1
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Rashid GMM, Rivière GN, Cottyn-Boitte B, Majira A, Cézard L, Sodré V, Lam R, Fairbairn JA, Baumberger S, Bugg TDH. Ether Bond Cleavage of a Phenylcoumaran β-5 Lignin Model Compound and Polymeric Lignin Catalysed by a LigE-type Etherase from Agrobacterium sp. Chembiochem 2024; 25:e202400132. [PMID: 38416537 DOI: 10.1002/cbic.202400132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
A LigE-type beta-etherase enzyme from lignin-degrading Agrobacterium sp. has been identified, which assists degradation of polymeric lignins. Testing against lignin dimer model compounds revealed that it does not catalyse the previously reported reaction of Sphingobium SYK-6 LigE, but instead shows activity for a β-5 phenylcoumaran lignin dimer. The reaction products did not contain glutathione, indicating a catalytic role for reduced glutathione in this enzyme. Three reaction products were identified: the major product was a cis-stilbene arising from C-C fragmentation involving loss of formaldehyde; two minor products were an alkene arising from elimination of glutathione, and an oxidised ketone, proposed to arise from reaction of an intermediate with molecular oxygen. Testing of the recombinant enzyme against a soda lignin revealed the formation of new signals by two-dimensional NMR analysis, whose chemical shifts are consistent with the formation of a stilbene unit in polymeric lignin.
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Affiliation(s)
- Goran M M Rashid
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Guillaume N Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Betty Cottyn-Boitte
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Amel Majira
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Laurent Cézard
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Victoria Sodré
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Richard Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Julia A Fairbairn
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Stéphanie Baumberger
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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2
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Bugg TDH. The chemical logic of enzymatic lignin degradation. Chem Commun (Camb) 2024; 60:804-814. [PMID: 38165282 PMCID: PMC10795516 DOI: 10.1039/d3cc05298b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Lignin is an aromatic heteropolymer, found in plant cell walls as 20-30% of lignocellulose. It represents the most abundant source of renewable aromatic carbon in the biosphere, hence, if it could be depolymerised efficiently, then it would be a highly valuable source of renewable aromatic chemicals. However, lignin presents a number of difficulties for biocatalytic or chemocatalytic breakdown. Research over the last 10 years has led to the identification of new bacterial enzymes for lignin degradation, and the use of metabolic engineering to generate useful bioproducts from microbial lignin degradation. The aim of this article is to discuss the chemical mechanisms used by lignin-degrading enzymes and microbes to break down lignin, and to describe current methods for generating aromatic bioproducts from lignin using enzymes and engineered microbes.
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Affiliation(s)
- Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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3
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An X, Cheng Y, Zang H, Li C. Biodegradation characteristics of lignin in pulping wastewater by the thermophilic Serratia sp. AXJ-M: Performance, genetic background, metabolic pathway and toxicity assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121230. [PMID: 36754200 DOI: 10.1016/j.envpol.2023.121230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The key to the efficient removal of pulping wastewater lies in the effective degradation of lignin at high temperature. There is thus an urgent need to seek effective eco-environmental techniques to overcome this environmental limit for lignin degradation. The soil isolate thermophilic Serratia sp. AXJ-M efficiently metabolizes lignin. Nevertheless, the underlying comprehensive molecular mechanism of lignin degradation by thermophilic AXJ-M is poorly understood. Here, strain AXJ-M showed excellent degradation ability toward diverse lignin-related aromatic compounds. Functional genome analysis and RNA-Seq disclosed several traits which in joint consideration suggest a high efficiency of AXJ-M representative to the lignin degradation and environmental adaptation. Multiomics analyses combined with GC-MS revealed seven potential lignin biodegradation pathways. DyP was predicted to be involved in the breakdown of the β-O-4 ether bond, Cα-Cβ bond and Cα oxidation of lignin by prokaryotic expression and gene knockout and complementation. Molecular docking deepens the understanding of the interaction between DyP and lignin. Toxicity assessment experiments clearly indicated that AXJ-M significantly reduced the toxicity of the metabolites. This work expands the knowledge about the degradation mechanism of thermophilic lignin-degrading bacteria, most importantly, offers a new perspective on potential applications in utilizing this strain in pulping wastewater bioremediation.
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Affiliation(s)
- Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang, 330045, PR China.
| | - Yi Cheng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Sciences, China Agricultural University, Beijing 100193, China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
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4
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Periplasmic expression of Pseudomonas fluorescens peroxidase Dyp1B and site-directed mutant Dyp1B enzymes enhances polymeric lignin degradation activity in Pseudomonas putida KT2440. Enzyme Microb Technol 2023; 162:110147. [DOI: 10.1016/j.enzmictec.2022.110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
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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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6
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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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Abstract
Lignin, a rigid polymer composed of phenolic subunits with high molecular weight and complex structure, ranks behind only cellulose in the contribution to the biomass of plants. Therefore, lignin can be used as a new environmentally friendly resource for the industrial production of a variety of polymers, dyes and adhesives. Since laccase was found to be able to degrade lignin, increasing attention had been paid to the valorization of lignin. Research has mainly focused on the identification of lignin-degrading enzymes, which play a key role in lignin biodegradation, and the potential application of lignin degradation products. In this review, we describe the source, catalytic specificity and enzyme reaction mechanism of the four classes of the lignin-degrading enzymes so far discovered. In addition, the major pathways of lignin biodegradation and the applications of the degradative products are also discussed. Lignin-degrading bacteria or enzymes can be used in combination with chemical pretreatment for the production of value-added chemicals from lignin, providing a promising strategy for lignin valorization.
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8
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Mueller J, Willett H, Feist AM, Niu W. Engineering Pseudomonas putida for Improved Utilization of Syringyl Aromatics. Biotechnol Bioeng 2022; 119:2541-2550. [PMID: 35524438 PMCID: PMC9378539 DOI: 10.1002/bit.28131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/22/2022] [Accepted: 05/01/2022] [Indexed: 11/08/2022]
Abstract
Lignin is a largely untapped source for the bioproduction of value‐added chemicals. Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic capabilities, and genetic amenability. Here we demonstrate the engineering of P. putida for the ability to metabolize syringic acid, one of the major products that comes from the breakdown of the syringyl component of lignin. The rational design was first applied for the construction of strain Sy‐1 by overexpressing a native vanillate demethylase. Subsequent adaptive laboratory evolution (ALE) led to the generation of mutations that achieved robust growth on syringic acid as a sole carbon source. The best mutant showed a 30% increase in the growth rate over the original engineered strain. Genomic sequencing revealed multiple mutations repeated in separate evolved replicates. Reverse engineering of mutations identified in agmR, gbdR, fleQ, and the intergenic region of gstB and yadG into the parental strain recaptured the improved growth of the evolved strains to varied extent. These findings thus reveal the ability of P. putida to utilize lignin more fully as a feedstock and make it a more economically viable chassis for chemical production.
