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Cui M, Wei Y, Tan J, Li T, Jiao X, Zhou Y. Biochemical investigations of polyphenol degradation enzymes in the phototrophic bacterium Rubrivivax gelatinosus. Biochem J 2023; 480:1753-1766. [PMID: 37903000 DOI: 10.1042/bcj20230387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is an important intermediate in the degradation of flavonoids and tannins by anaerobic bacteria. Recent studies have shed light on the enzymatic mechanism of phloroglucinol degradation in butyrate-forming anaerobic bacteria, including environmental and intestinal bacteria such as Clostridium and Flavonifractor sp. Phloroglucinol degradation gene clusters have also been identified in other metabolically diverse bacteria, although the polyphenol metabolism of these microorganisms remain largely unexplored. Here, we describe biochemical studies of polyphenol degradation enzymes found in the purple non-sulfur bacterium Rubrivivax gelatinosus IL144, an anaerobic photoheterotroph reported to utilize diverse organic compounds as carbon sources for growth. In addition to the phloroglucinol reductase and dihydrophloroglucinol cyclohydrolase that catalyze phloroglucinol degradation, we characterize a Mn2+-dependent phloretin hydrolase that catalyzes the cleavage of phloretin into phloroglucinol and phloretic acid. We also report a Mn2+-dependent decarboxylase (DeC) that catalyzes the reversible decarboxylation of 2,4,6-trihydroxybenzoate to form phloroglucinol. A bioinformatics search led to the identification of DeC homologs in diverse soil and gut bacteria, and biochemical studies of a DeC homolog from the human gut bacterium Flavonifractor plautii demonstrated that it is also a 2,4,6-trihydroxybenzoate decarboxylase. Our study expands the range of enzymatic mechanisms for phloroglucinol formation, and provides further biochemical insight into polyphenol metabolism in the anaerobic biosphere.
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Affiliation(s)
- Mengyu Cui
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Jason Tan
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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3
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Degradation of mycotoxins in mixtures by combined proteinous nanobiocatalysts: In silico, in vitro and in vivo. Int J Biol Macromol 2022; 218:866-877. [PMID: 35907453 DOI: 10.1016/j.ijbiomac.2022.07.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 01/13/2023]
Abstract
New combined proteinous (enzymatic) nanobiocatalysts capable of destructing mycotoxins in mixtures were developed and investigated in vitro and in vivo. Candidate enzymes for such combined biocatalysts were computationally screened using molecular docking of mycotoxins to the proteins. Catalytic characteristics of the 7 selected enzymes were estimated in the potential reactions with various mycotoxins (aflatoxin B1, citrinin, deoxynivalenol, ergotamine, fumonisin B1, gliotoxin, ochratoxin A, patulin, sterigmatocystin, T-2 toxin, zearalenone) at different pH values. To stabilize the enzymes hydrolyzing the mycotoxins, special biopolymers were selected using computer modeling. The poly(glutamic acid) was revealed as universal partner for the polyelectrolyte complexes with the selected enzymes. Finally, Sprague-Dawley rats were used for in vivo feeding experiments with feed contaminated by mycotoxin mixture at doses being up to orders of magnitude higher than maximum allowable limits. The treatment of contaminated feed by novel combined enzyme nanocomplexes significantly decreased negative effects of mycotoxin mixture on blood biochemical parameters which indicated huge damage to liver and kidneys of intoxicated animals. Such nanobiocatalysts and enzymatic treatment itself seem to be promising way for ensuring both food and feed chemical safety.
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4
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Rawat A, Dhakla S, Lama P, Pal TK. Fixation of carbon dioxide to aryl/aromatic carboxylic acids. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.101939] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Gao X, Wu M, Zhang W, Li C, Guo RT, Dai Y, Liu W, Mao S, Lu F, Qin HM. Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11616-11625. [PMID: 34553918 DOI: 10.1021/acs.jafc.1c04091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Salicylic acid (SA) decarboxylase from Trichosporon moniliiforme (TmSdc), which reversibly catalyses the decarboxylation of SA to yield phenol, is of significant interest because of its potential for the production of benzoic acid derivatives under environmentally friendly reaction conditions. TmSdc showed a preference for C2 hydroxybenzoate derivatives, with kcat/Km of SA being 3.2 × 103 M-1 s-1. Here, we presented the first crystal structures of TmSdc, including a complex with SA. The three conserved residues of Glu8, His169, and Asp298 are the catalytic residues within the TIM-barrel domain of TmSdc. Trp239 forms a unique hydrophobic recognition site by interacting with the phenyl ring of SA, while Arg235 is responsible for recognizing the hydroxyl group at the C2 of SA via hydrogen bond interactions. Using a semi-rational combinatorial active-site saturation test, we obtained the TmSdc mutant MT3 (Y64T/P191G/F195V/E302D), which exhibited a 26.4-fold increase in kcat/Km with SA, reaching 8.4 × 104 M-1 s-1. Steered molecular dynamics simulations suggested that the structural changes in MT3 relieved the steric hindrance within the substrate access channel and enlarged the substrate-binding pocket, leading to the increased activity by improving substrate access. Our data elucidate the unique substrate recognition mode and the substrate entrance tunnel of SA decarboxylase.
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Affiliation(s)
- Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Mian Wu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, P. R. China
| | - Yujie Dai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
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Aono R, Yoshihara T, Nishida H, Kino K. Screening and characterization of a novel reversible 4-hydroxyisophthalic acid decarboxylase from Cystobasidium slooffiae HTK3. Biosci Biotechnol Biochem 2021; 85:1658-1664. [PMID: 33942852 DOI: 10.1093/bbb/zbab082] [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: 02/25/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022]
Abstract
Owing to carboxylation activity, reversible decarboxylases can use CO2 as a C1-building block to produce useful carboxylic acids. Although many reversible decarboxylases can synthesize aromatic monocarboxylic acids, only a few reversible decarboxylases have been reported to date that catalyze the synthesis of aromatic dicarboxylic acids. In the present study, a reversible 4-hydroxyisophthalic acid decarboxylase was identified in Cystobasidium slooffiae HTK3. Furthermore, recombinant 4-hydroxyisophthalic acid decarboxylase was prepared, characterized, and used for 4-hydroxyisophthalic acid production from 4-hydroxybenzoic acid.
