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Wolf ME, Lalande AT, Newman BL, Bleem AC, Palumbo CT, Beckham GT, Eltis LD. The catabolism of lignin-derived p-methoxylated aromatic compounds by Rhodococcus jostii RHA1. Appl Environ Microbiol 2024; 90:e0215523. [PMID: 38380926 PMCID: PMC10952524 DOI: 10.1128/aem.02155-23] [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: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ΔpobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ΔpcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the β-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.IMPORTANCELignin, an abundant aromatic polymer found in plant biomass, is a promising renewable replacement for fossil fuels as a feedstock for the chemical industry. Strategies for upgrading lignin include processes that couple the catalytic fractionation of biomass and biocatalytic transformation of the resulting aromatic compounds with a microbial cell factory. Engineering microbial cell factories for this biocatalysis requires characterization of bacterial pathways involved in catabolizing lignin-derived aromatic compounds. This study identifies new pathways for lignin-derived aromatic degradation in Rhodococcus, a genus of bacteria well suited for biocatalysis. Additionally, we describe previously unknown activities of characterized enzymes on lignin-derived compounds, expanding their utility. This work advances the development of strategies to replace fossil fuel-based feedstocks with sustainable alternatives.
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Affiliation(s)
- Megan E. Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anne T. Lalande
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Brianne L. Newman
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Chad T. Palumbo
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
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2
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Kawazoe M, Takahashi K, Tokue Y, Hishiyama S, Seki H, Higuchi Y, Kamimura N, Masai E. Catabolic System of 5-Formylferulic Acid, a Downstream Metabolite of a β-5-Type Lignin-Derived Dimer, in Sphingobium lignivorans SYK-6. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19663-19671. [PMID: 38038961 DOI: 10.1021/acs.jafc.3c06128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Sphingobium lignivorans SYK-6 can assimilate various lignin-derived aromatic compounds, including a β-5-type (phenylcoumaran-type) dimer, dehydrodiconiferyl alcohol (DCA). SYK-6 converts DCA to a stilbene-type intermediate via multiple reaction steps and then to vanillin and 5-formylferulic acid (FFA). Here, we first elucidated the catabolic pathway of FFA, which is the only unknown pathway in DCA catabolism. Then, we identified and characterized the enzyme-encoding genes responsible for this pathway. Analysis of the metabolites revealed that FFA was converted to 5-carboxyferulic acid (CFA) through oxidation of the formyl group, followed by conversion to ferulic acid by decarboxylation. A comprehensive analysis of the aldehyde dehydrogenase genes in SYK-6 indicated that NAD+-dependent FerD (SLG_12800) is crucial for the conversion of FFA to CFA. LigW and LigW2, which are 5-carboxyvanillic acid decarboxylases involved in the catabolism of a 5,5-type dimer, were found to be involved in the conversion of CFA to ferulic acid, and LigW2 played a significant role. The ligW2 gene forms an operon with ferD, and their transcription was induced during growth in DCA.
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Affiliation(s)
- Mitsuru Kawazoe
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Kenji Takahashi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Yosuke Tokue
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Shojiro Hishiyama
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba 305-8687, Ibaraki, Japan
| | - Hayato Seki
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Yudai Higuchi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Niigata, Japan
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3
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Bleem A, Kato R, Kellermyer ZA, Katahira R, Miyamoto M, Niinuma K, Kamimura N, Masai E, Beckham GT. Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6. Cell Rep 2023; 42:112847. [PMID: 37515767 DOI: 10.1016/j.celrep.2023.112847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/21/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023] Open
Abstract
Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.
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Affiliation(s)
- Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Ryo Kato
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Zoe A Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Masahiro Miyamoto
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Koh Niinuma
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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4
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Higuchi Y, Ishimaru H, Yoshikawa T, Masuda T, Sakamoto C, Kamimura N, Masai E, Takeuchi D, Sonoki T. Successful selective production of vanillic acid from depolymerized sulfite lignin and its application to poly(ethylene vanillate) synthesis. BIORESOURCE TECHNOLOGY 2023:129450. [PMID: 37406831 DOI: 10.1016/j.biortech.2023.129450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Towards lignin upgrading, vanillic acid (VA), a lignin-derived guaiacyl compound, was produced from sulfite lignin for successfully synthesizing poly(ethylene vanillate), an aromatic polymer. The engineered Sphingobium sp. SYK-6-based strain in which the genes responsible for VA/3-O-methyl gallic acid O-demethylase and syringic acid O-demethylase were disrupted was able to produce vanillic acid (VA) from the mixture consisting of acetovanillone, vanillin, VA, and other low-molecular-weight aromatics obtained by Cu(OH)2-catalyzed alkaline depolymerization of sulfite lignin and membrane fractionation. From the bio-based VA, methyl-4-(2-hydroxyethoxy)-3-methoxybenzoate was synthesized via methylesterification, hydroxyethylation, and distillation, and then it was subjected to polymerization catalyzed by titanium tetraisopropoxide. The molecular weight of the obtained poly(ethylene vanillate) was evaluated to be Mw = 13,000 (Mw/Mn = 1.99) and its melting point was 261°C. The present work proved that poly(ethylene vanillate) is able to be synthesized using VA produced from lignin for the first time.
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Affiliation(s)
- Yudai Higuchi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Hiroya Ishimaru
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Takuya Yoshikawa
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan; Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Takao Masuda
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Chiho Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Daisuke Takeuchi
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Tomonori Sonoki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.
