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Kutraite I, Malys N. Development and Application of Whole-Cell Biosensors for the Detection of Gallic Acid. ACS Synth Biol 2023; 12:533-543. [PMID: 36724292 PMCID: PMC9942251 DOI: 10.1021/acssynbio.2c00537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Gallic acid is a prevalent secondary plant metabolite distinguished as one of the most effective free-radical scavengers among phenolic acids. This compound is also known for its cytotoxic, anti-inflammatory, and antimicrobial activities. Bulk quantities of gallic acid are conventionally produced by acid hydrolysis of tannins, a costly and environmentally hazardous process. With the aim to develop more sustainable approaches, microbial bioproduction strategies have been attempted recently. To advance synthetic biology and metabolic engineering of microorganisms for gallic acid production, we characterize here a transcription factor-based inducible system PpGalR/PPP_RS13150 that responds to the extracellular gallic acid in a dose-dependent manner in Pseudomonas putida KT2440. Surprisingly, this compound does not mediate induction when PpGalR/PPP_RS13150 is used in non-native host background. We show that the activation of the inducible system requires gallate dioxygenase activity encoded by galA gene. The 4-oxalomesaconic acid, an intermediate of gallic acid-metabolism, is identified as the effector molecule that interacts with the transcription factor GalR mediating activation of gene expression. Introduction of galA gene along galR enables development of biosensors suitable for detection and monitoring of gallic acid extracellularly using non-native hosts such as E. coli and C. necator. Moreover, the P. putida-based biosensor's applicability is demonstrated by detecting and measuring gallic acid in extracts of Camellia sinensis leaves. This study reports the strategy, which can be applied for developing gallic acid biosensors using bacterial species outside Pseudomonas genus.
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Affiliation(s)
- Ingrida Kutraite
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania
| | - Naglis Malys
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,Department
of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,
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2
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Tsagogiannis E, Vandera E, Primikyri A, Asimakoula S, Tzakos AG, Gerothanassis IP, Koukkou AI. Characterization of Protocatechuate 4,5-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and In Situ Reaction Monitoring in the NMR Tube. Int J Mol Sci 2021; 22:9647. [PMID: 34502555 PMCID: PMC8431788 DOI: 10.3390/ijms22179647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
The current study aims at the functional and kinetic characterization of protocatechuate (PCA) 4,5-dioxygenase (PcaA) from Pseudarthrobacter phenanthrenivorans Sphe3. This is the first single subunit Type II dioxygenase characterized in Actinobacteria. RT-PCR analysis demonstrated that pcaA and the adjacent putative genes implicated in the PCA meta-cleavage pathway comprise a single transcriptional unit. The recombinant PcaA is highly specific for PCA and exhibits Michaelis-Menten kinetics with Km and Vmax values of 21 ± 1.6 μM and 44.8 ± 4.0 U × mg-1, respectively, in pH 9.5 and at 20 °C. PcaA also converted gallate from a broad range of substrates tested. The enzymatic reaction products were identified and characterized, for the first time, through in situ biotransformation monitoring inside an NMR tube. The PCA reaction product demonstrated a keto-enol tautomerization, whereas the gallate reaction product was present only in the keto form. Moreover, the transcriptional levels of pcaA and pcaR (gene encoding a LysR-type regulator of the pathway) were also determined, showing an induction when cells were grown on PCA and phenanthrene. Studying key enzymes in biodegradation pathways is significant for bioremediation and for efficient biocatalysts development.
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Affiliation(s)
- Epameinondas Tsagogiannis
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Elpiniki Vandera
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Alexandra Primikyri
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Stamatia Asimakoula
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Andreas G. Tzakos
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Ioannis P. Gerothanassis
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
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3
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Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds. Sci Rep 2020; 10:12177. [PMID: 32699224 PMCID: PMC7376174 DOI: 10.1038/s41598-020-68984-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022] Open
Abstract
Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34540), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.