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Affiliation(s)
- Riku Aono
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tomoya Yoshihara
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Hotaka Nishida
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
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7
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Hofer G, Sheng X, Braeuer S, Payer SE, Plasch K, Goessler W, Faber K, Keller W, Himo F, Glueck SM. Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus oryzae. Chembiochem 2021; 22:652-656. [PMID: 33090643 PMCID: PMC7894528 DOI: 10.1002/cbic.202000600] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/06/2020] [Indexed: 12/19/2022]
Abstract
Broad substrate tolerance and excellent regioselectivity, as well as independence from sensitive cofactors have established benzoic acid decarboxylases from microbial sources as efficient biocatalysts. Robustness under process conditions makes them particularly attractive for preparative-scale applications. The divalent metal-dependent enzymes are capable of catalyzing the reversible non-oxidative (de)carboxylation of a variety of electron-rich (hetero)aromatic substrates analogously to the chemical Kolbe-Schmitt reaction. Elemental mass spectrometry supported by crystal structure elucidation and quantum chemical calculations verified the presence of a catalytically relevant Mg2+ complexed in the active site of 2,3-dihydroxybenoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao). This unique example with respect to the nature of the metal is in contrast to mechanistically related decarboxylases, which generally have Zn2+ or Mn2+ as the catalytically active metal.
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Affiliation(s)
- Gerhard Hofer
- Institute of Molecular BiosciencesBioTechMed GrazUniversity of Graz8010GrazAustria
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Simone Braeuer
- Department of Chemistry, Analytical ChemistryUniversity of Graz8010GrazAustria
| | - Stefan E. Payer
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Katharina Plasch
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Walter Goessler
- Department of Chemistry, Analytical ChemistryUniversity of Graz8010GrazAustria
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Walter Keller
- Institute of Molecular BiosciencesBioTechMed GrazUniversity of Graz8010GrazAustria
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Silvia M. Glueck
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
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8
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Ohde D, Thomas B, Bubenheim P, Liese A. Enhanced CO2 fixation in the biocatalytic carboxylation of resorcinol: Utilization of amines for amine scrubbing and in situ product precipitation. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Screening, gene cloning, and characterization of orsellinic acid decarboxylase from Arthrobacter sp. K8 for regio-selective carboxylation of resorcinol derivatives. J Biotechnol 2020; 323:128-135. [PMID: 32828832 DOI: 10.1016/j.jbiotec.2020.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 11/20/2022]
Abstract
Toward a sustainable synthesis of value-added chemicals, the method of CO2 utilization attracts great interest in chemical process engineering. Biotechnological CO2 fixation is a promising technology; however, efficient methods that can fix carbon dioxide are still limited. Instead, some parts of microbial decarboxylases allow the introduction of carboxy group into phenolic compounds using bicarbonate ion as a C1 building block. Here, we identified a unique decarboxylase from Arthrobacter sp. K8 that acts on resorcinol derivatives. A high-throughput colorimetric decarboxylase assay facilitated gene cloning of orsellinic acid decarboxylase from genomic DNA library of strain K8. Sequence analysis revealed that the orsellinic acid decarboxylase belonged to amidohydrolase 2 family, but shared low amino acid sequence identity with those of related decarboxylases. Enzymatic characterization unveiled that the decarboxylase introduces a carboxy group in a highly regio-selective manner. We applied the decarboxylase to enzymatic carboxylation of resorcinol derivatives. Using Escherichia coli expressing the decarboxylase gene as a whole cell biocatalyst, orsellinic acid, 2,4-dihydroxybenzoic acid, and 4-methoxysalicylic acid were produced in the presence of saturated bicarbonate. These findings could provide new insights into the production of useful phenolic acids from resorcinol derivatives.
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Song M, Zhang X, Liu W, Feng J, Cui Y, Yao P, Wang M, Guo RT, Wu Q, Zhu D. 2,3-Dihydroxybenzoic Acid Decarboxylase from Fusarium oxysporum: Crystal Structures and Substrate Recognition Mechanism. Chembiochem 2020; 21:2950-2956. [PMID: 32421914 DOI: 10.1002/cbic.202000244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/17/2020] [Indexed: 12/17/2022]
Abstract
A 2,3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum (2,3-DHBD_Fo) has a relatively high catalytic efficiency for the decarboxylation of 2,3-dihydroxybenzoic acid (DHBA) and carboxylation of catechol, thus it has a different substrate spectrum from other benzoic acid decarboxylases. We have determined the structures of 2,3-DHBD_Fo in its apo form and complexes with catechol or 2,5-dihydroxybenzoic acid at 1.55, 1.97, and 2.45 Å resolution, respectively. The crystal structures of 2,3-DHBD_Fo show that the enzyme exists as a homotetramer, and each active center has a Zn2+ ion coordinated by E8, H167, D291 and three water molecules. This is different from 2,6-DHBD from Rhizobium sporomusa, in which the Zn2+ ion is also coordinated with H10. Surprisingly, mutation of A10 of 2,3-DHBD_Fo to His resulted in almost complete loss of the enzyme activity. Enzyme-substrate docking and site-directed mutation studies indicate that residue R233Δ interacts with the 3-hydroxy group of 2,3-DHBA, and plays an important role in substrate recognition for this enzyme, thus revealing the molecular basis 2,3-dihydroxybenzoic acid decarboxylase.
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Affiliation(s)
- Mengkun Song
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Xuemei Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Weidong Liu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Jinghui Feng
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Yunfeng Cui
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Rey-Ting Guo
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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Novel 3,6-Dihydroxypicolinic Acid Decarboxylase-Mediated Picolinic Acid Catabolism in Alcaligenes faecalis JQ135. J Bacteriol 2019; 201:JB.00665-18. [PMID: 30692170 DOI: 10.1128/jb.00665-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
Picolinic acid (PA), a typical C-2-carboxylated pyridine derivative, is a metabolite of l-tryptophan and many other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize PA for growth. However, the precise mechanism of PA metabolism remains unknown. Alcaligenes faecalis strain JQ135 utilizes PA as its carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA), with no further degradation. A novel decarboxylase, PicC, was identified to be responsible for the decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. Although, PicC belonged to the amidohydrolase 2 family, it shows low similarity (<45%) compared to other reported amidohydrolase 2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated that picC was essential for PA degradation. The PicC was Zn2+-dependent nonoxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. The Km and k cat toward 3,6DHPA were observed to be 13.44 μM and 4.77 s-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity. This study provides new insights into the microbial metabolism of PA at molecular level.IMPORTANCE Picolinic acid is a natural toxic pyridine derived from l-tryptophan metabolism and other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6-dihydroxypicolinic acid was an intermediate in picolinic acid catabolism and further identified and characterized a novel amidohydrolase 2 family decarboxylase PicC. PicC was also shown to catalyze the decarboxylation of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding picolinic acid degradation and its underlying molecular mechanism.