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5
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Cai C, Xu Z, Li J, Zhou H, Jin M. Developing
Rhodococcus opacus
and
Sphingobium
sp. co‐culture systems for valorization of lignin‐derived dimers. Biotechnol Bioeng 2022; 119:3162-3177. [DOI: 10.1002/bit.28215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Chenggu Cai
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Zhaoxian Xu
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Jie Li
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Huarong Zhou
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
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The Catabolic System of Acetovanillone and Acetosyringone in Sphingobium sp. Strain SYK-6 Useful for Upgrading Aromatic Compounds Obtained through Chemical Lignin Depolymerization. Appl Environ Microbiol 2022; 88:e0072422. [PMID: 35938864 PMCID: PMC9397112 DOI: 10.1128/aem.00724-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acetovanillone is a major aromatic monomer produced in oxidative/base-catalyzed lignin depolymerization. However, the production of chemical products from acetovanillone has not been explored due to the lack of information on the microbial acetovanillone catabolic system. Here, the acvABCDEF genes were identified as specifically induced genes during the growth of Sphingobium sp. strain SYK-6 cells with acetovanillone and these genes were essential for SYK-6 growth on acetovanillone and acetosyringone (a syringyl-type acetophenone derivative). AcvAB and AcvF produced in Escherichia coli phosphorylated acetovanillone/acetosyringone and dephosphorylated the phosphorylated acetovanillone/acetosyringone, respectively. AcvCDE produced in Sphingobium japonicum UT26S carboxylated the reaction products generated from acetovanillone/acetosyringone by AcvAB and AcvF into vanilloyl acetic acid/3-(4-hydroxy-3,5-dimethoxyphenyl)-3-oxopropanoic acid. To demonstrate the feasibility of producing cis,cis-muconic acid from acetovanillone, a metabolic modification on a mutant of Pseudomonas sp. strain NGC7 that accumulates cis,cis-muconic acid from catechol was performed. The resulting strain expressing vceA and vceB required for converting vanilloyl acetic acid to vanillic acid and aroY encoding protocatechuic acid decarboxylase in addition to acvABCDEF successfully converted 1.2 mM acetovanillone to approximately equimolar cis,cis-muconic acid. Our results are expected to help improve the yield and purity of value-added chemical production from lignin through biological funneling. IMPORTANCE In the alkaline oxidation of lignin, aromatic aldehydes (vanillin, syringaldehyde, and p-hydroxybenzaldehyde), aromatic acids (vanillic acid, syringic acid, and p-hydroxybenzoic acid), and acetophenone-related compounds (acetovanillone, acetosyringone, and 4'-hydroxyacetophenone) are produced as major aromatic monomers. Also, base-catalyzed depolymerization of guaiacyl lignin resulted in vanillin, vanillic acid, guaiacol, and acetovanillone as primary aromatic monomers. To date, microbial catabolic systems of vanillin, vanillic acid, and guaiacol have been well characterized, and the production of value-added chemicals from them has also been explored. However, due to the lack of information on the microbial acetovanillone and acetosyringone catabolic system, chemical production from acetovanillone and acetosyringone has not been achieved. This study elucidated the acetovanillone/acetosyringone catabolic system and demonstrates the potential of using these genes for the production of value-added chemicals from these compounds.
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7
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Prekrasna I, Pavlovska M, Miryuta N, Dzhulai A, Dykyi E, Convey P, Kozeretska I, Bedernichek T, Parnikoza I. Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function. Microbes Environ 2022; 37. [PMID: 35705309 PMCID: PMC9530728 DOI: 10.1264/jsme2.me21069] [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] [Indexed: 11/12/2022] Open
Abstract
The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.
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Affiliation(s)
| | - Mariia Pavlovska
- State Institution National Antarctic Scientific Center.,National University of Life and Environmental Sciences of Ukraine
| | | | - Artem Dzhulai
- State Institution National Antarctic Scientific Center
| | - Evgen Dykyi
- State Institution National Antarctic Scientific Center
| | - Peter Convey
- British Antarctic Survey, NERC.,Department of Zoology, University of Johannesburg
| | | | | | - Ivan Parnikoza
- State Institution National Antarctic Scientific Center.,Institute of Molecular Biology and Genetics.,National University of "Kyiv-Mohyla Academy"
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8
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Hemati A, Nazari M, Asgari Lajayer B, Smith DL, Astatkie T. Lignocellulosics in plant cell wall and their potential biological degradation. Folia Microbiol (Praha) 2022; 67:671-681. [PMID: 35508797 DOI: 10.1007/s12223-022-00974-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
Lignocellulosic materials are composed of three main structural polymers: hemicellulose, cellulose, and lignin. Cellulose is a long chain molecule of glucose requiring a small number of enzymes for degradation due to its simple structure while lignin is a complex polymer of phenylpropane making its biochemical decomposition difficult. Under anaerobic conditions, lignocellulose breakdown is much easier and more rapid than aerobic conditions. Various studies have been carried out to estimate the rate of degradation of lignocellulosic materials. Microorganisms play a key role in the degradation of lignocellulosic materials because they produce a variety of hydrolytic enzymes including cellulase, proteases, xylanases, lipases, laccase, and phosphatases during the degradation of lignocellulosic materials. Based on the body of literature, microorganismal activity can provide useful information about the process of organic matter decomposition.