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5
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Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6. Sci Rep 2019; 9:18036. [PMID: 31792252 PMCID: PMC6888825 DOI: 10.1038/s41598-019-54490-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022] Open
Abstract
Vanillate and syringate are major intermediate metabolites generated during the microbial degradation of lignin. In Sphingobium sp. SYK-6, vanillate is O demethylated to protocatechuate by LigM; protocatechuate is then catabolized via the protocatechuate 4,5-cleavage pathway. Syringate is O demethylated to gallate by consecutive reactions catalyzed by DesA and LigM, and then gallate is subjected to ring cleavage by DesB. Here, we investigated the transcriptional regulation of desA, ligM, and desB involved in vanillate and syringate catabolism. Quantitative reverse transcription-PCR analyses indicated that the transcription of these genes was induced 5.8–37-fold in the presence of vanillate and syringate. A MarR-type transcriptional regulator, SLG_12870 (desR), was identified as the gene whose product bound to the desB promoter region. Analysis of a desR mutant indicated that the transcription of desB, ligM, and desR is negatively regulated by DesR. Purified DesR bound to the upstream regions of desB, ligM, and desR, and the inverted repeat sequences similar to each other in these regions were suggested to be essential for DNA binding of DesR. Vanillate and syringate inhibited DNA binding of DesR, indicating that these compounds are effector molecules of DesR. The transcription of desA was found to be regulated by an as-yet unidentified regulator.
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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7
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Shinoda E, Takahashi K, Abe N, Kamimura N, Sonoki T, Masai E. Isolation of a novel platform bacterium for lignin valorization and its application in glucose-free cis,cis-muconate production. ACTA ACUST UNITED AC 2019; 46:1071-1080. [DOI: 10.1007/s10295-019-02190-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/20/2019] [Indexed: 01/28/2023]
Abstract
Abstract
Microbial production of cis,cis-muconate (ccMA) from phenolic compounds obtained by chemical depolymerization of lignin is a promising approach to valorize lignin. Because microbial production requires a large amount of carbon and energy source, it is desirable to establish a ccMA-producing strain that utilizes lignin-derived phenols instead of general sources like glucose. We isolated Pseudomonas sp. strain NGC7 that grows well on various phenolic compounds derived from p-hydroxyphenyl, guaiacyl, and syringyl units of lignin. An NGC7 mutant of protocatechuate (PCA) 3,4-dioxygenase and ccMA cycloisomerase genes (NGC703) lost the ability to grow on vanillate and p-hydroxybenzoate but grew normally on syringate. Introduction of a plasmid carrying genes encoding PCA decarboxylase, flavin prenyltransferase, vanillate O-demethylase, and catechol 1,2-dioxygenase into NGC703 enabled production of 3.2 g/L ccMA from vanillate with a yield of 75% while growing on syringate. This strain also produced ccMA from birch lignin-derived phenols. All these results indicate the utility of NGC7 in glucose-free ccMA production.
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Affiliation(s)
- Eri Shinoda
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology Kamitomioka 940-2188 Nagaoka Niigata Japan
| | - Kenji Takahashi
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology Kamitomioka 940-2188 Nagaoka Niigata Japan
| | - Nanase Abe
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology Kamitomioka 940-2188 Nagaoka Niigata Japan
| | - Naofumi Kamimura
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology Kamitomioka 940-2188 Nagaoka Niigata Japan
| | - Tomonori Sonoki
- 0000 0001 0673 6172 grid.257016.7 Faculty of Agriculture and Life Science Hirosaki University 036-8561 Hirosaki Aomori Japan
| | - Eiji Masai
- 0000 0001 0671 2234 grid.260427.5 Department of Bioengineering Nagaoka University of Technology Kamitomioka 940-2188 Nagaoka Niigata Japan
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8
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Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019; 294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD-Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD-Memo families.
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Affiliation(s)
- A Maxwell Burroughs
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Margaret E Glasner
- the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, and
| | - Kevin P Barry
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Erika A Taylor
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - L Aravind
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,
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9
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Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:679-705. [PMID: 29052962 DOI: 10.1111/1758-2229.12597] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/26/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kenji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kosuke Mori
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takuma Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Fujita
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yudai Higuchi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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10
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Kuatsjah E, Chen HM, Withers SG, Eltis LD. Characterization of an extradiol dioxygenase involved in the catabolism of lignin-derived biphenyl. FEBS Lett 2017; 591:1001-1009. [DOI: 10.1002/1873-3468.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Eugene Kuatsjah
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
| | - Hong-Ming Chen
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
| | - Stephen G. Withers
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
| | - Lindsay D. Eltis
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
- Department of Microbiology and Immunology; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
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11
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Abstract
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.
