18059RostockGermany
| | - Christopher S. Lancefield
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
| | - Peter J. Deuss
- Department of Chemical Engineering (ENTEG)University of GroningenNijenborgh 49747 AGGroningenNetherlands
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17
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Klinger GE, Zhou Y, Foote JA, Wester AM, Cui Y, Alherech M, Stahl SS, Jackson JE, Hegg EL. Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin. CHEMSUSCHEM 2020; 13:4394-4399. [PMID: 32668064 PMCID: PMC7540407 DOI: 10.1002/cssc.202001238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Lignin may serve as a renewable feedstock for the production of chemicals and fuels if mild, scalable processes for its depolymerization can be devised. The use of small organic thiols represents a bioinspired strategy to cleave the β-O-4 bond, the most common linkage in lignin. In the present study, synthetic β-O-4 linked polymers were treated with organic thiols, yielding up to 90 % cleaved monomer products. Lignin extracted from poplar was also treated with organic thiols resulting in molecular weight reductions as high as 65 % (Mn ) in oxidized lignin. Thiol-based cleavage of other lignin linkages was also explored in small-molecule model systems to uncover additional potential pathways by which thiols might depolymerize lignin. The success of thiol-mediated cleavage on model dimers, polymers, and biomass-derived lignin illustrates the potential utility of small redox-active molecules to penetrate complex polymer matrices for depolymerization and subsequent valorization of lignin into fuels and chemicals.
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Affiliation(s)
- Grace E. Klinger
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
- Department of Biochemistry & Molecular BiologyMichigan State UniversityEast Lansing, MI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast Lansing, MI48824USA
| | - Yuting Zhou
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Juliet A. Foote
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Abby M. Wester
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Yanbin Cui
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - Manar Alherech
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - Shannon S. Stahl
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - James E. Jackson
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Eric L. Hegg
- Department of Biochemistry & Molecular BiologyMichigan State UniversityEast Lansing, MI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast Lansing, MI48824USA
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Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444. Microbiol Resour Announc 2020; 9:9/36/e00880-20. [PMID: 32883797 PMCID: PMC7471390 DOI: 10.1128/mra.00880-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria. Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria.
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19
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Common problems associated with the microbial productions of aromatic compounds and corresponding metabolic engineering strategies. Biotechnol Adv 2020; 41:107548. [DOI: 10.1016/j.biotechadv.2020.107548] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
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20
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Morales GM, Ali SS, Si H, Zhang W, Zhang R, Hosseini K, Sun J, Zhu D. Acidic Versus Alkaline Bacterial Degradation of Lignin Through Engineered Strain E. coli BL21(Lacc): Exploring the Differences in Chemical Structure, Morphology, and Degradation Products. Front Bioeng Biotechnol 2020; 8:671. [PMID: 32714907 PMCID: PMC7344149 DOI: 10.3389/fbioe.2020.00671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/29/2020] [Indexed: 11/30/2022] Open
Abstract
There is increasing interest in research on lignin biodegradation compounds as potential building blocks in applications related to renewable products. More attention is necessary to evaluate the effects of the initial pH conditions during the bacterial degradation of lignin. In this study we performed experiments on lignin biodegradation under acidic and mild alkaline conditions. For acidic biodegradation, lignin was chemically pretreated with hydrogen peroxide. Alkaline biodegradation was achieved by developing the bacterial growth on Luria and Bertani medium with alkali lignin as the sole carbon source. The mutant strain Escherichia coli BL21(Lacc) was used to carry out lignin biodegradation over 10 days of incubation. Results demonstrated that under acidic conditions there was a predominance of aliphatic compounds of the C3–C4 type. Alkaline biodegradation was produced in the context of oxidative stress, with a greater abundance of aryl compounds. The final pH values of acidic and alkaline biodegradation of lignin were 2.53 and 7.90, respectively. The results of the gas chromatography mass spectrometry analysis detected compounds such as crotonic acid, lactic acid and 3-hydroxybutanoic acid for acidic conditions, with potential applications for adhesives and polymer precursors. Under alkaline conditions, detected compounds included 2-phenylethanol and dehydroabietic acid, with potential applications for perfumery and anti tumor/anti-inflammatory medications. Size-exclusion chromatography analysis showed that the weight-average molecular weight of the alkaline biodegraded lignin increased by 6.75-fold compared to the acidic method, resulting in a repolymerization of its molecular structure. Lignin repolymerization coincided with an increase in the relative abundance of dehydroabietic acid and isovanillyl alcohol, from 2.70 and 3.96% on day zero to 13.43 and 10.26% on 10th day. The results of the Fourier-transformed Infrared spectroscopy detected the presence of C = O bond and OH functional group associated with carboxylic acids in the acidic method. In the alkaline method there was a greater preponderance of signals related to skeletal aromatic structures, the amine functional group and the C – O – bond. Lignin biodegradation products from E. coli BL21(Lacc), under different initial pH conditions, demonstrated a promising potential to enlarge the spectrum of renewable products for biorefinery activities.