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Affiliation(s)
- Arash Hemati
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mahtab Nazari
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Donald L Smith
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Tess Astatkie
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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9
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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10
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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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11
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Suzuki Y, Otsuka Y, Araki T, Kamimura N, Masai E, Nakamura M, Katayama Y. Lignin valorization through efficient microbial production of β-ketoadipate from industrial black liquor. BIORESOURCE TECHNOLOGY 2021; 337:125489. [PMID: 34320768 DOI: 10.1016/j.biortech.2021.125489] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Vanillin and vanillate are the major lignin-derived aromatic compounds produced through the alkaline oxidation of softwood lignin. Because the production of higher-value added chemicals from these compounds is essential for lignin valorization, the microbial production of β-ketoadipate, a promising raw material for the synthesis of novel nylons, from lignin was considered. Pseudomonas putida KT2440 was engineered to convert vanillin and vanillate to β-ketoadipate. By examining the culture conditions with an initial culture volume of 1 L, the engineered strain completely converted 25 g of vanillin and 25 g of vanillate and produced approximately 23 g of β-ketoadipate from each of them with a yield of 93% or higher. Furthermore, this strain showed the ability to efficiently produce β-ketoadipate from softwood lignin extracts in black liquor, a byproduct of pulp production. These results suggest that the production of β-ketoadipate from industrial black liquor is highly feasible for substantial lignin valorization.
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Affiliation(s)
- Yuzo Suzuki
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan.
| | - Yuichiro Otsuka
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Takuma Araki
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Naofumi Kamimura
- 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
| | - Masaya Nakamura
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687 Japan
| | - Yoshihiro Katayama
- Bio-based Solution Division, Kantechs Co. Ltd., Bunkyo, Tokyo 112-0004, Japan
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12
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Lubbers RJM, Dilokpimol A, Nousiainen PA, Cioc RC, Visser J, Bruijnincx PCA, de Vries RP. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories. Microb Cell Fact 2021; 20:151. [PMID: 34344380 PMCID: PMC8336404 DOI: 10.1186/s12934-021-01643-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/22/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. RESULTS Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. CONCLUSIONS This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Paula A Nousiainen
- Department of Chemistry, University of Helsinki, A. I. Virtasen Aukio 1, P.O. Box 55, 00014, Helsinki, Finland
| | - Răzvan C Cioc
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Pieter C A Bruijnincx
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
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13
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Morya R, Kumar M, Shekhar Thakur I. Bioconversion of syringyl lignin into malic acid by Burkholderia sp. ISTR5. BIORESOURCE TECHNOLOGY 2021; 330:124981. [PMID: 33756182 DOI: 10.1016/j.biortech.2021.124981] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Syringyl monomeric units are the most common intermediates encountered during hardwood lignin degradation. In the present study, efficient utilization of syringaldehyde (SAld), syringic acid (SAc) by Burkholderia sp. ISTR5 (R5) has been shown. The proteogenomic analysis of Burkholderia sp. ISTR5 was done to understand the enzymes involved in the degradation of syringaldehyde and syringic acid. Various proteins such as aldehyde dehydrogenase, laccase, and oxidoreductases were highly upregulated during growth on syringaldehyde and syringic acid. R5 completely transformed both the substrates SAld and SAc to other hydrocarbons in 48 h and 24 h, respectively. Moreover, bioconversion of syringyl lignins followed an unusual pathway and accumulated a considerable amount of industrially valuable chemical malic acid in the reaction titer. This study shows the robust chassis of R5 to cope with the aromatic aldehydic stress and simultaneous bioconversion into valuable products for an efficient biorefinery.
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Affiliation(s)
- Raj Morya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Madan Kumar
- Centre for Rural Development and Technology, IIT Delhi, New Delhi, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Amity School of Earth and Environmental Sciences, Amity University, Gurugram, Haryana, India.
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14
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Venkatesagowda B, Dekker RFH. Microbial demethylation of lignin: Evidence of enzymes participating in the removal of methyl/methoxyl groups. Enzyme Microb Technol 2021; 147:109780. [PMID: 33992403 DOI: 10.1016/j.enzmictec.2021.109780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 02/27/2021] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
Lignin is an abundant natural plant aromatic biopolymer containing various functional groups that can be exploited for activating lignin for potential commercial applications. Applications are hindered due to the presence of a high content of methyl/methoxyl groups that affects reactiveness. Various chemical and enzymatic approaches have been investigated to increase the functionality in transforming lignin. Among these is demethylation/demethoxylation, which increases the potential numbers of vicinal hydroxyl groups for applications as phenol-formaldehyde resins. Although the chemical route to lignin demethylation is well-studied, the biological route is still poorly explored. Bacteria and fungi have the ability to demethylate lignin and lignin-related compounds. Considering that appropriate microorganisms possess the biochemical machinery to demethylate lignin by cleaving O-methyl groups liberating methanol, and modify lignin by increasing the vicinal diol content that allows lignin to substitute for phenol in organic polymer syntheses. Certain bacteria through the actions of specific O-demethylases can modify various lignin-related compounds generating vicinal diols and liberating methanol or formaldehyde as end-products. The enzymes include: cytochrome P450-aryl-O-demethylase, monooxygenase, veratrate 3-O-demethylase, DDVA O-demethylase (LigX; lignin-related biphenyl 5,5'-dehydrodivanillate (DDVA)), vanillate O-demethylase, syringate O-demethylase, and tetrahydrofolate-dependent-O-demethylase. Although, the fungal counterparts have not been investigated in depth as in bacteria, O-demethylases, nevertheless, have been reported in demethylating various lignin substrates providing evidence of a fungal enzyme system. Few fungi appear to have the ability to secrete O-demethylases. The fungi can mediate lignin demethylation enzymatically (laccase, lignin peroxidase, manganese peroxidase, O-demethylase), or non-enzymatically in brown-rot fungi through the Fenton reaction. This review discusses details on the aspects of microbial (bacterial and fungal) demethylation of lignins and lignin-model compounds and provides evidence of enzymes identified as specific O-demethylases involved in demethylation.