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Affiliation(s)
- Joshua Mueller
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Howard Willett
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.,The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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9
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Isolation and characterization of microorganisms capable of cleaving the ether bond of 2-phenoxyacetophenone. Sci Rep 2022; 12:2874. [PMID: 35190591 PMCID: PMC8861056 DOI: 10.1038/s41598-022-06816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/07/2022] [Indexed: 11/08/2022] Open
Abstract
Lignin is a heterogeneous aromatic polymer and major component of plant cell walls. The β-O-4 alkyl aryl ether is the most abundant linkage within lignin. Given that lignin is effectively degraded on earth, as yet unknown ether bond-cleaving microorganisms could still exist in nature. In this study, we searched for microorganisms that transform 2-phenoxyacetophenone (2-PAP), a model compound for the β-O-4 linkage in lignin, by monitoring ether bond cleavage. We first isolated microorganisms that grew on medium including humic acid (soil-derived organic compound) as a carbon source. The isolated microorganisms were subsequently subjected to colorimetric assay for 2-PAP ether bond-cleaving activity; cells of the isolated strains were incubated with 2-PAP, and strains producing phenol via ether bond cleavage were selected using phenol-sensitive Gibbs reagent. This screening procedure enabled the isolation of various 2-PAP-transforming microorganisms, including 7 bacteria (genera: Acinetobacter, Cupriavidus, Nocardioides, or Streptomyces) and 1 fungus (genus: Penicillium). To our knowledge, these are the first microorganisms demonstrated to cleave the ether bond of 2-PAP. One Gram-negative bacterium, Acinetobacter sp. TUS-SO1, was characterized in detail. HPLC and GC-MS analyses revealed that strain TUS-SO1 oxidatively and selectively cleaves the ether bond of 2-PAP to produce phenol and benzoate. These results indicate that the transformation mechanism differs from that involved in reductive β-etherase, which has been well studied. Furthermore, strain TUS-SO1 efficiently transformed 2-PAP; glucose-grown TUS-SO1 cells converted 1 mM 2-PAP within only 12 h. These microorganisms might play important roles in the degradation of lignin-related compounds in nature.
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10
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Hirano Y, Izawa A, Hosoya T, Miyafuji H. Degradation mechanism of a lignin model compound during alkaline aerobic oxidation: formation of the vanillin precursor from the β-O-4 middle unit of softwood lignin. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have proposed plausible reaction pathways involved in the chemical conversion of softwood lignin to vanillin through alkaline aerobic oxidation.
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Affiliation(s)
- Yuki Hirano
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Akari Izawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takashi Hosoya
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hisashi Miyafuji
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
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11
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Rashid GMM, Bugg TDH. Enhanced biocatalytic degradation of lignin using combinations of lignin-degrading enzymes and accessory enzymes. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00431j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Combinations of lignin-oxidizing enzymes and accessory enzymes show enhanced activity for product formation from polymeric lignin.
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12
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Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6. Sci Rep 2020; 10:20614. [PMID: 33244017 PMCID: PMC7691349 DOI: 10.1038/s41598-020-77462-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Sphingobium sp. strain SYK-6 is an alphaproteobacterial degrader of lignin-derived aromatic compounds, which can degrade all the stereoisomers of β-aryl ether-type compounds. SYK-6 cells convert four stereoisomers of guaiacylglycerol-β-guaiacyl ether (GGE) into two enantiomers of α-(2-methoxyphenoxy)-β-hydroxypropiovanillone (MPHPV) through GGE α-carbon atom oxidation by stereoselective Cα-dehydrogenases encoded by ligD, ligL, and ligN. The ether linkages of the resulting MPHPV enantiomers are cleaved by stereoselective glutathione (GSH) S-transferases (GSTs) encoded by ligF, ligE, and ligP, generating (βR/βS)-α-glutathionyl-β-hydroxypropiovanillone (GS-HPV) and guaiacol. To date, it has been shown that the gene products of ligG and SLG_04120 (ligQ), both encoding GST, catalyze GSH removal from (βR/βS)-GS-HPV, forming achiral β-hydroxypropiovanillone. In this study, we verified the enzyme properties of LigG and LigQ and elucidated their roles in β-aryl ether catabolism. Purified LigG showed an approximately 300-fold higher specific activity for (βR)-GS-HPV than that for (βS)-GS-HPV, whereas purified LigQ showed an approximately six-fold higher specific activity for (βS)-GS-HPV than that for (βR)-GS-HPV. Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV. Furthermore, the disruption of both ligG and ligQ was observed to lead to the loss of the capability of SYK-6 to convert MPHPV. This suggests that GSH removal from GS-HPV catalyzed by LigG and LigQ, is essential for cellular GSH recycling during β-aryl ether catabolism.
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13
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Klinger GE, Zhou Y, Foote JA, Wester AM, Cui Y, Alherech M, Stahl SS, Jackson JE, Hegg EL. Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin. CHEMSUSCHEM 2020; 13:4394-4399. [PMID: 32668064 PMCID: PMC7540407 DOI: 10.1002/cssc.202001238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Lignin may serve as a renewable feedstock for the production of chemicals and fuels if mild, scalable processes for its depolymerization can be devised. The use of small organic thiols represents a bioinspired strategy to cleave the β-O-4 bond, the most common linkage in lignin. In the present study, synthetic β-O-4 linked polymers were treated with organic thiols, yielding up to 90 % cleaved monomer products. Lignin extracted from poplar was also treated with organic thiols resulting in molecular weight reductions as high as 65 % (Mn ) in oxidized lignin. Thiol-based cleavage of other lignin linkages was also explored in small-molecule model systems to uncover additional potential pathways by which thiols might depolymerize lignin. The success of thiol-mediated cleavage on model dimers, polymers, and biomass-derived lignin illustrates the potential utility of small redox-active molecules to penetrate complex polymer matrices for depolymerization and subsequent valorization of lignin into fuels and chemicals.