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Kirimura K, Araki M, Ishihara M, Ishii Y. Expanding Substrate Specificity of Salicylate Decarboxylase by Site-directed Mutagenesis for Expansion of the Entrance Region Connecting to the Substrate Access Tunnel. CHEM LETT 2019. [DOI: 10.1246/cl.180755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masahiro Araki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mana Ishihara
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshitaka Ishii
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics. Catalysts 2019. [DOI: 10.3390/catal9010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This review focuses on recent advances in the field of enzymatic carboxylation reactions of hydroxyaromatic compounds using HCO3− (as a CO2 source) to produce hydroxybenzoic and other phenolic acids in mild conditions with high selectivity and moderate to excellent yield. Nature offers an extensive portfolio of enzymes catalysing reversible decarboxylation of hydroxyaromatic acids, whose equilibrium can be pushed towards the side of the carboxylated products. Extensive structural and mutagenesis studies have allowed recent advances in the understanding of the reaction mechanism of decarboxylase enzymes, ultimately enabling an improved yield and expansion of the scope of the reaction. The topic is of particular relevance today as the scope of the carboxylation reactions can be extended to include lignin-related compounds in view of developing lignin biorefinery technology.
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14
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Selective carboxylation of substituted phenols with engineered Escherichia coli whole-cells. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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15
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Plasch K, Hofer G, Keller W, Hay S, Heyes DJ, Dennig A, Glueck SM, Faber K. Pressurized CO 2 as a carboxylating agent for the biocatalytic ortho-carboxylation of resorcinol. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2018; 20:1754-1759. [PMID: 29780282 PMCID: PMC5942041 DOI: 10.1039/c8gc00008e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 03/08/2018] [Indexed: 05/25/2023]
Abstract
The utilization of gaseous carbon dioxide instead of bicarbonate would greatly facilitate process development for enzyme catalyzed carboxylations on a large scale. As a proof-of-concept, 1,3-dihydroxybenzene (resorcinol) was carboxylated in the ortho-position using pressurized CO2 (∼30-40 bar) catalyzed by ortho-benzoic acid decarboxylases with up to 68% conversion. Optimization studies revealed tight pH-control and enzyme stability as the most important determinants.
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Affiliation(s)
- Katharina Plasch
- Department of Chemistry , Organic & Bioorganic Chemistry , University of Graz , Heinrichstrasse 28 , 8010 Graz , Austria . ;
| | - Gerhard Hofer
- Institute of Molecular Biosciences , University of Graz , Humboldstrasse 50 , 8010 Graz , Austria
| | - Walter Keller
- Institute of Molecular Biosciences , University of Graz , Humboldstrasse 50 , 8010 Graz , Austria
| | - Sam Hay
- Manchester Institute of Biotechnology , University of Manchester , 131 Princess Street , Manchester M1 7DN , UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology , University of Manchester , 131 Princess Street , Manchester M1 7DN , UK
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering , Graz University of Technology , Petersgasse 12 , 8010 Graz , Austria
| | - Silvia M Glueck
- Department of Chemistry , Organic & Bioorganic Chemistry , University of Graz , Heinrichstrasse 28 , 8010 Graz , Austria . ;
- Austrian Centre of Industrial Biotechnology (ACIB) , Petersgasse 14 , 8010 Graz , Austria
| | - Kurt Faber
- Department of Chemistry , Organic & Bioorganic Chemistry , University of Graz , Heinrichstrasse 28 , 8010 Graz , Austria . ;
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16
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Zhang X, Ren J, Yao P, Gong R, Wang M, Wu Q, Zhu D. Biochemical characterization and substrate profiling of a reversible 2,3-dihydroxybenzoic acid decarboxylase for biocatalytic Kolbe-Schmitt reaction. Enzyme Microb Technol 2018; 113:37-43. [PMID: 29602385 DOI: 10.1016/j.enzmictec.2018.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/04/2018] [Accepted: 02/20/2018] [Indexed: 11/30/2022]
Abstract
Reversible benzoic acid decarboxylases are versatile biocatalysts by taking advantage of both decarboxylation and carboxylation reactions, especially for the biocatalytic Kolbe-Schmitt reaction. In the course of developing a benzoic acid decarboxylase tool-box, a putative benzoic acid decarboxylase gene from Fusarium oxysporum was heterologously over-expressed in Escherichia coli, the recombinant protein was purified and characterized. The purified enzyme exhibited relatively high catalytic efficiencies for the decarboxylation of 2, 3-dihydroxybenzoic acid and carboxylation of catechol (kcat/Km = 2.03 × 102 and 1.88 mM-1 min-1, respectively), and thus characterized as 2, 3-dihydroxybenzoic acid decarboxylase (2, 3-DHBD_Fo). The enzyme also catalyzed the decarboxylation of various substituted salicylic acids with different groups at varied positions except 5-position and the carboxylation of phenol and the substituted phenols. In a preparative reaction, catechol was carboxylated into 2, 3-dihydroxybenoic acid with 95% conversion by adding dodecyldimethylbenzylammonium chloride into the reaction system, and the product was isolated in 72% yield. These results demonstrate that 2, 3-DHBD_Fo is a valuable addition to the benzoic acid decarboxylase tool-box with potential practical applications.
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Affiliation(s)
- Xuemei Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China; National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Jie Ren
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Rui Gong
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin, 300308, China.
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17
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Sheng X, Patskovsky Y, Vladimirova A, Bonanno JB, Almo SC, Himo F, Raushel FM. Mechanism and Structure of γ-Resorcylate Decarboxylase. Biochemistry 2018; 57:3167-3175. [PMID: 29283551 DOI: 10.1021/acs.biochem.7b01213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.