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Affiliation(s)
- Gabriel Murillo Morales
- Biofuels Institute, School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sameh S Ali
- Biofuels Institute, School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haibing Si
- Biofuels Institute, School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Weimin Zhang
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Rongxian Zhang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, China
| | - Keyvan Hosseini
- School of Public Affairs, University of Science and Technology of China, Hefei, China
| | - Jianzhong Sun
- Biofuels Institute, School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Daochen Zhu
- Biofuels Institute, School of Environmental Science and Safety Engineering, Jiangsu University, Zhenjiang, China.,Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
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21
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22
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Mnich E, Bjarnholt N, Eudes A, Harholt J, Holland C, Jørgensen B, Larsen FH, Liu M, Manat R, Meyer AS, Mikkelsen JD, Motawia MS, Muschiol J, Møller BL, Møller SR, Perzon A, Petersen BL, Ravn JL, Ulvskov P. Phenolic cross-links: building and de-constructing the plant cell wall. Nat Prod Rep 2020; 37:919-961. [PMID: 31971193 DOI: 10.1039/c9np00028c] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Covering: Up to 2019Phenolic cross-links and phenolic inter-unit linkages result from the oxidative coupling of two hydroxycinnamates or two molecules of tyrosine. Free dimers of hydroxycinnamates, lignans, play important roles in plant defence. Cross-linking of bound phenolics in the plant cell wall affects cell expansion, wall strength, digestibility, degradability, and pathogen resistance. Cross-links mediated by phenolic substituents are particularly important as they confer strength to the wall via the formation of new covalent bonds, and by excluding water from it. Four biopolymer classes are known to be involved in the formation of phenolic cross-links: lignins, extensins, glucuronoarabinoxylans, and side-chains of rhamnogalacturonan-I. Lignins and extensins are ubiquitous in streptophytes whereas aromatic substituents on xylan and pectic side-chains are commonly assumed to be particular features of Poales sensu lato and core Caryophyllales, respectively. Cross-linking of phenolic moieties proceeds via radical formation, is catalyzed by peroxidases and laccases, and involves monolignols, tyrosine in extensins, and ferulate esters on xylan and pectin. Ferulate substituents, on xylan in particular, are thought to be nucleation points for lignin polymerization and are, therefore, of paramount importance to wall architecture in grasses and for the development of technology for wall disassembly, e.g. for the use of grass biomass for production of 2nd generation biofuels. This review summarizes current knowledge on the intra- and extracellular acylation of polysaccharides, and inter- and intra-molecular cross-linking of different constituents. Enzyme mediated lignan in vitro synthesis for pharmaceutical uses are covered as are industrial exploitation of mutant and transgenic approaches to control cell wall cross-linking.
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Affiliation(s)
- Ewelina Mnich
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark.
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Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes. Appl Environ Microbiol 2020; 86:AEM.02026-19. [PMID: 31676477 DOI: 10.1128/aem.02026-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 11/20/2022] Open
Abstract
Lignin is the most abundant aromatic polymer in nature and a promising renewable source for the provision of aromatic platform chemicals and biofuels. β-Etherases are enzymes with a promising potential for application in lignin depolymerization due to their selectivity in the cleavage of β-O-4 aryl ether bonds. However, only a very limited number of these enzymes have been described and characterized so far. Using peptide pattern recognition (PPR) as well as phylogenetic analyses, 96 putatively novel β-etherases have been identified, some even originating from bacteria outside the order Sphingomonadales A set of 13 diverse enzymes was selected for biochemical characterization, and β-etherase activity was confirmed for all of them. Some enzymes displayed up to 3-fold higher activity than previously known β-etherases. Moreover, conserved sequence motifs specific for either LigE- or LigF-type enzymes were deduced from multiple-sequence alignments and the PPR-derived peptides. In combination with structural information available for the β-etherases LigE and LigF, insight into the potential structural and/or functional role of conserved residues within these sequence motifs is provided. Phylogenetic analyses further suggest the presence of additional bacterial enzymes with potential β-etherase activity outside the classical LigE- and LigF-type enzymes as well as the recently described heterodimeric β-etherases.IMPORTANCE The use of biomass as a renewable source and replacement for crude oil for the provision of chemicals and fuels is of major importance for current and future societies. Lignin, the most abundant aromatic polymer in nature, holds promise as a renewable starting material for the generation of required aromatic structures. However, a controlled and selective lignin depolymerization to yield desired aromatic structures is a very challenging task. In this regard, bacterial β-etherases are especially interesting, as they are able to cleave the most abundant bond type in lignin with high selectivity. With this study, we significantly expanded the toolbox of available β-etherases for application in lignin depolymerization and discovered more active as well as diverse enzymes than previously known. Moreover, the identification of further β-etherases by sequence database mining in the future will be facilitated considerably through our deduced etherase-specific sequence motifs.