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Affiliation(s)
- Grace E. Klinger
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
- Department of Biochemistry & Molecular BiologyMichigan State UniversityEast Lansing, MI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast Lansing, MI48824USA
| | - Yuting Zhou
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Juliet A. Foote
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Abby M. Wester
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Yanbin Cui
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - Manar Alherech
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - Shannon S. Stahl
- DOE Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonWI 53706USA
- Department of ChemistryUniversity of Wisconsin-MadisonMadisonWI53706USA
| | - James E. Jackson
- Department of ChemistryMichigan State UniversityEast Lansing, MI48824USA
| | - Eric L. Hegg
- Department of Biochemistry & Molecular BiologyMichigan State UniversityEast Lansing, MI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast Lansing, MI48824USA
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14
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Lemke RAS, Olson SM, Morse K, Karlen SD, Higbee A, Beebe ET, Ralph J, Coon JJ, Fox BG, Donohue TJ. A bacterial biosynthetic pathway for methylated furan fatty acids. J Biol Chem 2020; 295:9786-9801. [PMID: 32434926 PMCID: PMC7380195 DOI: 10.1074/jbc.ra120.013697] [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: 03/31/2020] [Revised: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Fatty acids play many important roles in cells and also in industrial processes. Furan fatty acids (FuFAs) are present in the lipids of some plant, fish, and microbial species and appear to function as second messengers in pathways that protect cells from membrane-damaging agents. We report here the results of chemical, genetic, and synthetic biology experiments to decipher the biosynthesis of the monomethylated FuFA, methyl 9-(3-methyl-5-pentylfuran-2-yl) nonanoate (9M5-FuFA), and its dimethyl counterpart, methyl 9-(3,4-dimethyl-5-pentylfuran-2-yl) nonanoate (9D5-FuFA), in two α-proteobacteria. Each of the steps in FuFA biosynthesis occurs on pre-existing phospholipid fatty acid chains, and we identified pathway intermediates and the gene products that catalyze 9M5-FuFA and 9D5-FuFA synthesis in Rhodobacter sphaeroides 2.4.1 and Rhodopseudomonas palustris CGA009. One previously unknown pathway intermediate was a methylated diunsaturated fatty acid, (10E,12E)-11-methyloctadeca-10,12-dienoic acid (11Me-10t,12t-18:2), produced from (11E)-methyloctadeca-11-enoic acid (11Me-12t-18:1) by a newly identified fatty acid desaturase, UfaD. We also show that molecular oxygen (O2) is the source of the oxygen atom in the furan ring of 9M5-FuFA, and our findings predict that an O2-derived oxygen atom is incorporated into 9M5-FuFA via a protein, UfaO, that uses the 11Me-10t,12t-18:2 fatty acid phospholipid chain as a substrate. We discovered that R. palustris also contains a SAM-dependent methylase, FufM, that produces 9D5-FuFA from 9M5-FuFA. These results uncover the biochemical sequence of intermediates in a bacterial pathway for 9M5-FuFA and 9D5-FuFA biosynthesis and suggest the existence of homologs of the enzymes identified here that could function in FuFA biosynthesis in other organisms.
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Affiliation(s)
- Rachelle A S Lemke
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA.,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Stephanie M Olson
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA.,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Kaitlin Morse
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Steven D Karlen
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Alan Higbee
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Emily T Beebe
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - John Ralph
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Brian G Fox
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA.,Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA .,Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
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15
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Granja-Travez RS, Persinoti GF, Squina FM, Bugg TDH. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 2020; 104:3305-3320. [PMID: 32088760 DOI: 10.1007/s00253-019-10318-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.
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Affiliation(s)
- Rommel Santiago Granja-Travez
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
| | | | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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16
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Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass. Curr Opin Chem Biol 2020; 55:26-33. [PMID: 31918394 DOI: 10.1016/j.cbpa.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 11/20/2022]
Abstract
The conversion of polymeric lignin from plant biomass into renewable chemicals is an important unsolved problem in the biorefinery concept. This article summarises recent developments in the discovery of bacterial enzymes for lignin degradation, our current understanding of their molecular mechanism of action, and their use to convert lignin or lignocellulose into aromatic chemicals. The review also discusses the recent developments in screening of metagenomic libraries for new biocatalysts, and the use of protein engineering to enhance lignin degradation activity.
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17
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Klinger GE, Zhou Y, Hao P, Robbins J, Aquilina JM, Jackson JE, Hegg EL. Biomimetic Reductive Cleavage of Keto Aryl Ether Bonds by Small-Molecule Thiols. CHEMSUSCHEM 2019; 12:4775-4779. [PMID: 31418534 DOI: 10.1002/cssc.201901742] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 06/10/2023]
Abstract
The nucleophilic and reductive properties of thiolates and thiols make them ideal candidates as redox mediators via the thiol/disulfide couple. One mechanism for biological lignin depolymerization entails reduction of keto aryl ether bonds by an SN 2 mechanism with the thiol redox mediator glutathione. In this study, mimicking this chemistry in a simple protein- and metal-free process, several small organic thiols are surveyed for their ability to cleave aryl keto ethers that model the β-O-4 linkages found in partially oxidized lignin. In polar aprotic solvents, β-mercaptoethanol and dithiothreitol yielded up to 100 % formation of phenol and acetophenone products from 2-phenoxyacetophenone, but not from its reduced alcohol congener. The effects of reaction conditions and of substituents on the aryl rings and the keto ether linkage are assessed. These results, together with activation barriers computed by quantum chemical simulations and direct observation of the expected intermediate thioether, point to an SN 2 mechanism. This study confirms that small organic thiols can reductively break down lignin-relevant keto aryl ether linkages.
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Affiliation(s)
- Grace E Klinger
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, Michigan, 48824, USA
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
| | - Yuting Zhou
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Pengchao Hao
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Jacob Robbins
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - Jake M Aquilina
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
| | - James E Jackson
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, Michigan, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, 164 Food Safety and Toxicology Building, East Lansing, Michigan, 48824, USA
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18
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Lee S, Kang M, Bae JH, Sohn JH, Sung BH. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front Bioeng Biotechnol 2019; 7:209. [PMID: 31552235 PMCID: PMC6733911 DOI: 10.3389/fbioe.2019.00209] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.