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Affiliation(s)
- Balaji Venkatesagowda
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada.
| | - Robert F H Dekker
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada; Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Engenharia Ambiental, Câmpus Londrina, CEP: 86036-370, Londrina, PR, Brazil.
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15
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Lopez-Echartea E, Suman J, Smrhova T, Ridl J, Pajer P, Strejcek M, Uhlik O. Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility. G3-GENES GENOMES GENETICS 2021; 11:6029021. [PMID: 33693598 PMCID: PMC8022969 DOI: 10.1093/g3journal/jkaa030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022]
Abstract
Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.
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Affiliation(s)
- Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 40 Prague, Czech Republic.,Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02 Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
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16
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Zhu D, Xu L, Sethupathy S, Si H, Ahmad F, Zhang R, Zhang W, Yang B, Sun J. Decoding lignin valorization pathways in the extremophilic Bacillus ligniniphilusL1 for vanillin biosynthesis. GREEN CHEMISTRY 2021; 23:9554-9570. [DOI: 10.1039/d1gc02692e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
An efficient bioconversion procedure for the accumulation of vanillin from lignin by pathway engineering and milking fermentation has been developed.
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Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Lingxia Xu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Haibing Si
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Fiaz Ahmad
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Rongxian Zhang
- School of chemistry and chemical engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Weimin Zhang
- 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, Guangzhou, China
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington 99354, USA
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
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17
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Yadav M, Pandey R, Chauhan NS. Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature. Front Microbiol 2020; 11:588545. [PMID: 33193247 PMCID: PMC7605359 DOI: 10.3389/fmicb.2020.588545] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Vanillin is a phenolic food additive commonly used for flavor, antimicrobial, and antioxidant properties. Though it is one of the widely used food additives, strategies of the human gut microbes to evade its antimicrobial activity await extensive elucidation. The current study explores the human gut microbiome with a multi-omics approach to elucidate its composition and metabolic machinery to counter vanillin bioactivity. A combination of SSU rRNA gene diversity, metagenomic RNA features diversity, phylogenetic affiliation of metagenome encoded proteins, uniformly (R = 0.99) indicates the abundance of Bacteroidetes followed by Firmicutes and Proteobacteria. Manual curation of metagenomic dataset identified gene clusters specific for the vanillin metabolism (ligV, ligK, and vanK) and intermediary metabolic pathways (pca and cat operon). Metagenomic dataset comparison identified the omnipresence of vanillin catabolic features across diverse populations. The metabolomic analysis brings forth the functionality of the vanillin catabolic pathway through the Protocatechuate branch of the beta-ketoadipate pathway. These results highlight the human gut microbial features and metabolic bioprocess involved in vanillin catabolism to overcome its antimicrobial activity. The current study advances our understanding of the human gut microbiome adaption toward changing dietary habits.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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18
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Suzuki Y, Okamura-Abe Y, Nakamura M, Otsuka Y, Araki T, Otsuka H, Navarro RR, Kamimura N, Masai E, Katayama Y. Development of the production of 2-pyrone-4,6-dicarboxylic acid from lignin extracts, which are industrially formed as by-products, as raw materials. J Biosci Bioeng 2020; 130:71-75. [DOI: 10.1016/j.jbiosc.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/07/2020] [Accepted: 02/01/2020] [Indexed: 10/24/2022]
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19
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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20
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Venkatesagowda B. Enzymatic demethylation of lignin for potential biobased polymer applications. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2019.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Hong H, Seo H, Kim KJ. Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls. Biochem Biophys Res Commun 2019; 514:765-771. [DOI: 10.1016/j.bbrc.2019.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/03/2019] [Indexed: 11/25/2022]
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22
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Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol Adv 2019; 37:107396. [PMID: 31075306 DOI: 10.1016/j.biotechadv.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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23
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Zhang R, Zhao CH, Chang HC, Chai MZ, Li BZ, Yuan YJ. Lignin valorization meets synthetic biology. Eng Life Sci 2019; 19:463-470. [PMID: 32625023 DOI: 10.1002/elsc.201800133] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/20/2019] [Accepted: 03/16/2019] [Indexed: 12/23/2022] Open
Abstract
Lignin, an abundant renewable resource in nature, is a highly heterogeneous biopolymer consisting of phenylpropanoid units. It is essential for sustainable utilization of biomass to convert lignin to value-added products. However, there are technical obstacles for lignin valorization due to intrinsic heterogeneity. The emerging of synthetic biology technologies brings new opportunities for lignin breakdown and utilization. In this review, we discussed the applications of synthetic biology on lignin conversion, especially the production of value-added products, such as aromatic chemicals, ring-cleaved chemicals from lignin-derived aromatics and bio-active substances. Synthetic biology will offer new potential strategies for lignin valorization by optimizing lignin degradation enzymes, building novel artificial converting pathways, and improving the chassis of model microorganisms.