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24
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Chan JC, Paice M, Zhang X. Enzymatic Oxidation of Lignin: Challenges and Barriers Toward Practical Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201901480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jou C. Chan
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
| | - Michael Paice
- FPInnovations Pulp Paper & Bioproducts 2665 East Mall Vancouver BC V6T 1Z4 Canada
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
- Pacific Northwest National Laboratory 520 Battelle Boulevard P.O. Box 999, MSIN P8-60 Richland WA-99352 USA
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25
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Klinger GE, Zhou Y, Hao P, Robbins J, Aquilina JM, Jackson JE, Hegg EL. Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small-Molecule Thiols. CHEMSUSCHEM 2019; 12:4775-4779. [PMID: 31418534 DOI: 10.1002/cssc.201901742] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 06/10/2023]
Abstract
The nucleophilic and reductive properties of thiolates and thiols make them ideal candidates as redox mediators via the thiol/disulfide couple. One mechanism for biological lignin depolymerization entails reduction of keto aryl ether bonds by an SN 2 mechanism with the thiol redox mediator glutathione. In this study, mimicking this chemistry in a simple protein- and metal-free process, several small organic thiols are surveyed for their ability to cleave aryl keto ethers that model the β-O-4 linkages found in partially oxidized lignin. In polar aprotic solvents, β-mercaptoethanol and dithiothreitol yielded up to 100 % formation of phenol and acetophenone products from 2-phenoxyacetophenone, but not from its reduced alcohol congener. The effects of reaction conditions and of substituents on the aryl rings and the keto ether linkage are assessed. These results, together with activation barriers computed by quantum chemical simulations and direct observation of the expected intermediate thioether, point to an SN 2 mechanism. This study confirms that small organic thiols can reductively break down lignin-relevant keto aryl ether linkages.
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Affiliation(s)
- Grace E Klinger
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, Michigan, 48824, USA
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
| | - Yuting Zhou
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Pengchao Hao
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Jacob Robbins
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Jake M Aquilina
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - James E Jackson
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
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26
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Prates ET, Crowley MF, Skaf MS, Beckham GT. Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG. J Phys Chem B 2019; 123:10142-10151. [DOI: 10.1021/acs.jpcb.9b06243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erica Teixeira Prates
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80403, United States
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo 13084-862, Brazil
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80403, United States
| | - Munir S. Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo 13084-862, Brazil
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80403, United States
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27
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Lee S, Kang M, Bae JH, Sohn JH, Sung BH. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front Bioeng Biotechnol 2019; 7:209. [PMID: 31552235 PMCID: PMC6733911 DOI: 10.3389/fbioe.2019.00209] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.
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Affiliation(s)
- Siseon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
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28
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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29
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Husarcikova J, Schallmey A. Whole-cell cascade for the preparation of enantiopure β-O-4 aryl ether compounds with glutathione recycling. J Biotechnol 2019; 293:1-7. [PMID: 30703467 DOI: 10.1016/j.jbiotec.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Bacterial β-etherases and glutathione lyases are glutathione-dependent enzymes that catalyze the selective cleavage of β-O-4 aryl ether bonds found in lignin. Their glutathione (GSH) dependence is regarded as major limitation for their application in the production of aromatics from lignin polymer and oligomers, as stoichiometric glutathione amounts are required. Thus, recycling of the GSH cofactor by a NAD(P)H-dependent glutathione reductase was proposed previously. Herein, the use of a whole-cell catalyst was studied for efficient β-O-4 aryl ether bond cleavage with intracellular GSH supply and recycling. After optimization of the whole-cell catalyst as well as reaction conditions, up to 5 mM lignin model substrate 2,6-methoxyphenoxy-α-veratrylglycerone (2,6-MP-VG) were efficiently converted into 2,6-methoxyphenol (2,6-MP) and veratryl glycerone (VG) without addition of external GSH. Unexpectedly, no glucose supply was required for glutathione recycling within the cells up to this substrate concentration. To demonstrate the applicability of this whole-cell approach, a whole-cell cascade combining a stereoselective β-etherase (either LigE from Sphingobium sp. SYK-6 or LigF-NA from Novosphingobium aromaticivorans) and a glutathione lyase (LigG-TD from Thiobacillus denitrificans) was employed in the kinetic resolution of racemic 2,6-MP-VG. This way, enantiopure (S)- and (R)-2,6-MP-VG were obtained on semi-preparative scale without the need for external GSH supply.