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Affiliation(s)
- Siseon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
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19
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Discovery of novel enzyme genes involved in the conversion of an arylglycerol-β-aryl ether metabolite and their use in generating a metabolic pathway for lignin valorization. Metab Eng 2019; 55:258-267. [DOI: 10.1016/j.ymben.2019.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/20/2022]
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20
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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21
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Husarcikova J, Schallmey A. Whole-cell cascade for the preparation of enantiopure β-O-4 aryl ether compounds with glutathione recycling. J Biotechnol 2019; 293:1-7. [PMID: 30703467 DOI: 10.1016/j.jbiotec.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Bacterial β-etherases and glutathione lyases are glutathione-dependent enzymes that catalyze the selective cleavage of β-O-4 aryl ether bonds found in lignin. Their glutathione (GSH) dependence is regarded as major limitation for their application in the production of aromatics from lignin polymer and oligomers, as stoichiometric glutathione amounts are required. Thus, recycling of the GSH cofactor by a NAD(P)H-dependent glutathione reductase was proposed previously. Herein, the use of a whole-cell catalyst was studied for efficient β-O-4 aryl ether bond cleavage with intracellular GSH supply and recycling. After optimization of the whole-cell catalyst as well as reaction conditions, up to 5 mM lignin model substrate 2,6-methoxyphenoxy-α-veratrylglycerone (2,6-MP-VG) were efficiently converted into 2,6-methoxyphenol (2,6-MP) and veratryl glycerone (VG) without addition of external GSH. Unexpectedly, no glucose supply was required for glutathione recycling within the cells up to this substrate concentration. To demonstrate the applicability of this whole-cell approach, a whole-cell cascade combining a stereoselective β-etherase (either LigE from Sphingobium sp. SYK-6 or LigF-NA from Novosphingobium aromaticivorans) and a glutathione lyase (LigG-TD from Thiobacillus denitrificans) was employed in the kinetic resolution of racemic 2,6-MP-VG. This way, enantiopure (S)- and (R)-2,6-MP-VG were obtained on semi-preparative scale without the need for external GSH supply.
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Affiliation(s)
- Jana Husarcikova
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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22
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Theoharaki C, Chronopoulou E, Vlachakis D, Ataya FS, Giannopoulos P, Maurikou S, Skopelitou K, Papageorgiou AC, Labrou NE. Delineation of the functional and structural properties of the glutathione transferase family from the plant pathogen Erwinia carotovora. Funct Integr Genomics 2018; 19:1-12. [PMID: 29938342 DOI: 10.1007/s10142-018-0618-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/24/2018] [Accepted: 05/31/2018] [Indexed: 01/09/2023]
Abstract
Erwinia carotovora, a widespread plant pathogen that causes soft rot disease in many plants, is considered a major threat in agriculture. Bacterial glutathione transferases (GSTs) play important roles in a variety of metabolic pathways and processes, such as the biodegradation of xenobiotics, protection against abiotic stress, and resistance against antimicrobial drugs. The GST family of canonical soluble enzymes from Erwinia carotovora subsp. atroseptica strain SCRI1043 (EcaGSTs) was investigated. Genome analysis showed the presence of six putative canonical cytoplasmic EcaGSTs, which were revealed by phylogenetic analysis to belong to the well-characterized GST classes beta, nu, phi, and zeta. The analysis also revealed the presence of two isoenzymes that were phylogenetically close to the omega class of GSTs, but formed a distinct class. The EcaGSTs were cloned and expressed in Escherichia coli, and their catalytic activity toward different electrophilic substrates was elucidated. The EcaGSTs catalyzed different types of reactions, although all enzymes were particularly active in reactions involving electrophile substitution. Gene and protein expression profiling conducted under normal culture conditions as well as in the presence of the herbicide alachlor and the xenobiotic 1-chloro-2,4-dinitrobenzene (CDNB) showed that the isoenzyme EcaGST1, belonging to the omega-like class, was specifically induced at both the protein and mRNA levels. EcaGST1 presumably participates in counteracting the xenobiotic toxicity and/or abiotic stress conditions, and may therefore represent a novel molecular target in the development of new chemical treatments to control soft rot diseases.
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Affiliation(s)
- Christina Theoharaki
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Evangelia Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.,Molecular Biology Department, Genetic Engineering Division, National Research Centre, 33 El-Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - Panagiotis Giannopoulos
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Sofia Maurikou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Katholiki Skopelitou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece
| | - Anastassios C Papageorgiou
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20521, Turku, Finland
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 118 55, Athens, Greece.
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23
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Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives. Appl Microbiol Biotechnol 2018; 102:5391-5401. [PMID: 29728724 DOI: 10.1007/s00253-018-9040-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 01/05/2023]
Abstract
Lignin is the major aromatic biopolymer in nature, and it is considered a valuable feedstock for the future supply of aromatics. Hence, its valorisation in biorefineries is of high importance, and various chemical and enzymatic approaches for lignin depolymerisation have been reported. Among the enzymes known to act on lignin, β-etherases offer the possibility for a selective cleavage of the β-O-4 aryl ether bonds present in lignin. These enzymes, together with glutathione lyases, catalyse a reductive, glutathione-dependent ether bond cleavage displaying high stereospecificity. β-Etherases and glutathione lyases both belong to the superfamily of glutathione transferases, and several structures have been solved recently. Additionally, different approaches for their application in lignin valorisation have been reported in the last years. This review gives an overview on the current knowledge on β-etherases and glutathione lyases, their biochemical and structural features, and critically discusses their potential for application in biorefineries.
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24
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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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25
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Marinović M, Nousiainen P, Dilokpimol A, Kontro J, Moore R, Sipilä J, de Vries RP, Mäkelä MR, Hildén K. Selective Cleavage of Lignin β- O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:2878-2882. [PMID: 30271687 PMCID: PMC6156110 DOI: 10.1021/acssuschemeng.7b03619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/19/2018] [Indexed: 05/06/2023]
Abstract
Production of value-added compounds from a renewable aromatic polymer, lignin, has proven to be challenging. Chemical procedures, involving harsh reaction conditions, are costly and often result in nonselective degradation of lignin linkages. Therefore, enzymatic catalysis with selective cleavage of lignin bonds provides a sustainable option for lignin valorization. In this study, we describe the first functionally characterized fungal intracellular β-etherase from the wood-degrading white-rot basidiomycete Dichomitus squalens. This enzyme, Ds-GST1, from the glutathione-S-transferase superfamily selectively cleaved the β-O-4 aryl ether bond of a dimeric lignin model compound in a glutathione-dependent reaction. Ds-GST1 also demonstrated activity on polymeric synthetic lignin fractions, shown by a decrease in molecular weight distribution of the laccase-oxidized guaiacyl dehydrogenation polymer. In addition to a possible role of Ds-GST1 in intracellular catabolism of lignin-derived aromatic compounds, the cleavage of the most abundant linkages in lignin under mild reaction conditions makes this biocatalyst an attractive green alternative in biotechnological applications.