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Affiliation(s)
- Renkuan Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Chen-Hui Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Han-Chen Chang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Meng-Zhe Chai
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Bing-Zhi Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
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24
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Nishimura M, Kawakami S, Otsuka H. Molecular cloning and characterization of vanillin dehydrogenase from Streptomyces sp. NL15-2K. BMC Microbiol 2018; 18:154. [PMID: 30355315 PMCID: PMC6201588 DOI: 10.1186/s12866-018-1309-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/10/2018] [Indexed: 12/03/2022] Open
Abstract
Background Streptomyces sp. NL15-2K, previously isolated from the forest soil, features an extensive catabolic network for lignin-derived aromatic compounds, including pathways transforming ferulic acid to vanillin, vanillic acid, and protocatechuic acid. To successfully use Streptomyces sp. NL15-2K as a biocatalyst for vanillin production, it is necessary to characterize the vanillin dehydrogenase (VDH) that degrades the produced vanillin to vanillic acid, as well as the gene encoding this enzyme. Here, we cloned the VDH-encoding gene (vdh) from strain NL15-2K and comprehensively characterized its gene product. Results The vdh open reading frame contains 1488 bp and encodes a 496-amino-acid protein with a calculated molecular mass of 51,705 Da. Whereas the apparent native molecular mass of recombinant VDH was estimated to be 214 kDa by gel filtration analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a subunit molecular mass of ca. 56 kDa, indicating that VDH is a homotetramer. The recombinant enzyme showed optimal activity at 45 °C and pH 9.5. The VDH substrate specificity followed this order: vanillin (100%) > protocatechualdehyde (91%) > benzaldehyde (79%) > p-hydroxybenzaldehyde (56%) > isovanillin (49%) ≈ salicylaldehyde (48%) > anisaldehyde (15%) ≈ veratraldehyde (12%). Although peptide mass fingerprinting and BLAST searches indicated that this enzyme is a salicylaldehyde dehydrogenase (SALDH), the determined kinetic parameters clearly demonstrated that the enzyme is a vanillin dehydrogenase. Lastly, phylogenetic analysis revealed that VDH from Streptomyces sp. NL15-2K forms an independent branch in the phylogenetic tree and, hence, is evolutionarily distinct from other VDHs and SALDHs whose activities have been confirmed experimentally. Conclusions Our findings not only enhance the understanding of the enzymatic properties of VDH and the characteristics of its amino acid sequence, but also contribute to the development of Streptomyces sp. NL15-2K into a biocatalyst for the biotransformation of ferulic acid to vanillin. Electronic supplementary material The online version of this article (10.1186/s12866-018-1309-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Motohiro Nishimura
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima, 731-0153, Japan.
| | - Susumu Kawakami
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima, 731-0153, Japan
| | - Hideaki Otsuka
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima, 731-0153, Japan
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25
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Zhang R, Li C, Wang J, Yan Y. Microbial Ligninolysis: Toward a Bottom-Up Approach for Lignin Upgrading. Biochemistry 2018; 58:1501-1510. [DOI: 10.1021/acs.biochem.8b00920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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26
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Takahashi K, Miyake K, Hishiyama S, Kamimura N, Masai E. Two novel decarboxylase genes play a key role in the stereospecific catabolism of dehydrodiconiferyl alcohol in Sphingobium sp. strain SYK-6. Environ Microbiol 2018. [PMID: 29528542 DOI: 10.1111/1462-2920.14099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Sphingobium sp. strain SYK-6 is able to use a phenylcoumaran-type biaryl, dehydrodiconiferyl alcohol (DCA), as a sole source of carbon and energy. In SYK-6 cells, the alcohol group of the B-ring side chain of DCA was first oxidized to the carboxyl group, and then the alcohol group of the A-ring side chain was oxidized to generate 5-(2-carboxyvinyl)-2-(4-hydroxy-3-methoxyphenyl)-7-methoxy-2,3-dihydrobenzofuran-3-carboxylate (DCA-CC). We identified phcF, phcG and phcH, which conferred the ability to convert DCA-CC into 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl)acrylate (DCA-S) in a host strain. These genes exhibited no significant sequence similarity with known enzyme genes, whereas phcF and phcG, which contain a DUF3237 domain of unknown function, showed 32% amino acid sequence identity with each other. The DCA-CC conversion activities were markedly decreased by disruption of phcF and phcG, indicating that phcF and phcG play dominant roles in the conversion of DCA-CC. Purified PhcF and PhcG catalysed the decarboxylation of the A-ring side chain of DCA-CC, producing DCA-S, and showed enantiospecificity towards (+)- and (-)-DCA-CC respectively. PhcF and PhcG formed homotrimers, and their Km for DCA-CC were determined to be 84 μM and 103 μM, and Vmax were 307 μmol⋅min-1 ⋅mg-1 and 137 μmol⋅min-1 ⋅mg-1 respectively. In conclusion, PhcF and PhcG are enantiospecific decarboxylases involved in phenylcoumaran catabolism.
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Affiliation(s)
- Kenji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Kyohei Miyake
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shojiro Hishiyama
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Wu W, Liu F, Singh S. Toward engineering E. coli with an autoregulatory system for lignin valorization. Proc Natl Acad Sci U S A 2018; 115:2970-2975. [PMID: 29500185 PMCID: PMC5866589 DOI: 10.1073/pnas.1720129115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics' toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. This study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization.