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Affiliation(s)
- Jana Husarcikova
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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30
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Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ. A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β( R)-aryl ether bond reveals the diversity of bacterial β-etherases. J Biol Chem 2018; 294:1877-1890. [PMID: 30541921 PMCID: PMC6369299 DOI: 10.1074/jbc.ra118.006548] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/07/2018] [Indexed: 11/12/2022] Open
Abstract
Lignin is a heterogeneous polymer of aromatic subunits that is a major component of lignocellulosic plant biomass. Understanding how microorganisms deconstruct lignin is important for understanding the global carbon cycle and could aid in developing systems for processing plant biomass into valuable commodities. Sphingomonad bacteria use stereospecific glutathione S-transferases (GSTs) called β-etherases to cleave the β-aryl ether (β-O-4) bond, the most common bond between aromatic subunits in lignin. Previously characterized bacterial β-etherases are homodimers that fall into two distinct GST subclasses: LigE homologues, which cleave the β(R) stereoisomer of the bond, and LigF homologues, which cleave the β(S) stereoisomer. Here, we report on a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond of the di-aromatic compound β-(2-methoxyphenoxy)-γ-hydroxypropiovanillone (MPHPV). BaeAB's subunits are phylogenetically distinct from each other and from other β-etherases, although they are evolutionarily related to LigF, despite the fact that BaeAB and LigF cleave different β-aryl ether bond stereoisomers. We identify amino acid residues in BaeAB's BaeA subunit important for substrate binding and catalysis, including an asparagine that is proposed to activate the GSH cofactor. We also show that BaeAB homologues from other sphingomonads can cleave β(R)-MPHPV and that they may be as common in bacteria as LigE homologues. Our results suggest that the ability to cleave the β-aryl ether bond arose independently at least twice in GSTs and that BaeAB homologues may be important for cleaving the β(R)-aryl ether bonds of lignin-derived oligomers in nature.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Larissa M Yusko
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Alyssa V Niles
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Kevin A Walters
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Emily T Beebe
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Kirk A Vander Meulen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Steven D Karlen
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,the Departments of Biochemistry
| | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center, and.,Civil and Environmental Engineering, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center, and.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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31
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Lechner U, Türkowsky D, Dinh TTH, Al‐Fathi H, Schwoch S, Franke S, Gerlach M, Koch M, von Bergen M, Jehmlich N, Dang TCH. Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill. Microb Biotechnol 2018; 11:1137-1156. [PMID: 30117290 PMCID: PMC6196390 DOI: 10.1111/1751-7915.13301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/07/2018] [Indexed: 12/17/2022] Open
Abstract
The herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was a major component of Agent Orange, which was used as a defoliant in the Vietnam War. Little is known about its degradation under anoxic conditions. Established enrichment cultures using soil from an Agent Orange bioremediation plant in southern Vietnam with pyruvate as potential electron donor and carbon source were shown to degrade 2,4,5-T via ether cleavage to 2,4,5-trichlorophenol (2,4,5-TCP), which was further dechlorinated to 3,4-dichlorophenol. Pyruvate was initially fermented to hydrogen, acetate and propionate. Hydrogen was then used as the direct electron donor for ether cleavage of 2,4,5-T and subsequent dechlorination of 2,4,5-TCP. 16S rRNA gene amplicon sequencing indicated the presence of bacteria and archaea mainly belonging to the Firmicutes, Bacteroidetes, Spirochaetes, Chloroflexi and Euryarchaeota. Desulfitobacterium hafniense was identified as the dechlorinating bacterium. Metaproteomics of the enrichment culture indicated higher protein abundances of 60 protein groups in the presence of 2,4,5-T. A reductive dehalogenase related to RdhA3 of D. hafniense showed the highest fold change, supporting its function in reductive dehalogenation of 2,4,5-TCP. Despite an ether-cleaving enzyme not being detected, the inhibition of ether cleavage but not of dechlorination, by 2-bromoethane sulphonate, suggested that the two reactions are catalysed by different organisms.
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Affiliation(s)
- Ute Lechner
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Dominique Türkowsky
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Thu Hang Dinh
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
- Present address:
Vietnamese Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Hassan Al‐Fathi
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Schwoch
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Franke
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | | | - Mandy Koch
- Institute of Chemistry/Food and Environmental ChemistryMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Martin von Bergen
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Cam Ha Dang
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
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32
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Marjamaa K, Kruus K. Enzyme biotechnology in degradation and modification of plant cell wall polymers. PHYSIOLOGIA PLANTARUM 2018; 164:106-118. [PMID: 29987848 DOI: 10.1111/ppl.12800] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 05/28/2023]
Abstract
Lignocelluloses are abundant raw materials for production of fuels, chemicals and materials. The purpose of this paper is to review the enzyme-types and enzyme-technologies studied and applied in the processing of the lignocelluloses into different products. The enzymes here are mostly glycoside hydrolases, esterases and different redox enzymes. Enzymatic hydrolysis of lignocellulosic polysaccharides to platform sugars has been widely studied leading to development of advanced commercial products for this purpose. Restricted hydrolysis or oxidation of cellulosic fibers have been applied in processing of pulps to paper products, nanocelluloses and textile fibers. Oxidation, transglycosylation and derivatization have been utilized in functionalization of fibers, cellulosic surfaces and polysaccharides. Enzymatic polymerization, depolymerization and grafting methods are being developed for lignin valorization.
