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Kumagawa E, Katsumata M, Ohta Y. Catalytic and molecular properties of alkaliphilic and thermotolerant β-etherase from Altererythrobacter sp. B11. Biosci Biotechnol Biochem 2023; 87:1183-1192. [PMID: 37403406 DOI: 10.1093/bbb/zbad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Phenylpropanone monomers, including guaiacyl hydroxypropanone, are important precursors for the synthesis of various chemicals. The monomers are obtained in a three-step cascade reaction catalyzed by a group of enzymes in the β-etherase system that cleaves the β-O-4 bond, the major bond in lignin. In this study, one of the β-etherase of the glutathione-S-transferase superfamily, AbLigF2, was discovered in genus Altererythrobacter, and the recombinant etherase was characterized. The enzyme showed maximal activity at 45 °C, maintained 30% of its activity after 2 h at 50 °C, and was the most thermostable among the previously reported enzymes. Moreover, N13, S14, and S115, located near the thiol group of glutathione, had a significant effect on the maximum reaction rate of enzyme activity. This study suggests that AbLigF2 has the potential to serve as a thermostable enzyme for lignin utilization and provides insights into its catalytic mechanism.
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Affiliation(s)
- Eri Kumagawa
- Graduate School of Science and Technology, Gunma University, Gunma, Japan
| | - Madoka Katsumata
- Gunma University Center for Food Science and Wellness, Gunma, Japan
| | - Yukari Ohta
- Gunma University Center for Food Science and Wellness, Gunma, Japan
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Kato R, Maekawa K, Kobayashi S, Hishiyama S, Katahira R, Nambo M, Higuchi Y, Kuatsjah E, Beckham GT, Kamimura N, Masai E. Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers. Appl Environ Microbiol 2023; 89:e0017123. [PMID: 37184397 PMCID: PMC10304671 DOI: 10.1128/aem.00171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the Cα hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD+-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases. IMPORTANCE In many catalytic depolymerization processes of lignin polymers, aryl-ether bonds are selectively cleaved, leaving carbon-carbon bonds between aromatic units intact, including dimers and oligomers with β-1 linkages. Therefore, elucidating the catabolic system of β-1-type lignin-derived compounds will aid in the establishment of biological funneling of heterologous lignin-derived aromatic compounds to value-added products. Here, we found that threo-DGPD was converted by successive stereoselective oxidation and reduction at the Cα position by multiple alcohol dehydrogenases to erythro-DGPD, which is further catabolized. This system is very similar to that developed to obtain enantiopure alcohols from racemic alcohols by artificially combining two enantiocomplementary alcohol dehydrogenases. The results presented here demonstrate that SYK-6 has evolved to catabolize all four stereoisomers of DGPD by incorporating this stereoinversion system into its native β-1-type dimer catabolic system.
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Affiliation(s)
- Ryo Kato
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Kodai Maekawa
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shota Kobayashi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shojiro Hishiyama
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Miki Nambo
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yudai Higuchi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Xu Z, Peng B, Kitata RB, Nicora CD, Weitz KK, Pu Y, Shi T, Cort JR, Ragauskas AJ, Yang B. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:117. [PMID: 36316752 PMCID: PMC9620641 DOI: 10.1186/s13068-022-02214-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. RESULTS This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography-mass spectrometry (GC-MS) and two-dimensional 1H-13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C-C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C-O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. CONCLUSIONS Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.
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Affiliation(s)
- Zhangyang Xu
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Bo Peng
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Reta Birhanu Kitata
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Carrie D. Nicora
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Karl K. Weitz
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Yunqiao Pu
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - John R. Cort
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Arthur J. Ragauskas
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ,grid.411461.70000 0001 2315 1184Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA ,grid.411461.70000 0001 2315 1184Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Bin Yang
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
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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: 1.4] [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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