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Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Yury Patskovsky
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Anna Vladimirova
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Jeffrey B Bonanno
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Steven C Almo
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
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18
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Luo J, Larrosa I. C-H Carboxylation of Aromatic Compounds through CO 2 Fixation. CHEMSUSCHEM 2017; 10:3317-3332. [PMID: 28722818 PMCID: PMC5601192 DOI: 10.1002/cssc.201701058] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/19/2017] [Indexed: 05/24/2023]
Abstract
Carbon dioxide (CO2 ) represents the most abundant and accessible carbon source on Earth. Thus the ability to transform CO2 into valuable commodity chemicals through the construction of C-C bonds is an invaluable strategy. Carboxylic acids and derivatives, the main products obtained by carboxylation of carbon nucleophiles by reaction of CO2 , have wide application in pharmaceuticals and advanced materials. Among the variety of carboxylation methods currently available, the direct carboxylation of C-H bonds with CO2 has attracted much attention owing to advantages from a step- and atom-economical point of view. In particular, the prevalence of (hetero)aromatic carboxylic acids and derivatives among biologically active compounds has led to significant interest in the development of methods for their direct carboxylation from CO2 . Herein, the latest achievements in the area of direct C-H carboxylation of (hetero)aromatic compounds with CO2 will be discussed.
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Affiliation(s)
- Junfei Luo
- School of Materials Science and Chemical EngineeringNingbo UniversityNingbo315211P.R. China
| | - Igor Larrosa
- School of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUnited Kingdom
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19
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Biogenetic Relationships of Bioactive Sponge Merotriterpenoids. Mar Drugs 2017; 15:md15090285. [PMID: 28891968 PMCID: PMC5618424 DOI: 10.3390/md15090285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 02/01/2023] Open
Abstract
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied. In this review, an in depth structural analysis of sponge merotriterpenoids, including the adociasulfate family of kinesin motor protein inhibitors, provides insight into their biosynthesis. Several key structural features provide clues to the relationships between compounds. All adociasulfates appear to be derived from only four different hydroquinone hexaprenyl diphosphate precursors, each varying in the number and position of epoxidations. Proton-initiated cyclization of these precursors can lead to all carbon skeletons observed amongst sponge merotriterpenoids. Consideration of the enzymes involved in the proposed biosynthetic route suggests a bacterial source, and a hypothetical gene cluster was constructed that may facilitate discovery of the authentic pathway from the sponge metagenome. A similar rationale can be extended to other sponge meroterpenoids, for which no biosynthetic pathways have yet been identified.
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20
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Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1. J Bacteriol 2016; 198:1755-1763. [PMID: 27068590 DOI: 10.1128/jb.00250-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (hndA) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various Burkholderia species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis. IMPORTANCE Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily.
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21
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Fujii T, Sato A, Okamoto Y, Yamauchi T, Kato S, Yoshida M, Oikawa T, Hata Y. The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005 provides insights into the reaction mechanism of enzymes in its original family. Proteins 2016; 84:1029-42. [PMID: 27040018 DOI: 10.1002/prot.25046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 11/08/2022]
Abstract
Maleylacetate reductase plays a crucial role in catabolism of resorcinol by catalyzing the NAD(P)H-dependent reduction of maleylacetate, at a carbon-carbon double bond, to 3-oxoadipate. The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005, GraC, has been elucidated by the X-ray diffraction method at 1.5 Å resolution. GraC is a homodimer, and each subunit consists of two domains: an N-terminal NADH-binding domain adopting an α/β structure and a C-terminal functional domain adopting an α-helical structure. Such structural features show similarity to those of the two existing families of enzymes in dehydroquinate synthase-like superfamily. However, GraC is distinct in dimer formation and activity expression mechanism from the families of enzymes. Two subunits in GraC have different structures from each other in the present crystal. One subunit has several ligands mimicking NADH and the substrate in the cleft and adopts a closed domain arrangement. In contrast, the other subunit does not contain any ligand causing structural changes and adopts an open domain arrangement. The structure of GraC reveals those of maleylacetate reductase both in the coenzyme, substrate-binding state and in the ligand-free state. The comparison of both subunit structures reveals a conformational change of the Tyr326 loop for interaction with His243 on ligand binding. Structures of related enzymes suggest that His243 is likely a catalytic residue of GraC. Mutational analyses of His243 and Tyr326 support the catalytic roles proposed from structural information. The crystal structure of GraC characterizes the maleylacetate reductase family as a third family in the dehydroquinate synthase-like superfamily. Proteins 2016; 84:1029-1042. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomomi Fujii
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ai Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuko Okamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takae Yamauchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Shiro Kato
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Masahiro Yoshida
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Tadao Oikawa
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, 564-8680, Japan.,Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Yasuo Hata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
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22
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Ren J, Yao P, Yu S, Dong W, Chen Q, Feng J, Wu Q, Zhu D. An Unprecedented Effective Enzymatic Carboxylation of Phenols. ACS Catal 2015. [DOI: 10.1021/acscatal.5b02529] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Ren
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Peiyuan Yao
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Shanshan Yu
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Wenyue Dong
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qijia Chen
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Jinhui Feng
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Laboratory
for Industrial Enzymes and Tianjin Engineering Research Center for
Biocatalytic Technology Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
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23
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Sato M, Sakurai N, Suzuki H, Shibata D, Kino K. Enzymatic carboxylation of hydroxystilbenes by the γ-resorcylic acid decarboxylase from Rhizobium radiobacter WU-0108 under reverse reaction conditions. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 2015; 81:7656-65. [PMID: 26319878 DOI: 10.1128/aem.02422-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
The Rhodococcus jostii RHA1 gene cluster required for γ-resorcylate (GRA) catabolism was characterized. The cluster includes tsdA, tsdB, tsdC, tsdD, tsdR, tsdT, and tsdX, which encode GRA decarboxylase, resorcinol 4-hydroxylase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, an IclR-type regulator, a major facilitator superfamily transporter, and a putative hydrolase, respectively. The tsdA gene conferred GRA decarboxylase activity on Escherichia coli. Purified TsdB oxidized NADH in the presence of resorcinol, suggesting that tsdB encodes a unique NADH-specific single-component resorcinol 4-hydroxylase. Mutations in either tsdA or tsdB resulted in growth deficiency on GRA. The tsdC and tsdD genes conferred hydroxyquinol 1,2-dioxygenase and maleylacetate reductase activities, respectively, on E. coli. Inactivation of tsdT significantly retarded the growth of RHA1 on GRA. The growth retardation was partially suppressed under acidic conditions, suggesting the involvement of tsdT in GRA uptake. Reverse transcription-PCR analysis revealed that the tsd genes constitute three transcriptional units, the tsdBADC and tsdTX operons and tsdR. Transcription of the tsdBADC and tsdTX operons was induced during growth on GRA. Inactivation of tsdR derepressed transcription of the tsdBADC and tsdTX operons in the absence of GRA, suggesting that tsd gene transcription is negatively regulated by the tsdR-encoded regulator. Binding of TsdR to the tsdR-tsdB and tsdT-tsdR intergenic regions was inhibited by the addition of GRA, indicating that GRA interacts with TsdR as an effector molecule.