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Affiliation(s)
- Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
| | - Kristiina Kruus
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
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33
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Osman WHW, Lin MI, Kondo K, Nagata T, Katahira M. Characterization of the glutathione S-transferases that belong to the GSTFuA class in Ceriporiopsis subvermispora: Implications in intracellular detoxification and metabolism of wood-derived compounds. Int J Biol Macromol 2018. [DOI: 10.1016/j.ijbiomac.2018.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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34
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Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives. Appl Microbiol Biotechnol 2018; 102:5391-5401. [PMID: 29728724 DOI: 10.1007/s00253-018-9040-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 01/05/2023]
Abstract
Lignin is the major aromatic biopolymer in nature, and it is considered a valuable feedstock for the future supply of aromatics. Hence, its valorisation in biorefineries is of high importance, and various chemical and enzymatic approaches for lignin depolymerisation have been reported. Among the enzymes known to act on lignin, β-etherases offer the possibility for a selective cleavage of the β-O-4 aryl ether bonds present in lignin. These enzymes, together with glutathione lyases, catalyse a reductive, glutathione-dependent ether bond cleavage displaying high stereospecificity. β-Etherases and glutathione lyases both belong to the superfamily of glutathione transferases, and several structures have been solved recently. Additionally, different approaches for their application in lignin valorisation have been reported in the last years. This review gives an overview on the current knowledge on β-etherases and glutathione lyases, their biochemical and structural features, and critically discusses their potential for application in biorefineries.
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35
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Moraes EC, Alvarez TM, Persinoti GF, Tomazetto G, Brenelli LB, Paixão DAA, Ematsu GC, Aricetti JA, Caldana C, Dixon N, Bugg TDH, Squina FM. Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:75. [PMID: 29588660 PMCID: PMC5863372 DOI: 10.1186/s13068-018-1073-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/09/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. RESULTS The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. CONCLUSION The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.
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Affiliation(s)
- Eduardo C. Moraes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Thabata M. Alvarez
- Master Program in Industrial Biotechnology, Universidade Positivo (UP), Curitiba, Brazil
| | - Gabriela F. Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Geizecler Tomazetto
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Livia B. Brenelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Douglas A. A. Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Gabriela C. Ematsu
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Juliana A. Aricetti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Neil Dixon
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | | | - Fabio M. Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
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Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin. Appl Environ Microbiol 2018; 84:AEM.02670-17. [PMID: 29374031 DOI: 10.1128/aem.02670-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/19/2018] [Indexed: 12/11/2022] Open
Abstract
Sphingobium sp. strain SYK-6 converts four stereoisomers of arylglycerol-β-guaiacyl ether into achiral β-hydroxypropiovanillone (HPV) via three stereospecific reaction steps. Here, we determined the HPV catabolic pathway and characterized the HPV catabolic genes involved in the first two steps of the pathway. In SYK-6 cells, HPV was oxidized to vanilloyl acetic acid (VAA) via vanilloyl acetaldehyde (VAL). The resulting VAA was further converted into vanillate through the activation of VAA by coenzyme A. A syringyl-type HPV analog, β-hydroxypropiosyringone (HPS), was also catabolized via the same pathway. SLG_12830 (hpvZ), which belongs to the glucose-methanol-choline oxidoreductase family, was isolated as the HPV-converting enzyme gene. An hpvZ mutant completely lost the ability to convert HPV and HPS, indicating that hpvZ is essential for the conversion of both the substrates. HpvZ produced in Escherichia coli oxidized both HPV and HPS and other 3-phenyl-1-propanol derivatives. HpvZ localized to both the cytoplasm and membrane of SYK-6 and used ubiquinone derivatives as electron acceptors. Thirteen gene products of the 23 aldehyde dehydrogenase (ALDH) genes in SYK-6 were able to oxidize VAL into VAA. Mutant analyses suggested that multiple ALDH genes, including SLG_20400, contribute to the conversion of VAL. We examined whether the genes encoding feruloyl-CoA synthetase (ferA) and feruloyl-CoA hydratase/lyase (ferB and ferB2) are involved in the conversion of VAA. Only FerA exhibited activity toward VAA; however, disruption of ferA did not affect VAA conversion. These results indicate that another enzyme system is involved in VAA conversion.IMPORTANCE Cleavage of the β-aryl ether linkage is the most essential process in lignin biodegradation. Although the bacterial β-aryl ether cleavage pathway and catabolic genes have been well documented, there have been no reports regarding the catabolism of HPV or HPS, the products of cleavage of β-aryl ether compounds. HPV and HPS have also been found to be obtained from lignin by chemoselective catalytic oxidation by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O2, followed by cleavage of the β-aryl ether with zinc. Therefore, value-added chemicals are expected to be produced from these compounds. In this study, we determined the SYK-6 catabolic pathways for HPV and HPS and identified the catabolic genes involved in the first two steps of the pathways. Since SYK-6 catabolizes HPV through 2-pyrone-4,6-dicarboxylate, which is a building block for functional polymers, characterization of HPV catabolism is important not only for understanding the bacterial lignin catabolic system but also for lignin utilization.