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Affiliation(s)
- Weihua Wu
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550
| | - Fang Liu
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550
| | - Seema Singh
- Biomass Science & Conversion Technologies Department, Sandia National Laboratories, Livermore, CA 94550;
- Joint BioEnergy Institute, Emeryville, CA 94608
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108
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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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Taubert M, Stöckel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, Rösch P, Popp J, Küsel K. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environ Microbiol 2017; 20:369-384. [DOI: 10.1111/1462-2920.14010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/16/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
| | - Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Patricia Geesink
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
| | - Sophie Girnus
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology; Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology; Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
- Institute of Biochemistry, Pharmacy and Psychology; University of Leipzig, Brüderstraße 32; 04103 Leipzig Germany
- Department of Chemistry and Bioscience; University of Aalborg, Fredrik Bajers Vej 7H; 9220 Aalborg East Denmark
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics; Friedrich Schiller University Jena, Helmholtzweg 4; 07743 Jena Germany
- Leibniz-Institute of Photonic Technology, Albert-Einstein-Straße 9; 07745 Jena Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity; Friedrich Schiller University Jena, Dornburger Str. 159; 07743 Jena Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E; 04103 Leipzig Germany
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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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Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals. Sci Rep 2017; 7:8420. [PMID: 28827602 PMCID: PMC5566326 DOI: 10.1038/s41598-017-07895-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/06/2017] [Indexed: 11/26/2022] Open
Abstract
Naturally, many aerobic organisms degrade lignin-derived aromatics through conserved intermediates including protocatechuate and catechol. Employing this microbial approach offers a potential solution for valorizing lignin into valuable chemicals for a potential lignocellulosic biorefinery and enabling bioeconomy. In this study, two hybrid biochemical routes combining lignin chemical depolymerization, plant metabolic engineering, and synthetic pathway reconstruction were demonstrated for valorizing lignin into value-added products. In the biochemical route 1, alkali lignin was chemically depolymerized into vanillin and syringate as major products, which were further bio-converted into cis, cis-muconic acid (ccMA) and pyrogallol, respectively, using engineered Escherichia coli strains. In the second biochemical route, the shikimate pathway of Tobacco plant was engineered to accumulate protocatechuate (PCA) as a soluble intermediate compound. The PCA extracted from the engineered Tobacco was further converted into ccMA using the engineered E. coli strain. This study reports a direct process for converting lignin into ccMA and pyrogallol as value-added chemicals, and more importantly demonstrates benign methods for valorization of polymeric lignin that is inherently heterogeneous and recalcitrant. Our approach also validates the promising combination of plant engineering with microbial chassis development for the production of value added and speciality chemicals.
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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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A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde. Sci Rep 2017; 7:44422. [PMID: 28294121 PMCID: PMC5353671 DOI: 10.1038/srep44422] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/07/2017] [Indexed: 01/18/2023] Open
Abstract
Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed similar kcat/Km values for syringaldehyde (2100 s−1·mM−1) and vanillin (1700 s−1·mM−1), whereas LigV substantially preferred vanillin (8800 s−1·mM−1) over syringaldehyde (1.4 s−1·mM−1). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster.
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Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 2016; 113:E5802-E5811. [PMID: 27634497 DOI: 10.1073/pnas.1606043113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.
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35
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Datta S, Annapure US, Timson DJ. Characterization of Cd36_03230p, a putative vanillin dehydrogenase from Candida dubliniensis. RSC Adv 2016. [DOI: 10.1039/c6ra22209a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite its annotation as such, Cd36_03230p is not a vanillin dehydrogenase.
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Affiliation(s)
- Suprama Datta
- School of Biological Sciences
- Queen's University Belfast
- Medical Biology Centre
- Belfast BT9 7BL
- UK
| | - Uday S. Annapure
- Food Engineering and Technology Department
- Institute of Chemical Technology (ICT)
- Mumbai 400 019
- India
| | - David J. Timson
- School of Biological Sciences
- Queen's University Belfast
- Medical Biology Centre
- Belfast BT9 7BL
- UK
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36
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Membrane-associated glucose-methanol-choline oxidoreductase family enzymes PhcC and PhcD are essential for enantioselective catabolism of dehydrodiconiferyl alcohol. Appl Environ Microbiol 2015; 81:8022-36. [PMID: 26362985 DOI: 10.1128/aem.02391-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/09/2015] [Indexed: 01/06/2023] Open
Abstract
Sphingobium sp. strain SYK-6 is able to degrade various lignin-derived biaryls, including a phenylcoumaran-type compound, dehydrodiconiferyl alcohol (DCA). In SYK-6 cells, the alcohol group of the B-ring side chain of DCA is initially oxidized to the carboxyl group to generate 3-(2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydrobenzofuran-5-yl) acrylic acid (DCA-C). Next, the alcohol group of the A-ring side chain of DCA-C is oxidized to the carboxyl group, and then the resulting metabolite is catabolized through vanillin and 5-formylferulate. In this study, the genes involved in the conversion of DCA-C were identified and characterized. The DCA-C oxidation activities in SYK-6 were enhanced in the presence of flavin adenine dinucleotide and an artificial electron acceptor and were induced ca. 1.6-fold when the cells were grown with DCA. Based on these observations, SLG_09480 (phcC) and SLG_09500 (phcD), encoding glucose-methanol-choline oxidoreductase family proteins, were presumed to encode DCA-C oxidases. Analyses of phcC and phcD mutants indicated that PhcC and PhcD are essential for the conversion of (+)-DCA-C and (-)-DCA-C, respectively. When phcC and phcD were expressed in SYK-6 and Escherichia coli, the gene products were mainly observed in their membrane fractions. The membrane fractions of E. coli that expressed phcC and phcD catalyzed the specific conversion of DCA-C into the corresponding carboxyl derivatives. In the oxidation of DCA-C, PhcC and PhcD effectively utilized ubiquinone derivatives as electron acceptors. Furthermore, the transcription of a putative cytochrome c gene was significantly induced in SYK-6 grown with DCA. The DCA-C oxidation catalyzed by membrane-associated PhcC and PhcD appears to be coupled to the respiratory chain.