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25
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Wuensch C, Pavkov-Keller T, Steinkellner G, Gross J, Fuchs M, Hromic A, Lyskowski A, Fauland K, Gruber K, Glueck SM, Faber K. Regioselective Enzymatic β-Carboxylation of para-Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases. Adv Synth Catal 2015; 357:1909-1918. [PMID: 26190963 PMCID: PMC4498466 DOI: 10.1002/adsc.201401028] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/07/2015] [Indexed: 11/17/2022]
Abstract
We report on a 'green' method for the utilization of carbon dioxide as C1 unit for the regioselective synthesis of (E)-cinnamic acids via regioselective enzymatic carboxylation of para-hydroxystyrenes. Phenolic acid decarboxylases from bacterial sources catalyzed the β-carboxylation of para-hydroxystyrene derivatives with excellent regio- and (E/Z)-stereoselectivity by exclusively acting at the β-carbon atom of the C=C side chain to furnish the corresponding (E)-cinnamic acid derivatives in up to 40% conversion at the expense of bicarbonate as carbon dioxide source. Studies on the substrate scope of this strategy are presented and a catalytic mechanism is proposed based on molecular modelling studies supported by mutagenesis of amino acid residues in the active site.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Johannes Gross
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Michael Fuchs
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Andrzej Lyskowski
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Kerstin Fauland
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
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26
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Pesci L, Glueck SM, Gurikov P, Smirnova I, Faber K, Liese A. Biocatalytic carboxylation of phenol derivatives: kinetics and thermodynamics of the biological Kolbe-Schmitt synthesis. FEBS J 2015; 282:1334-45. [PMID: 25652582 DOI: 10.1111/febs.13225] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/24/2015] [Accepted: 02/02/2015] [Indexed: 11/28/2022]
Abstract
Microbial decarboxylases, which catalyse the reversible regioselective ortho-carboxylation of phenolic derivatives in anaerobic detoxification pathways, have been studied for their reverse carboxylation activities on electron-rich aromatic substrates. Ortho-hydroxybenzoic acids are important building blocks in the chemical and pharmaceutical industries and are currently produced via the Kolbe-Schmitt process, which requires elevated pressures and temperatures (≥ 5 bar, ≥ 100 °C) and often shows incomplete regioselectivities. In order to resolve bottlenecks in view of preparative-scale applications, we studied the kinetic parameters for 2,6-dihydroxybenzoic acid decarboxylase from Rhizobium sp. in the carboxylation- and decarboxylation-direction using 1,2-dihydroxybenzene (catechol) as starting material. The catalytic properties (K(m), V(max)) are correlated with the overall thermodynamic equilibrium via the Haldane equation, according to a reversible random bi-uni mechanism. The model was subsequently verified by comparing experimental results with simulations. This study provides insights into the catalytic behaviour of a nonoxidative aromatic decarboxylase and reveals key limitations (e.g. substrate oxidation, CO2 pressure, enzyme deactivation, low turnover frequency) in view of the employment of this system as a 'green' alternative to the Kolbe-Schmitt processes.
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Affiliation(s)
- Lorenzo Pesci
- Institute of Technical Biocatalysis, Hamburg University of Technology, Germany
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Chowdhury PP, Sarkar J, Basu S, Dutta TK. Metabolism of 2-hydroxy-1-naphthoic acid and naphthalene via gentisic acid by distinctly different sets of enzymes in Burkholderia sp. strain BC1. Microbiology (Reading) 2014; 160:892-902. [DOI: 10.1099/mic.0.077495-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia sp. strain BC1, a soil bacterium, isolated from a naphthalene balls manufacturing waste disposal site, is capable of utilizing 2-hydroxy-1-naphthoic acid (2H1NA) and naphthalene individually as the sole source of carbon and energy. To deduce the pathway for degradation of 2H1NA, metabolites isolated from resting cell culture were identified by a combination of chromatographic and spectrometric analyses. Characterization of metabolic intermediates, oxygen uptake studies and enzyme activities revealed that strain BC1 degrades 2H1NA via 2-naphthol, 1,2,6-trihydroxy-1,2-dihydronaphthalene and gentisic acid. In addition, naphthalene was found to be degraded via 1,2-dihydroxy-1,2-dihydronaphthalene, salicylic acid and gentisic acid, with the putative involvement of the classical nag pathway. Unlike most other Gram-negative bacteria, metabolism of salicylic acid in strain BC1 involves a dual pathway, via gentisic acid and catechol, with the latter being metabolized by catechol 1,2-dioxygenase. Involvement of a non-oxidative decarboxylase in the enzymic transformation of 2H1NA to 2-naphthol indicates an alternative catabolic pathway for the bacterial degradation of hydroxynaphthoic acid. Furthermore, the biochemical observations on the metabolism of structurally similar compounds, naphthalene and 2-naphthol, by similar but different sets of enzymes in strain BC1 were validated by real-time PCR analyses.
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Affiliation(s)
- Piyali Pal Chowdhury
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, India
| | - Jayita Sarkar
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, India
| | - Soumik Basu
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, India
| | - Tapan K. Dutta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, India
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The gene PatG involved in the biosynthesis pathway of patulin, a food-borne mycotoxin, encodes a 6-methylsalicylic acid decarboxylase. Int J Food Microbiol 2014; 171:77-83. [DOI: 10.1016/j.ijfoodmicro.2013.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/08/2013] [Accepted: 11/18/2013] [Indexed: 11/23/2022]
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Wuensch C, Gross J, Steinkellner G, Lyskowski A, Gruber K, Glueck SM, Faber K. Regioselective ortho-carboxylation of phenols catalyzed by benzoic acid decarboxylases: a biocatalytic equivalent to the Kolbe–Schmitt reaction. RSC Adv 2014. [DOI: 10.1039/c3ra47719c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Pushing the equilibrium of regio-complementary carboxylation of phenols and hydroxystyrene derivatives. J Biotechnol 2013; 168:264-70. [PMID: 23880442 DOI: 10.1016/j.jbiotec.2013.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/18/2013] [Accepted: 07/12/2013] [Indexed: 11/22/2022]
Abstract
The enzymatic carboxylation of electron-rich aromatics, which represents a promising 'green' equivalent to the chemical Kolbe-Schmitt reaction, is thermodynamically disfavored and is therefore impeded by incomplete conversions. Optimization of the reaction conditions, such as pH, temperature, substrate concentration and the use of organic co-solvents and/or ionic liquids allowed to push the conversion in favor of carboxylation by a factor of up to 50%. Careful selection of the type of bicarbonate salt used as CO2 source was crucial to ensure optimal activities. Among two types of carboxylases tested with their natural substrates, benzoic acid decarboxylase from Rhizobium sp. proved to be significantly more stable than phenolic acid decarboxylase from Mycobacterium colombiense; it tolerated reaction temperatures of up to 50 °C and substrate concentrations of up to 100mM and allowed efficient biocatalyst recycling.