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37
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Marinović M, Nousiainen P, Dilokpimol A, Kontro J, Moore R, Sipilä J, de Vries RP, Mäkelä MR, Hildén K. Selective Cleavage of Lignin β- O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:2878-2882. [PMID: 30271687 PMCID: PMC6156110 DOI: 10.1021/acssuschemeng.7b03619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/19/2018] [Indexed: 05/06/2023]
Abstract
Production of value-added compounds from a renewable aromatic polymer, lignin, has proven to be challenging. Chemical procedures, involving harsh reaction conditions, are costly and often result in nonselective degradation of lignin linkages. Therefore, enzymatic catalysis with selective cleavage of lignin bonds provides a sustainable option for lignin valorization. In this study, we describe the first functionally characterized fungal intracellular β-etherase from the wood-degrading white-rot basidiomycete Dichomitus squalens. This enzyme, Ds-GST1, from the glutathione-S-transferase superfamily selectively cleaved the β-O-4 aryl ether bond of a dimeric lignin model compound in a glutathione-dependent reaction. Ds-GST1 also demonstrated activity on polymeric synthetic lignin fractions, shown by a decrease in molecular weight distribution of the laccase-oxidized guaiacyl dehydrogenation polymer. In addition to a possible role of Ds-GST1 in intracellular catabolism of lignin-derived aromatic compounds, the cleavage of the most abundant linkages in lignin under mild reaction conditions makes this biocatalyst an attractive green alternative in biotechnological applications.
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Affiliation(s)
- Mila Marinović
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Paula Nousiainen
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Adiphol Dilokpimol
- Fungal
Physiology, Westerdijk Fungal Biodiversity Institute & Fungal
Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jussi Kontro
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Robin Moore
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Jussi Sipilä
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Ronald P. de Vries
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
- Fungal
Physiology, Westerdijk Fungal Biodiversity Institute & Fungal
Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miia R. Mäkelä
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Kristiina Hildén
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
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Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. J Biol Chem 2018; 293:4955-4968. [PMID: 29449375 PMCID: PMC5892560 DOI: 10.1074/jbc.ra117.001268] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Indexed: 01/01/2023] Open
Abstract
As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Craig A Bingman
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Douglas R Wassarman
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | | | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Robert W Smith
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | | | - Brian G Fox
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Civil and Environmental Engineering
| | - Joshua J Coon
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Chemistry.,the Genome Center of Wisconsin, and.,Biomolecular Chemistry, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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Gall DL, Kontur WS, Lan W, Kim H, Li Y, Ralph J, Donohue TJ, Noguera DR. In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units. Appl Environ Microbiol 2018; 84:e02076-17. [PMID: 29180366 PMCID: PMC5772236 DOI: 10.1128/aem.02076-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/16/2017] [Indexed: 11/30/2022] Open
Abstract
New environmentally sound technologies are needed to derive valuable compounds from renewable resources. Lignin, an abundant polymer in terrestrial plants comprised predominantly of guaiacyl and syringyl monoaromatic phenylpropanoid units, is a potential natural source of aromatic compounds. In addition, the plant secondary metabolite tricin is a recently discovered and moderately abundant flavonoid in grasses. The most prevalent interunit linkage between guaiacyl, syringyl, and tricin units is the β-ether linkage. Previous studies have shown that bacterial β-etherase pathway enzymes catalyze glutathione-dependent cleavage of β-ether bonds in dimeric β-ether lignin model compounds. To date, however, it remains unclear whether the known β-etherase enzymes are active on lignin polymers. Here we report on enzymes that catalyze β-ether cleavage from bona fide lignin, under conditions that recycle the cosubstrates NAD+ and glutathione. Guaiacyl, syringyl, and tricin derivatives were identified as reaction products when different model compounds or lignin fractions were used as substrates. These results demonstrate an in vitro enzymatic system that can recycle cosubstrates while releasing aromatic monomers from model compounds as well as natural and engineered lignin oligomers. These findings can improve the ability to produce valuable aromatic compounds from a renewable resource like lignin.IMPORTANCE Many bacteria are predicted to contain enzymes that could convert renewable carbon sources into substitutes for compounds that are derived from petroleum. The β-etherase pathway present in sphingomonad bacteria could cleave the abundant β-O-4-aryl ether bonds in plant lignin, releasing a biobased source of aromatic compounds for the chemical industry. However, the activity of these enzymes on the complex aromatic oligomers found in plant lignin is unknown. Here we demonstrate biodegradation of lignin polymers using a minimal set of β-etherase pathway enzymes, the ability to recycle needed cofactors (glutathione and NAD+) in vitro, and the release of guaiacyl, syringyl, and tricin as depolymerized products from lignin. These observations provide critical evidence for the use and future optimization of these bacterial β-etherase pathway enzymes for industrial-level biotechnological applications designed to derive high-value monomeric aromatic compounds from lignin.