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12
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Opportunities and challenges in biological lignin valorization. Curr Opin Biotechnol 2016; 42:40-53. [DOI: 10.1016/j.copbio.2016.02.030] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/24/2016] [Indexed: 02/08/2023]
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13
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Nishitani Y, Simons JR, Kanai T, Atomi H, Miki K. Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase. Acta Crystallogr F Struct Biol Commun 2016; 72:427-33. [PMID: 27303894 PMCID: PMC4909241 DOI: 10.1107/s2053230x16006920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
The TK2203 protein from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (262 residues, 29 kDa) is a putative extradiol dioxygenase catalyzing the cleavage of C-C bonds in catechol derivatives. It contains three metal-binding residues, but has no significant sequence similarity to proteins for which structures have been determined. Here, the first crystal structure of the TK2203 protein was determined at 1.41 Å resolution to investigate its functional role. Structure analysis reveals that this protein shares the same fold and catalytic residues as other extradiol dioxygenases, strongly suggesting the same enzymatic activity. Furthermore, the important region contributing to substrate selectivity is discussed.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jan-Robert Simons
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, Sanbancho, Chiyoda-ku, Tokyo, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, Sanbancho, Chiyoda-ku, Tokyo, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, Sanbancho, Chiyoda-ku, Tokyo, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- JST, CREST, Sanbancho, Chiyoda-ku, Tokyo, Japan
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14
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Kotake T, Matsuzawa J, Suzuki-Minakuchi C, Okada K, Nojiri H, Iwata K. Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase, in the fluorene degradation pathway from Rhodococcus sp. strain DFA3. Biosci Biotechnol Biochem 2016; 80:719-25. [DOI: 10.1080/09168451.2015.1123605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Type II extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase (FlnD1D2) involved in the fluorene degradation pathway of Rhodococcus sp. DFA3 was purified to homogeneity from a heterologously expressing Escherichia coli. Gel filtration chromatography and SDS-PAGE suggested that FlnD1D2 is an α4β4 heterooctamer and that the molecular masses of these subunits are 30 and 9.9 kDa, respectively. The optimum pH and temperature for enzyme activity were 8.0 and 30 °C, respectively. Assessment of metal ion effects suggested that exogenously supplied Fe2+ increases enzyme activity 3.2-fold. FlnD1D2 catalyzed meta-cleavage of 2′-carboxy-2,3-dihydroxybiphenyl homologous compounds, but not single-ring catecholic compounds. The Km and kcat/Km values of FlnD1D2 for 2,3-dihidroxybiphenyl were 97.2 μM and 1.5 × 10−2 μM−1sec−1, and for 2,2′,3-trihydroxybiphenyl, they were 168.0 μM and 0.5 × 10−2 μM−1sec−1, respectively. A phylogenetic tree of the large and small subunits of type II extradiol dioxygenases suggested that FlnD1D2 constitutes a novel subgroup among heterooligomeric type II extradiol dioxygenases.
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Affiliation(s)
- Tatsuro Kotake
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Jun Matsuzawa
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | | | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Kenichi Iwata
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
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15
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Wang P, Chen X, Li C, Gao X, Zhu D, Xie B, Qin Q, Zhang X, Su H, Zhou B, Xun L, Zhang Y. Structural and molecular basis for the novel catalytic mechanism and evolution of
DddP
, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold. Mol Microbiol 2015; 98:289-301. [DOI: 10.1111/mmi.13119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Wang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiu‐Lan Chen
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Chun‐Yang Li
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - De‐yu Zhu
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bin‐Bin Xie
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Qi‐Long Qin
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xi‐Ying Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Hai‐Nan Su
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bai‐Cheng Zhou
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Lu‐ying Xun
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
| | - Yu‐Zhong Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
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