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Affiliation(s)
- Mila Marinović
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Paula Nousiainen
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Adiphol Dilokpimol
- Fungal
Physiology, Westerdijk Fungal Biodiversity Institute & Fungal
Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jussi Kontro
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Robin Moore
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Jussi Sipilä
- Department
of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, A.I. Virtasen aukio 1, FI-00014 Helsinki, Finland
| | - Ronald P. de Vries
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
- Fungal
Physiology, Westerdijk Fungal Biodiversity Institute & Fungal
Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miia R. Mäkelä
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Kristiina Hildén
- Division
of Microbiology and Biotechnology, Department of Food and Environmental
Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
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26
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Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. J Biol Chem 2018; 293:4955-4968. [PMID: 29449375 PMCID: PMC5892560 DOI: 10.1074/jbc.ra117.001268] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Indexed: 01/01/2023] Open
Abstract
As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases.
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Affiliation(s)
- Wayne S Kontur
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Craig A Bingman
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Charles N Olmsted
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Douglas R Wassarman
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | | | - Daniel L Gall
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center
| | - Robert W Smith
- the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | | | - Brian G Fox
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,the Departments of Biochemistry
| | - Daniel R Noguera
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Civil and Environmental Engineering
| | - Joshua J Coon
- From the Wisconsin Energy Institute.,the Department of Energy Great Lakes Bioenergy Research Center.,Chemistry.,the Genome Center of Wisconsin, and.,Biomolecular Chemistry, and
| | - Timothy J Donohue
- From the Wisconsin Energy Institute, .,the Department of Energy Great Lakes Bioenergy Research Center.,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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27
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Gall DL, Kontur WS, Lan W, Kim H, Li Y, Ralph J, Donohue TJ, Noguera DR. In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units. Appl Environ Microbiol 2018; 84:e02076-17. [PMID: 29180366 PMCID: PMC5772236 DOI: 10.1128/aem.02076-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/16/2017] [Indexed: 11/30/2022] Open
Abstract
New environmentally sound technologies are needed to derive valuable compounds from renewable resources. Lignin, an abundant polymer in terrestrial plants comprised predominantly of guaiacyl and syringyl monoaromatic phenylpropanoid units, is a potential natural source of aromatic compounds. In addition, the plant secondary metabolite tricin is a recently discovered and moderately abundant flavonoid in grasses. The most prevalent interunit linkage between guaiacyl, syringyl, and tricin units is the β-ether linkage. Previous studies have shown that bacterial β-etherase pathway enzymes catalyze glutathione-dependent cleavage of β-ether bonds in dimeric β-ether lignin model compounds. To date, however, it remains unclear whether the known β-etherase enzymes are active on lignin polymers. Here we report on enzymes that catalyze β-ether cleavage from bona fide lignin, under conditions that recycle the cosubstrates NAD+ and glutathione. Guaiacyl, syringyl, and tricin derivatives were identified as reaction products when different model compounds or lignin fractions were used as substrates. These results demonstrate an in vitro enzymatic system that can recycle cosubstrates while releasing aromatic monomers from model compounds as well as natural and engineered lignin oligomers. These findings can improve the ability to produce valuable aromatic compounds from a renewable resource like lignin.IMPORTANCE Many bacteria are predicted to contain enzymes that could convert renewable carbon sources into substitutes for compounds that are derived from petroleum. The β-etherase pathway present in sphingomonad bacteria could cleave the abundant β-O-4-aryl ether bonds in plant lignin, releasing a biobased source of aromatic compounds for the chemical industry. However, the activity of these enzymes on the complex aromatic oligomers found in plant lignin is unknown. Here we demonstrate biodegradation of lignin polymers using a minimal set of β-etherase pathway enzymes, the ability to recycle needed cofactors (glutathione and NAD+) in vitro, and the release of guaiacyl, syringyl, and tricin as depolymerized products from lignin. These observations provide critical evidence for the use and future optimization of these bacterial β-etherase pathway enzymes for industrial-level biotechnological applications designed to derive high-value monomeric aromatic compounds from lignin.
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Affiliation(s)
- Daniel L Gall
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wayne S Kontur
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wu Lan
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hoon Kim
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Yanding Li
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - John Ralph
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J Donohue
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel R Noguera
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
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Abstract
Many potentially toxic electrophilic xenobiotics and some endogenous compounds are detoxified by conversion to the corresponding glutathione S-conjugate, which is metabolized to the N-acetylcysteine S-conjugate (mercapturate) and excreted. Some mercapturate pathway components, however, are toxic. Bioactivation (toxification) may occur when the glutathione S-conjugate (or mercapturate) is converted to a cysteine S-conjugate that undergoes a β-lyase reaction. If the sulfhydryl-containing fragment produced in this reaction is reactive, toxicity may ensue. Some drugs and halogenated workplace/environmental contaminants are bioactivated by this mechanism. On the other hand, cysteine S-conjugate β-lyases occur in nature as a means of generating some biologically useful sulfhydryl-containing compounds.