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31
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Ienaga S, Kosaka S, Honda Y, Ishii Y, Kirimura K. p-Aminosalicylic Acid Production by Enzymatic Kolbe–Schmitt Reaction Using Salicylic Acid Decarboxylases Improved through Site-Directed Mutagenesis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Saori Ienaga
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Sachiyo Kosaka
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Yuki Honda
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Yoshitaka Ishii
- Environmental Information and Science Course, School of Social Information Studies, Otsuma Women’s University
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
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Abstract
A new route to Cbz-(S)-dolaphenine, a recurring element in bioactive peptidic natural products, has been implemented, which closely parallels the biogenetic pathway. Cyclodehydration of 11 to yield thiazoline 2 allows for a Ni(0)-promoted decarbonylative aromatization to provide the thiazole framework with retention of stereochemistry.
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Affiliation(s)
- Pablo García-Reynaga
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
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33
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Wuensch C, Glueck SM, Gross J, Koszelewski D, Schober M, Faber K. Regioselective enzymatic carboxylation of phenols and hydroxystyrene derivatives. Org Lett 2012; 14:1974-7. [PMID: 22471935 PMCID: PMC3593611 DOI: 10.1021/ol300385k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic carboxylation of phenol and styrene derivatives using (de)carboxylases in carbonate buffer proceeded in a highly regioselective fashion: Benzoic acid (de)carboxylases selectively formed o-hydroxybenzoic acid derivatives, phenolic acid (de)carboxylases selectively acted at the β-carbon atom of styrenes forming (E)-cinnamic acids.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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34
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Kirimura K, Yanaso S, Kosaka S, Koyama K, Hattori T, Ishii Y. Production ofp-Aminosalicylic Acid through Enzymatic Kolbe–Schmitt Reaction Catalyzed by Reversible Salicylic Acid Decarboxylase. CHEM LETT 2011. [DOI: 10.1246/cl.2011.206] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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Kirimura K, Gunji H, Wakayama R, Hattori T, Ishii Y. Enzymatic Kolbe-Schmitt reaction to form salicylic acid from phenol: enzymatic characterization and gene identification of a novel enzyme, Trichosporon moniliiforme salicylic acid decarboxylase. Biochem Biophys Res Commun 2010; 394:279-84. [PMID: 20188702 DOI: 10.1016/j.bbrc.2010.02.154] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 02/23/2010] [Indexed: 10/19/2022]
Abstract
Salicylic acid decarboxylase (Sdc) can produce salicylic acid from phenol; it was found in the yeast Trichosporon moniliiforme WU-0401 and was for the first time enzymatically characterized, with the sdc gene heterologously expressed. Sdc catalyzed both reactions: decarboxylation of salicylic acid to phenol and the carboxylation of phenol to form salicylic acid without any byproducts. Both reactions were detected without the addition of any cofactors and occurred even in the presence of oxygen, suggesting that this Sdc is reversible, nonoxidative, and oxygen insensitive. Therefore, it is readily applicable in the selective production of salicylic acid from phenol, the enzymatic Kolbe-Schmitt reaction. The deduced amino acid sequence of the gene, sdc, encoding Sdc comprises 350 amino acid residues corresponding to a 40-kDa protein. The recombinant Escherichia coli BL21(DE3) expressing sdc converted phenol to salicylic acid with a 27% (mol/mol) yield at 30 degrees C for 9h.
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Affiliation(s)
- Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku 169-8555, Tokyo, Japan.
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Rachid S, Revermann O, Dauth C, Kazmaier U, Müller R. Characterization of a novel type of oxidative decarboxylase involved in the biosynthesis of the styryl moiety of chondrochloren from an acylated tyrosine. J Biol Chem 2010; 285:12482-9. [PMID: 20080978 DOI: 10.1074/jbc.m109.079707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myxobacteria are soil-dwelling bacteria notable for several unique behavioral features, such as cellular movement by gliding and the formation of multicellular fruiting bodies. More recently they have gained recognition as producers of several unique polyketide and nonribosomal polypeptide metabolites with potential therapeutic value. The biosynthesis of these compounds often involves highly unusual mechanisms including the formation of the chloro-hydroxy-styryl moiety of the chondrochloren antibiotic produced by Chondromyces crocatus Cm c5. Here it is shown that the final product of the chondrochloren megasynthetase is the novel natural product pre-chondrochloren, a carboxylated and saturated derivative of chondrochloren. This compound was isolated from strains harboring mutants of a hypothetical oxidative decarboxylase (CndG) identified in the chondrochloren gene cluster. CndG was heterologously expressed in Escherichia coli and shown to be an FAD-dependent oxidative decarboxylase. Biochemical characterization of the protein was achieved using the intermediate described above as the substrate and yielded chondrochloren by oxidative decarboxylation. It was also demonstrated that the CndG post-assembly line modification of pre-chondrochloren is essential for the biological activity of chondrochloren.
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Affiliation(s)
- Shwan Rachid
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Center for Infection Research, Saarland University, 66041 Saarbrücken, Germany
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Abstract
Dwindling petroleum feedstocks and increased CO(2)-concentrations in the atmosphere currently open the concept of using CO(2) as raw material for the synthesis of well-defined organic compounds. In parallel to recent advances in the chemical CO(2)-fixation, enzymatic (biocatalytic) carboxylation is currently being investigated at an increased pace. On the one hand, this critical review provides a concise overview on highly specific biosynthetic pathways for CO(2)-fixation and, on the other hand, a summary of biodegradation (detoxification) processes involving enzymes which possess relaxed substrate specificities, which allow their application for the regioselective carboxylation of organic substrates to furnish the corresponding carboxylic acids (145 references).