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Affiliation(s)
- Daniel L Gall
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wayne S Kontur
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wu Lan
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hoon Kim
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Yanding Li
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - John Ralph
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J Donohue
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel R Noguera
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
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Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:679-705. [PMID: 29052962 DOI: 10.1111/1758-2229.12597] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/26/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kenji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kosuke Mori
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takuma Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Fujita
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yudai Higuchi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Naresh Kumar M, Ravikumar R, Thenmozhi S, Kirupa Sankar M. Development of natural cellulase inhibitor mediated intensified biological pretreatment technology using Pleurotus florida for maximum recovery of cellulose from paddy straw under solid state condition. BIORESOURCE TECHNOLOGY 2017; 244:353-361. [PMID: 28780270 DOI: 10.1016/j.biortech.2017.07.105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 05/28/2023]
Abstract
Inhibitor mediated intensified bio-pretreatment (IMBP) technology using natural cellulase inhibitor (NCI) for maximum cellulose recovery from paddy straw was studied. Pretreatment was carried out under solid state condition. Supplementation of 8% NCI in pretreatment medium improves cellulose recovery and delignification by 1.2 and 1.5-fold respectively, compared to conventional bio-pretreatment due to inhibition of 61% of cellulase activity in IMBP. Further increase in NCI concentration showed negative effect on Pleurotus florida growth and suppress the laccase productivity by 1.1-fold. Laccase activity in IMBP was found to be 2.0U/mL on 19thday, which is higher than (1.5U/mL) conventional bio-pretreatment. Physico-chemical modifications in paddy straw before and after pretreatment were analysed by SEM, ATR-FTIR, XRD and TGA. According to these findings, the IMBP technology can be a viable eco-friendly technology for sustainable production of bioethanol with maximum cellulose recovery.
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Affiliation(s)
- Manickam Naresh Kumar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
| | - Rajarathinam Ravikumar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India.
| | - Senniyappan Thenmozhi
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
| | - Muthuvelu Kirupa Sankar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
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43
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Gall DL, Ralph J, Donohue TJ, Noguera DR. Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol 2017; 45:120-126. [DOI: 10.1016/j.copbio.2017.02.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/06/2017] [Accepted: 02/24/2017] [Indexed: 11/30/2022]
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44
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Wang W, Zhang C, Sun X, Su S, Li Q, Linhardt RJ. Efficient, environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes. World J Microbiol Biotechnol 2017; 33:125. [DOI: 10.1007/s11274-017-2286-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
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45
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Mnich E, Vanholme R, Oyarce P, Liu S, Lu F, Goeminne G, Jørgensen B, Motawie MS, Boerjan W, Ralph J, Ulvskov P, Møller BL, Bjarnholt N, Harholt J. Degradation of lignin β-aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK-6. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:581-593. [PMID: 27775869 PMCID: PMC5399005 DOI: 10.1111/pbi.12655] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/25/2016] [Accepted: 10/10/2016] [Indexed: 05/02/2023]
Abstract
Lignin is a major polymer in the secondary plant cell wall and composed of hydrophobic interlinked hydroxyphenylpropanoid units. The presence of lignin hampers conversion of plant biomass into biofuels; plants with modified lignin are therefore being investigated for increased digestibility. The bacterium Sphingomonas paucimobilis produces lignin-degrading enzymes including LigD, LigF and LigG involved in cleaving the most abundant lignin interunit linkage, the β-aryl ether bond. In this study, we expressed the LigD, LigF and LigG (LigDFG) genes in Arabidopsis thaliana to introduce postlignification modifications into the lignin structure. The three enzymes were targeted to the secretory pathway. Phenolic metabolite profiling and 2D HSQC NMR of the transgenic lines showed an increase in oxidized guaiacyl and syringyl units without concomitant increase in oxidized β-aryl ether units, showing lignin bond cleavage. Saccharification yield increased significantly in transgenic lines expressing LigDFG, showing the applicability of our approach. Additional new information on substrate specificity of the LigDFG enzymes is also provided.
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Affiliation(s)
- Ewelina Mnich
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - Paula Oyarce
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - Sarah Liu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | | | - Bodil Jørgensen
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Mohammed S. Motawie
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Peter Ulvskov
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Birger L. Møller
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Carlsberg Research LaboratoryCopenhagenDenmark
| | - Nanna Bjarnholt
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Jesper Harholt
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Carlsberg Research LaboratoryCopenhagenDenmark
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Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
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Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
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47
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Ohta Y, Hasegawa R, Kurosawa K, Maeda AH, Koizumi T, Nishimura H, Okada H, Qu C, Saito K, Watanabe T, Hatada Y. Enzymatic Specific Production and Chemical Functionalization of Phenylpropanone Platform Monomers from Lignin. CHEMSUSCHEM 2017; 10:425-433. [PMID: 27878983 PMCID: PMC5299523 DOI: 10.1002/cssc.201601235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/31/2016] [Indexed: 05/04/2023]
Abstract
Enzymatic catalysis is an ecofriendly strategy for the production of high-value low-molecular-weight aromatic compounds from lignin. Although well-definable aromatic monomers have been obtained from synthetic lignin-model dimers, enzymatic-selective synthesis of platform monomers from natural lignin has not been accomplished. In this study, we successfully achieved highly specific synthesis of aromatic monomers with a phenylpropane structure directly from natural lignin using a cascade reaction of β-O-4-cleaving bacterial enzymes in one pot. Guaiacylhydroxylpropanone (GHP) and the GHP/syringylhydroxylpropanone (SHP) mixture are exclusive monomers from lignin isolated from softwood (Cryptomeria japonica) and hardwood (Eucalyptus globulus). The intermediate products in the enzymatic reactions show the capacity to accommodate highly heterologous substrates at the substrate-binding sites of the enzymes. To demonstrate the applicability of GHP as a platform chemical for bio-based industries, we chemically generate value-added GHP derivatives for bio-based polymers. Together with these chemical conversions for the valorization of lignin-derived phenylpropanone monomers, the specific and enzymatic production of the monomers directly from natural lignin is expected to provide a new stream in "white biotechnology" for sustainable biorefineries.