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29
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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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30
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31
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Gall DL, Ralph J, Donohue TJ, Noguera DR. Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol 2017; 45:120-126. [DOI: 10.1016/j.copbio.2017.02.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 02/06/2017] [Accepted: 02/24/2017] [Indexed: 11/30/2022]
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32
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Mnich E, Vanholme R, Oyarce P, Liu S, Lu F, Goeminne G, Jørgensen B, Motawie MS, Boerjan W, Ralph J, Ulvskov P, Møller BL, Bjarnholt N, Harholt J. Degradation of lignin β-aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK-6. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:581-593. [PMID: 27775869 PMCID: PMC5399005 DOI: 10.1111/pbi.12655] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/25/2016] [Accepted: 10/10/2016] [Indexed: 05/02/2023]
Abstract
Lignin is a major polymer in the secondary plant cell wall and composed of hydrophobic interlinked hydroxyphenylpropanoid units. The presence of lignin hampers conversion of plant biomass into biofuels; plants with modified lignin are therefore being investigated for increased digestibility. The bacterium Sphingomonas paucimobilis produces lignin-degrading enzymes including LigD, LigF and LigG involved in cleaving the most abundant lignin interunit linkage, the β-aryl ether bond. In this study, we expressed the LigD, LigF and LigG (LigDFG) genes in Arabidopsis thaliana to introduce postlignification modifications into the lignin structure. The three enzymes were targeted to the secretory pathway. Phenolic metabolite profiling and 2D HSQC NMR of the transgenic lines showed an increase in oxidized guaiacyl and syringyl units without concomitant increase in oxidized β-aryl ether units, showing lignin bond cleavage. Saccharification yield increased significantly in transgenic lines expressing LigDFG, showing the applicability of our approach. Additional new information on substrate specificity of the LigDFG enzymes is also provided.
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Affiliation(s)
- Ewelina Mnich
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - Paula Oyarce
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - Sarah Liu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | | | - Bodil Jørgensen
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Mohammed S. Motawie
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- Department of Plant Systems BiologyVIBGhentBelgium
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research CenterWisconsin Energy InstituteMadisonWIUSA
| | - Peter Ulvskov
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Birger L. Møller
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Carlsberg Research LaboratoryCopenhagenDenmark
| | - Nanna Bjarnholt
- Plant Biochemistry LaboratoryDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Jesper Harholt
- Section for Plant GlycobiologyDepartment of Plant Biology and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Carlsberg Research LaboratoryCopenhagenDenmark
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33
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Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
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Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
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34
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Ohta Y, Hasegawa R, Kurosawa K, Maeda AH, Koizumi T, Nishimura H, Okada H, Qu C, Saito K, Watanabe T, Hatada Y. Enzymatic Specific Production and Chemical Functionalization of Phenylpropanone Platform Monomers from Lignin. CHEMSUSCHEM 2017; 10:425-433. [PMID: 27878983 PMCID: PMC5299523 DOI: 10.1002/cssc.201601235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/31/2016] [Indexed: 05/04/2023]
Abstract
Enzymatic catalysis is an ecofriendly strategy for the production of high-value low-molecular-weight aromatic compounds from lignin. Although well-definable aromatic monomers have been obtained from synthetic lignin-model dimers, enzymatic-selective synthesis of platform monomers from natural lignin has not been accomplished. In this study, we successfully achieved highly specific synthesis of aromatic monomers with a phenylpropane structure directly from natural lignin using a cascade reaction of β-O-4-cleaving bacterial enzymes in one pot. Guaiacylhydroxylpropanone (GHP) and the GHP/syringylhydroxylpropanone (SHP) mixture are exclusive monomers from lignin isolated from softwood (Cryptomeria japonica) and hardwood (Eucalyptus globulus). The intermediate products in the enzymatic reactions show the capacity to accommodate highly heterologous substrates at the substrate-binding sites of the enzymes. To demonstrate the applicability of GHP as a platform chemical for bio-based industries, we chemically generate value-added GHP derivatives for bio-based polymers. Together with these chemical conversions for the valorization of lignin-derived phenylpropanone monomers, the specific and enzymatic production of the monomers directly from natural lignin is expected to provide a new stream in "white biotechnology" for sustainable biorefineries.
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Affiliation(s)
- Yukari Ohta
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Ryoichi Hasegawa
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Kanako Kurosawa
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Allyn H. Maeda
- Research and Development Center for Marine BiosciencesJapan Agency for Marine-Earth Science and Technology, JAMSTEC2-15 NatsushimaYokosukaKanagawa237-0061Japan
| | - Toshio Koizumi
- Department of Applied ChemistryNational Defense Academy1-10-20 HashirimizuYokosukaKanagawa239-8686Japan
| | - Hiroshi Nishimura
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Hitomi Okada
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Chen Qu
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Kaori Saito
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere, RISHKyoto UniversityGokasho, UjiKyoto611-0011Japan
| | - Yuji Hatada
- Department of Life Sciences and Green ChemistrySaitama Institute of Technology1690 FusaijiFukayaSaitama369-0293Japan
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35
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Rais D, Zibek S. Biotechnological and Biochemical Utilization of Lignin. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:469-518. [PMID: 28540404 DOI: 10.1007/10_2017_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.
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Affiliation(s)
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
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36
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Wang C, Ouyang X, Su S, Liang X, Zhang C, Wang W, Yuan Q, Li Q. Effect of sulfonated lignin on enzymatic activity of the ligninolytic enzymes Cα-dehydrogenase LigD and β-etherase LigF. Enzyme Microb Technol 2016; 93-94:59-69. [DOI: 10.1016/j.enzmictec.2016.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/05/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
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37
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Njiojob CN, Bozell JJ, Long BK, Elder T, Key RE, Hartwig WT. Enantioselective Syntheses of Lignin Models: An Efficient Synthesis of β-O-4 Dimers and Trimers by Using the Evans Chiral Auxiliary. Chemistry 2016; 22:12506-17. [PMID: 27459234 DOI: 10.1002/chem.201601592] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/27/2023]
Abstract
We describe an efficient five-step, enantioselective synthesis of (R,R)- and (S,S)-lignin dimer models possessing a β-O-4 linkage, by using the Evans chiral aldol reaction as a key step. Mitsunobu inversion of the (R,R)- or (S,S)-isomers generates the corresponding (R,S)- and (S,R)-diastereomers. We further extend this approach to the enantioselective synthesis of a lignin trimer model. These lignin models are synthesized with excellent ee (>99 %) and high overall yields. The lignin dimer models can be scaled up to provide multigram quantities that are not attainable by using previous methodologies. These lignin models will be useful in degradation studies probing the selectivity of enzymatic, microbial, and chemical processes that deconstruct lignin.