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Affiliation(s)
- Silvia M Glueck
- Research Centre Applied Biocatalysis, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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38
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Abstract
Paenibacillus sp. (formerly Bacillus macerans) strain JJ-1b is able to grow on 4-hydroxybenzoate (4HB) as a sole source of carbon and energy and is known to degrade 4HB via the protocatechuate (PCA) 2,3-cleavage pathway. However, none of the genes involved in this pathway have been identified. In this study, we identified and characterized the JJ-1b genes for the 4HB catabolic pathway via the PCA 2,3-cleavage pathway, which consisted of praR and praABEGFDCHI. Based on the enzyme activities of cell extracts of Escherichia coli carrying praI, praA, praH, praB, praC, and praD, these genes were found to code for 4HB 3-hydroxylase, PCA 2,3-dioxygenase, 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase, 2-hydroxymuconate-6-semialdehyde dehydrogenase, 4-oxalocrotonate (OCA) tautomerase, and OCA decarboxylase, respectively, which are involved in the conversion of 4HB into 2-hydroxypenta-2,4-dienoate (HPD). The praE, praF, and praG gene products exhibited 45 to 61% amino acid sequence identity to the corresponding enzymes responsible for the catabolism of HPD to pyruvate and acetyl coenzyme A. The deduced amino acid sequence of praR showed similarity with those of IclR-type transcriptional regulators. Reverse transcription-PCR analysis revealed that praABEGFDCHI constitute an operon, and these genes were expressed during the growth of JJ-1b on 4HB and PCA. praR-praABEGFDCHI conferred the ability to grow on 4HB to E. coli, suggesting that praEGF were functional for the conversion of HPD to pyruvate and acetyl coenzyme A. A promoter analysis suggested that praR encodes a repressor of the pra operon.
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39
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Parshetti G, Saratale G, Telke A, Govindwar S. Biodegradation of hazardous triphenylmethane dye methyl violet by Rhizobium radiobacter (MTCC 8161). J Basic Microbiol 2009; 49 Suppl 1:S36-42. [DOI: 10.1002/jobm.200800200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Fujii T, Goda Y, Yoshida M, Oikawa T, Hata Y. Crystallization and preliminary X-ray diffraction studies of maleylacetate reductase from Rhizobium sp. strain MTP-10005. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:737-9. [PMID: 18678945 DOI: 10.1107/s1744309108022537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 07/18/2008] [Indexed: 11/10/2022]
Abstract
Maleylacetate reductase (EC 1.3.1.32), which catalyzes the reduction of maleylacetate to 3-oxoadipate, plays an important role in the aerobic microbial catabolism of resorcinol. The enzyme has been crystallized at 293 K by the sitting-drop vapour-diffusion method supplemented with a microseeding technique, using ammonium sulfate as the precipitating agent. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 56.85, b = 121.13, c = 94.09 A, beta = 101.48 degrees , and contained one dimeric molecule in the asymmetric unit. It diffracted to 1.79 A resolution.
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Affiliation(s)
- Tomomi Fujii
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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41
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Lupa B, Lyon D, Shaw LN, Sieprawska-Lupa M, Wiegel J. Properties of the reversible nonoxidative vanillate / 4-hydroxybenzoate decarboxylase fromBacillus subtilis. Can J Microbiol 2008; 54:75-81. [DOI: 10.1139/w07-113] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus subtilis (ATCC 6051) reversibly decarboxylates vanillate and 4-hydroxybenzoate under both aerobic and anoxic conditions. Thus, we have identified on the basis of gene sequence homology with Sedimentibacter hydroxybenzoicus and Streptomyces sp. strain D7, a putative B. subtilis hydroxybenzoate decarboxylase. The native form of this enzyme is encoded by 3 genes yclBCD (GI Sequence Identification Nos.: 2632649, 2632650, 2632651) that we have renamed during this research as bsdBCD to align with existing nomenclature. The bsdD gene is reported in the database to be 690 bp; however, our sequence analysis revealed that the size of this gene is in fact 228 bp, an observation that results in a shortening of YclD (i.e., BsdD) from 229 to 75 aa. The corresponding bsdBCD genes were cloned into Escherichia coli , and the heterologously expressed enzyme was assayed for activity. The decarboxylase exhibited a narrow substrate range, with only 2 of the tested substrates, vanillate (Kmapp = 4 mmol·L–1) and 4-hydroxybenzoate (Kmapp = ~1 mmol·L–1), being decarboxylated. The recombinant enzyme had properties similar to that of the native enzyme in respect to specific activity, kinetic properties, bidirectional decarboxylase–carboxylase activity, oxygen insensitivity, and substrate specificity.
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Affiliation(s)
- Boguslaw Lupa
- Department of Microbiology, 212 Biological Sciences Building, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
| | - Delina Lyon
- Department of Microbiology, 212 Biological Sciences Building, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
| | - Lindsey N. Shaw
- Department of Microbiology, 212 Biological Sciences Building, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
| | - Magdalena Sieprawska-Lupa
- Department of Microbiology, 212 Biological Sciences Building, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
| | - Juergen Wiegel
- Department of Microbiology, 212 Biological Sciences Building, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
- Department of Microbiology, The University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
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Iwasaki Y, Kino K, Nishide H, Kirimura K. Regioselective and enzymatic production of gamma-resorcylic acid from resorcinol using recombinant Escherichia coli cells expressing a novel decarboxylase gene. Biotechnol Lett 2007; 29:819-22. [PMID: 17415666 DOI: 10.1007/s10529-007-9309-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/04/2007] [Accepted: 01/05/2007] [Indexed: 10/23/2022]
Abstract
A recombinant Escherichia coli, expressing the rdc gene, which encodes a gamma-resorcylic acid decarboxylase (Rdc) reversibly catalyzing regioselective carboxylation of resorcinol derived from Rhizobium radiobacter WU-0108, converted 20 mM resorcinol to gamma-resorcylic acid with a 44% (mol/mol) yield at 30 degrees C for 7 h. The recombinant E. coli cells were recyclable at least five times for use as biocatalysts.