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37
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Boyd DR, Sharma ND, Malone JF, McIntyre PBA, McRoberts C, Floyd S, Allen CCR, Gohil A, Coles SJ, Horton PN, Stevenson PJ. Toluene dioxygenase-catalyzed synthesis and reactions of cis-diol metabolites derived from 2- and 3-methoxyphenols. J Org Chem 2015; 80:3429-39. [PMID: 25756661 DOI: 10.1021/jo5028968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using toluene dioxygenase as biocatalyst, enantiopure cis-dihydrodiol and cis-tetrahydrodiol metabolites, isolated as their ketone tautomers, were obtained from meta and ortho methoxyphenols. Although these isomeric phenol substrates are structurally similar, the major bioproducts from each of these biotransformations were found at different oxidation levels. The relatively stable cyclohexenone cis-diol metabolite from meta methoxyphenol was isolated, while the corresponding metabolite from ortho methoxyphenol was rapidly bioreduced to a cyclohexanone cis-diol. The chemistry of the 3-methoxycyclohexenone cis-diol product was investigated and elimination, aromatization, hydrogenation, regioselective O-exchange, Stork-Danheiser transposition and O-methylation reactions were observed. An offshoot of this technology provided a two-step chemoenzymatic synthesis, from meta methoxyphenol, of a recently reported chiral fungal metabolite; this synthesis also established the previously unassigned absolute configuration.
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Affiliation(s)
- Derek R Boyd
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Narain D Sharma
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - John F Malone
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Peter B A McIntyre
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Colin McRoberts
- §Agri-food and Biosciences Institute for Northern Ireland, Belfast, BT9 5PX, U.K
| | - Stewart Floyd
- §Agri-food and Biosciences Institute for Northern Ireland, Belfast, BT9 5PX, U.K
| | - Christopher C R Allen
- ‡School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5AG, U.K
| | - Amit Gohil
- ‡School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5AG, U.K
| | - Simon J Coles
- ∥National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Peter N Horton
- ∥National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Paul J Stevenson
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
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Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, Schlüter A, Pühler A, Bartosik D. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Front Microbiol 2015; 6:152. [PMID: 26074880 PMCID: PMC4447125 DOI: 10.3389/fmicb.2015.00152] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/09/2015] [Indexed: 12/31/2022] Open
Abstract
The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Adam Pyzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Sebastian Mielnicki
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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Ding W, Si M, Zhang W, Zhang Y, Chen C, Zhang L, Lu Z, Chen S, Shen X. Functional characterization of a vanillin dehydrogenase in Corynebacterium glutamicum. Sci Rep 2015; 5:8044. [PMID: 25622822 PMCID: PMC4306973 DOI: 10.1038/srep08044] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/29/2014] [Indexed: 11/09/2022] Open
Abstract
Vanillin dehydrogenase (VDH) is a crucial enzyme involved in the degradation of lignin-derived aromatic compounds. Herein, the VDH from Corynebacterium glutamicum was characterized. The relative molecular mass (Mr) determined by SDS-PAGE was ~51 kDa, whereas the apparent native Mr values revealed by gel filtration chromatography were 49.5, 92.3, 159.0 and 199.2 kDa, indicating the presence of dimeric, trimeric and tetrameric forms. Moreover, the enzyme showed its highest level of activity toward vanillin at pH 7.0 and 30°C, and interestingly, it could utilize NAD(+) and NADP(+) as coenzymes with similar efficiency and showed no obvious difference toward NAD(+) and NADP(+). In addition to vanillin, this enzyme exhibited catalytic activity toward a broad range of substrates, including p-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, o-phthaldialdehyde, cinnamaldehyde, syringaldehyde and benzaldehyde. Conserved catalytic residues or putative cofactor interactive sites were identified based on sequence alignment and comparison with previous studies, and the function of selected residues were verified by site-directed mutagenesis analysis. Finally, the vdh deletion mutant partially lost its ability to grow on vanillin, indicating the presence of alternative VDH(s) in Corynebacterium glutamicum. Taken together, this study contributes to understanding the VDH diversity from bacteria and the aromatic metabolism pathways in C. glutamicum.