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Affiliation(s)
- Costyl N Njiojob
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
| | - Joseph J Bozell
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Brian K Long
- Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas Elder
- Southern Research Station, USDA Forest Service, Auburn, AL, 36849, USA
| | - Rebecca E Key
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
| | - William T Hartwig
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN, 37996, USA
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38
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Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem 2016; 291:10228-38. [PMID: 26940872 PMCID: PMC4858972 DOI: 10.1074/jbc.m115.700427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 12/23/2022] Open
Abstract
There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
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Affiliation(s)
- Jose Henrique Pereira
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Richard A Heins
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Ryan P McAndrew
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kai Deng
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Paul D Adams
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720
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39
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Bacterial Enzymes for Lignin Oxidation and Conversion to Renewable Chemicals. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Rosini E, Allegretti C, Melis R, Cerioli L, Conti G, Pollegioni L, D'Arrigo P. Cascade enzymatic cleavage of the β-O-4 linkage in a lignin model compound. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01591j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The optimized Lig enzymatic system reached the full bioconversion of a racemic mixture of GGE, a lignin model compound.
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Affiliation(s)
- Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
| | - Chiara Allegretti
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Roberta Melis
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Lorenzo Cerioli
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Gianluca Conti
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
| | - Paola D'Arrigo
- The Protein Factory
- Politecnico di Milano and Università degli Studi dell'Insubria
- 20131 Milano
- Italy
- Dipartimento di Chimica
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41
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Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J Biol Chem 2015; 291:5234-46. [PMID: 26637355 PMCID: PMC4777856 DOI: 10.1074/jbc.m115.694307] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.
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Affiliation(s)
- Kate E Helmich
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Jose Henrique Pereira
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Richard A Heins
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Ryan P McAndrew
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Craig Bingman
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Deng
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Bacteriology, University of Wisconsin, Madison, Wisconsin 53706,
| | - Paul D Adams
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720, and
| | - George N Phillips
- the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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42
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Cragg SM, Beckham GT, Bruce NC, Bugg TDH, Distel DL, Dupree P, Etxabe AG, Goodell BS, Jellison J, McGeehan JE, McQueen-Mason SJ, Schnorr K, Walton PH, Watts JEM, Zimmer M. Lignocellulose degradation mechanisms across the Tree of Life. Curr Opin Chem Biol 2015; 29:108-19. [PMID: 26583519 PMCID: PMC7571853 DOI: 10.1016/j.cbpa.2015.10.018] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022]
Abstract
Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.
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Affiliation(s)
- Simon M Cragg
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK.
| | - Gregg T Beckham
- National Renewable Energy Laboratory, National Bioenergy Centre, Golden, CO 80401 USA
| | - Neil C Bruce
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel L Distel
- Ocean Genome Legacy, Marine Science Center, Northeastern University, Boston, MA, USA
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Amaia Green Etxabe
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Barry S Goodell
- Department of Sustainable Biomaterials, 216 ICTAS II Bldg., Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Jody Jellison
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - John E McGeehan
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Simon J McQueen-Mason
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | | | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Martin Zimmer
- Leibniz-Center for Tropical Marine Ecology (ZMT) GmbH, Fahrenheitstrasse 6, 28359 Bremen, Germany
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43
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Combination of six enzymes of a marine Novosphingobium converts the stereoisomers of β-O-4 lignin model dimers into the respective monomers. Sci Rep 2015; 5:15105. [PMID: 26477321 PMCID: PMC4609964 DOI: 10.1038/srep15105] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/16/2015] [Indexed: 11/23/2022] Open
Abstract
Lignin, an aromatic polymer of phenylpropane units joined predominantly by β-O-4 linkages, is the second most abundant biomass component on Earth. Despite the continuous discharge of terrestrially produced lignin into marine environments, few studies have examined lignin degradation by marine microorganisms. Here, we screened marine isolates for β-O-4 cleavage activity and determined the genes responsible for this enzymatic activity in one positive isolate. Novosphingobium sp. strain MBES04 converted all four stereoisomers of guaiacylglycerol-β-guaiacyl ether (GGGE), a structural mimic of lignin, to guaiacylhydroxypropanone as an end metabolite in three steps involving six enzymes, including a newly identified Nu-class glutathione-S-transferase (GST). In silico searches of the strain MBES04 genome revealed that four GGGE-metabolizing GST genes were arranged in a cluster. Transcriptome analysis demonstrated that the lignin model compounds GGGE and (2-methoxyphenoxy)hydroxypropiovanillone (MPHPV) enhanced the expression of genes in involved in energy metabolism, including aromatic-monomer assimilation, and evoked defense responses typically expressed upon exposure to toxic compounds. The findings from this study provide insight into previously unidentified bacterial enzymatic systems and the physiological acclimation of microbes associated with the biological transformation of lignin-containing materials in marine environments.
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44
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Phylogenetic and kinetic characterization of a suite of dehydrogenases from a newly isolated bacterium, strain SG61-1L, that catalyze the turnover of guaiacylglycerol-β-guaiacyl ether stereoisomers. Appl Environ Microbiol 2015; 81:8164-76. [PMID: 26386069 PMCID: PMC4651090 DOI: 10.1128/aem.01573-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022] Open
Abstract
Lignin is a complex aromatic polymer found in plant cell walls that makes up 15 to 40% of plant biomass. The degradation of lignin substructures by bacteria is of emerging interest because it could provide renewable alternative feedstocks and intermediates for chemical manufacturing industries. We have isolated a bacterium, strain SG61-1L, that rapidly degrades all of the stereoisomers of one lignin substructure, guaiacylglycerol-β-guaiacyl ether (GGE), which contains a key β-O-4 linkage found in most intermonomer linkages in lignin. In an effort to understand the rapid degradation of GGE by this bacterium, we heterologously expressed and kinetically characterized a suite of dehydrogenase candidates for the first known step of GGE degradation. We identified a clade of active GGE dehydrogenases and also several other dehydrogenases outside this clade that were all able to oxidize GGE. Several candidates exhibited stereoselectivity toward the GGE stereoisomers, while others had higher levels of catalytic performance than previously described GGE dehydrogenases for all four stereoisomers, indicating a variety of potential applications for these enzymes in the manufacture of lignin-derived commodities.