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Affiliation(s)
- Yukari Ohta
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Ryoichi Hasegawa
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Kanako Kurosawa
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Allyn H. Maeda
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Toshio Koizumi
- Department of Applied ChemistryNational Defense Academy1-10-20 HashirimizuYokosukaKanagawa239-8686Japan
| | - Hiroshi Nishimura
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Hitomi Okada
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Chen Qu
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Kaori Saito
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Yuji Hatada
- Department of Life Sciences and Green ChemistrySaitama Institute of Technology1690 FusaijiFukayaSaitama369-0293Japan
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48
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Njiojob CN, Bozell JJ, Long BK, Elder T, Key RE, Hartwig WT. Enantioselective Syntheses of Lignin Models: An Efficient Synthesis of β-O-4 Dimers and Trimers by Using the Evans Chiral Auxiliary. Chemistry 2016; 22:12506-17. [PMID: 27459234 DOI: 10.1002/chem.201601592] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/27/2023]
Abstract
We describe an efficient five-step, enantioselective synthesis of (R,R)- and (S,S)-lignin dimer models possessing a β-O-4 linkage, by using the Evans chiral aldol reaction as a key step. Mitsunobu inversion of the (R,R)- or (S,S)-isomers generates the corresponding (R,S)- and (S,R)-diastereomers. We further extend this approach to the enantioselective synthesis of a lignin trimer model. These lignin models are synthesized with excellent ee (>99 %) and high overall yields. The lignin dimer models can be scaled up to provide multigram quantities that are not attainable by using previous methodologies. These lignin models will be useful in degradation studies probing the selectivity of enzymatic, microbial, and chemical processes that deconstruct lignin.
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Affiliation(s)
- Costyl N Njiojob
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
| | - Joseph J Bozell
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Brian K Long
- Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas Elder
- Southern Research Station, USDA Forest Service, Auburn, AL, 36849, USA
| | - Rebecca E Key
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
| | - William T Hartwig
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
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49
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Wadke N, Kandasamy D, Vogel H, Lah L, Wingfield BD, Paetz C, Wright LP, Gershenzon J, Hammerbacher A. The Bark-Beetle-Associated Fungus, Endoconidiophora polonica, Utilizes the Phenolic Defense Compounds of Its Host as a Carbon Source. PLANT PHYSIOLOGY 2016; 171:914-31. [PMID: 27208235 PMCID: PMC4902585 DOI: 10.1104/pp.15.01916] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
Norway spruce (Picea abies) is periodically attacked by the bark beetle Ips typographus and its fungal associate, Endoconidiophora polonica, whose infection is thought to be required for successful beetle attack. Norway spruce produces terpenoid resins and phenolics in response to fungal and bark beetle invasion. However, how the fungal associate copes with these chemical defenses is still unclear. In this study, we investigated changes in the phenolic content of Norway spruce bark upon E. polonica infection and the biochemical factors mediating these changes. Although genes encoding the rate-limiting enzymes in Norway spruce stilbene and flavonoid biosynthesis were actively transcribed during fungal infection, there was a significant time-dependent decline of the corresponding metabolites in fungal lesions. In vitro feeding experiments with pure phenolics revealed that E. polonica transforms both stilbenes and flavonoids to muconoid-type ring-cleavage products, which are likely the first steps in the degradation of spruce defenses to substrates that can enter the tricarboxylic acid cycle. Four genes were identified in E. polonica that encode catechol dioxygenases carrying out these reactions. These enzymes catalyze the cleavage of phenolic rings with a vicinal dihydroxyl group to muconoid products accepting a wide range of Norway spruce-produced phenolics as substrates. The expression of these genes and E. polonica utilization of the most abundant spruce phenolics as carbon sources both correlated positively with fungal virulence in several strains. Thus, the pathways for the degradation of phenolic compounds in E. polonica, initiated by catechol dioxygenase action, are important to the infection, growth, and survival of this bark beetle-vectored fungus and may play a major role in the ability of I. typographus to colonize spruce trees.
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Affiliation(s)
- Namita Wadke
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Dineshkumar Kandasamy
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Ljerka Lah
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Brenda D Wingfield
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Christian Paetz
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Louwrance P Wright
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Almuth Hammerbacher
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
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50
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Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem 2016; 291:10228-38. [PMID: 26940872 PMCID: PMC4858972 DOI: 10.1074/jbc.m115.700427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 12/23/2022] Open
Abstract
There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
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Affiliation(s)
- Jose Henrique Pereira
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Richard A Heins
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Ryan P McAndrew
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kai Deng
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Paul D Adams
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720
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