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Affiliation(s)
- Wei Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Meiru Si
- 1] State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China [2] Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Weipeng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yaoling Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Can Chen
- 1] State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China [2] Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lei Zhang
- 1] State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China [2] Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhiqiang Lu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Shaolin Chen
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xihui Shen
- 1] State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China [2] Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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Investigation of the Amycolatopsis sp. strain ATCC 39116 vanillin dehydrogenase and its impact on the biotechnical production of vanillin. Appl Environ Microbiol 2012; 79:81-90. [PMID: 23064333 DOI: 10.1128/aem.02358-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The actinomycete Amycolatopsis sp. strain ATCC 39116 is capable of synthesizing large amounts of vanillin from ferulic acid, which is a natural cell wall component of higher plants. The desired intermediate vanillin is subject to undesired catabolism caused by the metabolic activity of a hitherto unknown vanillin dehydrogenase (VDH(ATCC 39116)). In order to prevent the oxidation of vanillin to vanillic acid and thereby to obtain higher yields and concentrations of vanillin, the responsible vanillin dehydrogenase in Amycolatopsis sp. ATCC 39116 was investigated for the first time by using data from our genome sequence analysis and further bioinformatic approaches. The vdh gene was heterologously expressed in Escherichia coli, and the encoded vanillin dehydrogenase was characterized in detail. VDH(ATCC 39116) was purified to apparent electrophoretic homogeneity and exhibited NAD(+)-dependent activity toward vanillin, coniferylaldehyde, cinnamaldehyde, and benzaldehyde. The enzyme showed its highest level of activity toward vanillin at pH 8.0 and at a temperature of 44°C. In a next step, a precise vdh deletion mutant of Amycolatopsis sp. ATCC 39116 was generated. The mutant lost its ability to grow on vanillin and did not show vanillin dehydrogenase activity. A 2.3-times-higher vanillin concentration and a substantially reduced amount of vanillic acid occurred with the Amycolatopsis sp. ATCC 39116 Δvdh::Km(r) mutant when ferulic acid was provided for biotransformation in a cultivation experiment on a 2-liter-bioreactor scale. Based on these results and taking further metabolic engineering into account, the Amycolatopsis sp. ATCC 39116 Δvdh::Km(r) mutant represents an optimized and industrially applicable platform for the biotechnological production of natural vanillin.
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Kasai D, Kamimura N, Tani K, Umeda S, Abe T, Fukuda M, Masai E. Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6. FEMS Microbiol Lett 2012; 332:68-75. [PMID: 22515452 DOI: 10.1111/j.1574-6968.2012.02576.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/12/2012] [Accepted: 04/16/2012] [Indexed: 11/28/2022] Open
Abstract
Sphingobium sp. strain SYK-6 is able to degrade various lignin-derived aromatic compounds including ferulate, vanillate, and syringate. In the SYK-6 cells, ferulate is converted to vanillin and acetyl-coenzyme A (acetyl-CoA) through the reactions catalyzed by feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase encoded by ferA and ferB, respectively. Here, we characterized the transcriptional regulation of ferBA controlled by a MarR-type transcriptional regulator, FerC. The ferC gene is located upstream of ferB. Reverse transcription (RT)-PCR analysis suggested that the ferBA genes form an operon. Quantitative RT-PCR analyses of SYK-6 and its mutant cells revealed that the transcription of the ferBA operon is negatively regulated by FerC, and feruloyl-CoA was identified as an inducer. The transcription start site of ferB was mapped at 30 nucleotides upstream from the ferB initiation codon. Purified His-tagged FerC bound to the ferC-ferB intergenic region. This region contains an inverted repeat sequence, which overlaps with a part of the -10 sequence and the transcriptional start site of ferB. The binding of FerC to the operator sequence was inhibited by the addition of feruloyl-CoA, indicating that FerC interacts with feruloyl-CoA as an effector molecule. Furthermore, hydroxycinnamoyl-CoAs, including p-coumaroyl-CoA, caffeoyl-CoA, and sinapoyl-CoA also acted as effector.
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Affiliation(s)
- Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Bugg TDH, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 2011; 28:1883-96. [PMID: 21918777 DOI: 10.1039/c1np00042j] [Citation(s) in RCA: 455] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.
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Nakamura T, Ichinose H, Wariishi H. Cloning and heterologous expression of two aryl-aldehyde dehydrogenases from the white-rot basidiomycete Phanerochaete chrysosporium. Biochem Biophys Res Commun 2010; 394:470-5. [PMID: 20175998 DOI: 10.1016/j.bbrc.2010.01.131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 01/31/2010] [Indexed: 11/16/2022]
Abstract
We identified two aryl-aldehyde dehydrogenase proteins (PcALDH1 and PcALDH2) from the white-rot basidiomycete Phanerochaete chrysosporium. Both PcALDHs were translationally up-regulated in response to exogenous addition of vanillin, one of the key aromatic compounds in the pathway of lignin degradation by basidiomycetes. To clarify the catalytic functions of PcALDHs, we isolated full-length cDNAs encoding these proteins and heterologously expressed the recombinant enzymes using a pET/Escherichia coli system. The open reading frames of both PcALDH1 and PcALDH2 consisted of 1503 nucleotides. The deduced amino acid sequences of both proteins showed high homologies with aryl-aldehyde dehydrogenases from other organisms and contained ten conserved domains of ALDHs. Moreover, a novel glycine-rich motif "GxGxxxG" was located at the NAD(+)-binding site. The recombinant PcALDHs catalyzed dehydrogenation reactions of several aryl-aldehyde compounds, including vanillin, to their corresponding aromatic acids. These results strongly suggested that PcALDHs metabolize aryl-aldehyde compounds generated during fungal degradation of lignin and various aromatic xenobiotics.
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Affiliation(s)
- Tomofumi Nakamura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Gosling A, Zachariou M, Straffon M. Purification and characterisation of a 4-hydroxy benzaldehyde dehydrogenase cloned from Acinetobacter baylyi. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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