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45
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Picart P, de María PD, Schallmey A. From gene to biorefinery: microbial β-etherases as promising biocatalysts for lignin valorization. Front Microbiol 2015; 6:916. [PMID: 26388858 PMCID: PMC4560021 DOI: 10.3389/fmicb.2015.00916] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/21/2015] [Indexed: 11/13/2022] Open
Abstract
The set-up of biorefineries for the valorization of lignocellulosic biomass will be core in the future to reach sustainability targets. In this area, biomass-degrading enzymes are attracting significant research interest for their potential in the production of chemicals and biofuels from renewable feedstock. Glutathione-dependent β-etherases are emerging enzymes for the biocatalytic depolymerization of lignin, a heterogeneous aromatic polymer abundant in nature. They selectively catalyze the reductive cleavage of β-O-4 aryl-ether bonds which account for 45–60% of linkages present in lignin. Hence, application of β-etherases in lignin depolymerization would enable a specific lignin breakdown, selectively yielding (valuable) low-molecular-mass aromatics. Albeit β-etherases have been biochemically known for decades, only very recently novel β-etherases have been identified and thoroughly characterized for lignin valorization, expanding the enzyme toolbox for efficient β-O-4 aryl-ether bond cleavage. Given their emerging importance and potential, this mini-review discusses recent developments in the field of β-etherase biocatalysis covering all aspects from enzyme identification to biocatalytic applications with real lignin samples.
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Affiliation(s)
- Pere Picart
- Institute of Biotechnology, RWTH Aachen University , Aachen, Germany
| | | | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig , Braunschweig, Germany
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46
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Tsuji Y, Vanholme R, Tobimatsu Y, Ishikawa Y, Foster CE, Kamimura N, Hishiyama S, Hashimoto S, Shino A, Hara H, Sato-Izawa K, Oyarce P, Goeminne G, Morreel K, Kikuchi J, Takano T, Fukuda M, Katayama Y, Boerjan W, Ralph J, Masai E, Kajita S. Introduction of chemically labile substructures into Arabidopsis lignin through the use of LigD, the Cα-dehydrogenase from Sphingobium sp. strain SYK-6. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:821-32. [PMID: 25580543 DOI: 10.1111/pbi.12316] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/07/2014] [Accepted: 11/25/2014] [Indexed: 05/19/2023]
Abstract
Bacteria-derived enzymes that can modify specific lignin substructures are potential targets to engineer plants for better biomass processability. The Gram-negative bacterium Sphingobium sp. SYK-6 possesses a Cα-dehydrogenase (LigD) enzyme that has been shown to oxidize the α-hydroxy functionalities in β-O-4-linked dimers into α-keto analogues that are more chemically labile. Here, we show that recombinant LigD can oxidize an even wider range of β-O-4-linked dimers and oligomers, including the genuine dilignols, guaiacylglycerol-β-coniferyl alcohol ether and syringylglycerol-β-sinapyl alcohol ether. We explored the possibility of using LigD for biosynthetically engineering lignin by expressing the codon-optimized ligD gene in Arabidopsis thaliana. The ligD cDNA, with or without a signal peptide for apoplast targeting, has been successfully expressed, and LigD activity could be detected in the extracts of the transgenic plants. UPLC-MS/MS-based metabolite profiling indicated that levels of oxidized guaiacyl (G) β-O-4-coupled dilignols and analogues were significantly elevated in the LigD transgenic plants regardless of the signal peptide attachment to LigD. In parallel, 2D NMR analysis revealed a 2.1- to 2.8-fold increased level of G-type α-keto-β-O-4 linkages in cellulolytic enzyme lignins isolated from the stem cell walls of the LigD transgenic plants, indicating that the transformation was capable of altering lignin structure in the desired manner.
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Affiliation(s)
- Yukiko Tsuji
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Yuki Tobimatsu
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Yasuyuki Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Clifton E Foster
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
- Michigan State University, East Lansing, MI, USA
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | | | - Saki Hashimoto
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Amiu Shino
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Hirofumi Hara
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Kuala Lumpur, Malaysia
| | - Kanna Sato-Izawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Paula Oyarce
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Jun Kikuchi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | | | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | | | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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47
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Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 2015; 29:10-7. [PMID: 26121945 DOI: 10.1016/j.cbpa.2015.06.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/29/2015] [Accepted: 06/08/2015] [Indexed: 11/22/2022]
Abstract
The aromatic heteropolymer lignin is a major component of plant cell walls, and is produced industrially from paper/pulp manufacture and cellulosic bioethanol production. Conversion of lignin into renewable chemicals is a major unsolved problem in the development of a biomass-based biorefinery. The review describes recent developments in the understanding of bacterial enzymes for lignin breakdown, such as DyP peroxidases, bacterial laccases, and beta-etherase enzymes. The use of pathway engineering methods to construct genetically modified microbes to convert lignin to renewable chemicals (e.g. vanillin, adipic acid) via fermentation is discussed, and the search for novel applications for lignin (e.g. carbon fibre).
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48
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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49
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Njiojob CN, Rhinehart JL, Bozell JJ, Long BK. Synthesis of Enantiomerically Pure Lignin Dimer Models for Catalytic Selectivity Studies. J Org Chem 2015; 80:1771-80. [DOI: 10.1021/jo502685k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Costyl N. Njiojob
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
for Renewable
Carbon, University of Tennessee, Knoxville, Tennessee 37917, United States
| | - Jennifer L. Rhinehart
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Joseph J. Bozell
- Center
for Renewable
Carbon, University of Tennessee, Knoxville, Tennessee 37917, United States
| | - Brian K. Long
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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50
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Picart P, Müller C, Mottweiler J, Wiermans L, Bolm C, Domínguez de María P, Schallmey A. From gene towards selective biomass valorization: bacterial β-etherases with catalytic activity on lignin-like polymers. CHEMSUSCHEM 2014; 7:3164-71. [PMID: 25186983 DOI: 10.1002/cssc.201402465] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/15/2014] [Indexed: 05/07/2023]
Abstract
Microbial β-etherases, which selectively cleave the β-O-4 aryl ether linkage present in lignin, hold great promise for future applications in lignin valorization. However, very few members have been reported so far and little is known about these enzymes. By using a database mining approach, four novel bacterial β-etherases were identified, recombinantly produced in Escherichia coli, and investigated together with known β-etherases in the conversion of various lignin and non-lignin-type model compounds. The resulting activities revealed the significant influence of the substituents at the phenyl ring adjacent to the ether bond. Finally, β-etherase activity on polymeric substrates, measured by using a fluorescently labeled synthetic lignin, was also proven; this underlined the applicability of the enzymes for the conversion of lignin into renewable chemicals.
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Affiliation(s)
- Pere Picart
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen (Germany)
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