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Affiliation(s)
- Yuichiro Iwasaki
- Department of Applied Chemistry, School of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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Yoshida M, Oikawa T, Obata H, Abe K, Mihara H, Esaki N. Biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005: identification and functional analysis of its gene cluster. J Bacteriol 2006; 189:1573-81. [PMID: 17158677 PMCID: PMC1855702 DOI: 10.1128/jb.01675-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium Rhizobium sp. strain MTP-10005. The cluster consists of the graRDAFCBEK genes, and graA, graB, graC, and graD were heterologously expressed in Escherichia coli. Enzymological studies showed that graD, graA, graC, and graB encode the reductase (GraD) and oxygenase (GraA) components of a resorcinol hydroxylase (EC 1.14.13.x), a maleylacetate reductase (GraC) (EC 1.3.1.32), and a hydroxyquinol 1,2-dioxygenase (GraB) (EC 1.13.11.37). Bioinformatic analyses suggested that graE, graR, and graK encode a protein with an unknown function (GraE), a MarR-type transcriptional regulator (GraR), and a benzoate transporter (GraK). Quantitative reverse transcription-PCR of graF, which encodes gamma-resorcylate decarboxylase, revealed that the maximum relative mRNA expression level ([5.93 +/- 0.82] x 10(-4)) of graF was detected in the total RNA of the cells after one hour of cultivation when gamma-resorcylate was used as the sole carbon source. Reverse transcription-PCR of graDAFCBE showed that these genes are transcribed as a single mRNA and that the transcription of the gene cluster is induced by gamma-resorcylate. These results suggested that the graDAFCBE genes are responsible as an operon for the growth of Rhizobium sp. strain MTP-10005 on gamma-resorcylate and are probably regulated by GraR at the transcriptional level. This is the first report of the gamma-resorcylate catabolic pathway in an aerobic bacterium.
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Affiliation(s)
- Masahiro Yoshida
- Department of Biotechnology, Faculty of Engineering, Kansai University, Suita, Osaka-Fu 564-8680, Japan
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44
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Goto M, Hayashi H, Miyahara I, Hirotsu K, Yoshida M, Oikawa T. Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. J Biol Chem 2006; 281:34365-73. [PMID: 16963440 DOI: 10.1074/jbc.m607270200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reversible 2,6-dihydroxybenzoate decarboxylase from Rhizobium sp. strain MTP-10005 belongs to a nonoxidative decarboxylase family. We have determined the structures of the following three forms of the enzyme: the native form, the complex with the true substrate (2,6-dihydroxybenzoate), and the complex with 2,3-dihydroxybenzaldehyde at 1.7-, 1.9-, and 1.7-A resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of one (alphabeta)8 triose-phosphate isomerase-barrel domain with three functional linkers and one C-terminal tail. The native enzyme possesses one Zn2+ ion liganded by Glu8, His10, His164, Asp287, and a water molecule at the active site center, although the enzyme has been reported to require no cofactor for its catalysis. The substrate carboxylate takes the place of the water molecule and is coordinated to the Zn2+ ion. The 2-hydroxy group of the substrate is hydrogen-bonded to Asp287, which forms a triad together with His218 and Glu221 and is assumed to be the catalytic base. On the basis of the geometrical consideration, substrate specificity is uncovered, and the catalytic mechanism is proposed for the novel Zn2+-dependent decarboxylation.
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Affiliation(s)
- Masaru Goto
- Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan
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Matsui T, Yoshida T, Hayashi T, Nagasawa T. Purification, characterization, and gene cloning of 4-hydroxybenzoate decarboxylase of Enterobacter cloacae P240. Arch Microbiol 2006; 186:21-9. [PMID: 16758158 DOI: 10.1007/s00203-006-0117-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2005] [Revised: 03/13/2006] [Accepted: 05/02/2006] [Indexed: 10/24/2022]
Abstract
We found the occurrence of 4-hydroxybenzoate decarboxylase in Enterobacter cloacae P240, isolated from soils under anaerobic conditions, and purified the enzyme to homogeneity. The purified enzyme was a homohexamer of identical 60 kDa subunits. The purified decarboxylase catalyzed the nonoxidative decarboxylation of 4-hydroxybenzoate without requiring any cofactors. Its Km value for 4-hydroxybenzoate was 596 microM. The enzyme also catalyzed decarboxylation of 3,4-dihydroxybenzoate, for which the Km value was 6.80 mM. In the presence of 3 M KHCO3 and 20 mM phenol, the decarboxylase catalyzed the reverse carboxylation reaction of phenol to form 4-hydroxybenzoate with a molar conversion yield of 19%. The Km value for phenol was calculated to be 14.8 mM. The gene encoding the 4-hydroxybenzoate decarboxylase was isolated from E. cloacae P240. Nucleotide sequencing of recombinant plasmids revealed that the 4-hydroxybenzoate decarboxylase gene codes for a 475-amino-acid protein. The amino acid sequence of the enzyme is similar to those of 4-hydroxybenzoate decarboxylase of Clostridium hydroxybenzoicum (53% identity), VdcC protein (vanillate decarboxylase) of Streptomyces sp. strain D7 (72%) and 3-octaprenyl-4-hydroxybenzoate decarboxylase of Escherichia coli (28%). The hypothetical proteins, showing 96-97% identities to the primary structure of E. cloacae P240 4-hydroxybenzoate decarboxylase, were found in several bacterial strains.
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Affiliation(s)
- Tsuyoshi Matsui
- Department of Biomolecular Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
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46
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Matsui T, Yoshida T, Yoshimura T, Nagasawa T. Regioselective carboxylation of 1,3-dihydroxybenzene by 2,6-dihydroxybenzoate decarboxylase of Pandoraea sp. 12B-2. Appl Microbiol Biotechnol 2006; 73:95-102. [PMID: 16683134 DOI: 10.1007/s00253-006-0437-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 03/17/2006] [Accepted: 03/23/2006] [Indexed: 11/28/2022]
Abstract
We found a bacterium, Pandoraea sp. 12B-2, of which whole cells catalyzed not only the decarboxylation of 2,6-dihydroxybenzoate but also the regioselective carboxylation of 1,3-dihydroxybenzene to 2,6-dihydroxybenzoate. The whole cells of Pandoraea sp. 12B-2 also catalyzed the regioselective carboxylation of phenol and 1,2-dihydroxybenzene to 4-hydroxybenzoate and 2,3-dihydroxybenzoate, respectively. The molar conversion ratio of the carboxylation reaction depended on the concentration of KHCO(3) in the reaction mixture. Only 5 or 48 % of 1,3-dihydroxybenzene added was converted into 2,6-dihydroxybenzoate in the presence of 0.1 M or 3 M KHCO(3), respectively. The addition of acetone to the reaction mixture increased the initial rate of the carboxylation reaction, but the final molar conversion yield reached almost the same value. When the efficient production of 2,6-dihydroxybenzoate was optimized using the whole cells of Pandoraea sp. 12B-2, the productivity of 2,6-dihydroxybenzoate topped out at 1.43 M, which was the highest value so far reported. No formation of any other products was observed after the carboxylation reaction.
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Affiliation(s)
- Tsuyoshi Matsui
- Department of Biomolecular Science, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
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