1
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Rodrigues AV, Moriarty NW, Kakumanu R, DeGiovanni A, Pereira JH, Gin JW, Chen Y, Baidoo EEK, Petzold CJ, Adams PD. Characterization of lignin degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid (PDC). J Biol Chem 2024:107736. [PMID: 39222681 DOI: 10.1016/j.jbc.2024.107736] [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: 03/19/2024] [Revised: 07/22/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is CHMS dehydrogenase, which acts on the substrate 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS). We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.
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Affiliation(s)
- Andria V Rodrigues
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States.
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Andy DeGiovanni
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Bioengineering, University of California Berkeley, Berkeley California 94720, United States.
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2
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Yang H, Qian Z, Liu Y, Yu F, Huang T, Zhang B, Peng T, Hu Z. Comparative genomics reveals evidence of polycyclic aromatic hydrocarbon degradation in the moderately halophilic genus Pontibacillus. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132724. [PMID: 37839372 DOI: 10.1016/j.jhazmat.2023.132724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a common class of persistent organic pollutants (POPs) that are widely distributed in various environments and pose significant threats to both environmental and human health. The genus Pontibacillus, a type of moderately halophilic bacteria, has demonstrated potential for biodegrading aromatic compounds in high-salinity environments. However, no previous study has comprehensively investigated the PAH degradation mechanisms and environmental adaptability in the genus Pontibacillus. In this study, we sequenced the whole genome of the PAH-degrading strain Pontibacillus chungwhensis HN14 and conducted a comparative genomics analysis of genes associated with PAH degradation, as well as salt and arsenic tolerance using ten other Pontibacillus sp. strains. Here, we elucidated potential degradation pathways for benzo[a]pyrene and phenanthrene, which were initiated by cytochrome P450 monooxygenases, in most Pontibacillus strains. Moreover, four Pontibacillus strains were selected to investigate the biodegradation of benzo[a]pyrene and phenanthrene under high-salt (5% NaCl) stress, and all four strains exhibited exceptional degradation abilities. The results of comparative genomics and phenotypic analyses demonstrate that the genus Pontibacillus have the potential to degrade polycyclic aromatic hydrocarbons in high-salinity environments, thus providing valuable insights for biodegradation in extreme environments.
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Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Bing Zhang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China; Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou 515063, Guangdong, PR China.
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3
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Pimviriyakul P, Buttranon S, Soithongcharoen S, Supawatkon C, Disayabootr K, Watthaisong P, Tinikul R, Jaruwat A, Chaiyen P, Chitnumsub P, Maenpuen S. Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii. Arch Biochem Biophys 2023; 747:109768. [PMID: 37769893 DOI: 10.1016/j.abb.2023.109768] [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: 08/24/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
3,4-Dihydroxyphenylacetate (DHPA) 2,3-dioxygenase (EC 1.13.11.15) from Acinetobacter baumannii (AbDHPAO) is an enzyme that catalyzes the 2,3-extradiol ring-cleavage of DHPA in the p-hydroxyphenylacetate (HPA) degradation pathway. While the biochemical reactions of various DHPAOs have been reported, only structures of DHPAO from Brevibacterium fuscum and their homologs are available. Here, we report the X-ray structure and biochemical characterization of an Fe2+-specific AbDHPAO that shares 12% sequence identity to the enzyme from B. fuscum. The 1.8 Å X-ray structure of apo-AbDHPAO was determined with four subunits per asymmetric unit, consistent with a homotetrameric structure. Interestingly, the αβ-sandwiched fold of the AbDHPAO subunit is different from the dual β-barrel-like motif of the well-characterized B. fuscum DHPAO structures; instead, it is similar to the structures of non-DHPA extradiol dioxygenases from Comamonas sp. and Sphingomonas paucimobilis. Similarly, these extradiol dioxygenases share the same chemistry owing to a conserved 2-His-1-carboxylate catalytic motif. Structure analysis and molecular docking suggested that the Fe2+ cofactor and substrate binding sites consist of the conserved residues His12, His57, and Glu238 forming a 2-His-1-carboxylate motif ligating to Fe2+ and DHPA bound with Fe2+ in an octahedral coordination. In addition to DHPA, AbDHPAO can also use other 3,4-dihydroxyphenylacetate derivatives with different aliphatic carboxylic acid substituents as substrates, albeit with low reactivity. Altogether, this report provides a better understanding of the structure and biochemical properties of AbDHPAO and its homologs, which is advancing further modification of DHPAO in future applications.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Supacha Buttranon
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Sahachat Soithongcharoen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Cheerapat Supawatkon
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Kasidis Disayabootr
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand.
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Li YX, Lin W, Han YH, Wang YQ, Wang T, Zhang H, Zhang Y, Wang SS. Biodegradation of p-hydroxybenzoic acid in Herbaspirillum aquaticum KLS-1 isolated from tailing soil: Characterization and molecular mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131669. [PMID: 37236108 DOI: 10.1016/j.jhazmat.2023.131669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The wide distribution of p-hydroxybenzoic acid (PHBA) in the environments has attracted great concerns due to its potential risks to organisms. Bioremediation is considered a green way to remove PHBA from environment. Here, a new PHBA-degrading bacterium Herbaspirillum aquaticum KLS-1was isolated and its PHBA degradation mechanisms were fully evaluated. Results showed that strain KLS-1 could utilize PHBA as the sole carbon source and completely degrade 500 mg/L PHBA within 18 h. The optimal conditions for bacterial growth and PHBA degradation were pH values of 6.0-8.0, temperatures of 30 °C-35 °C, shaking speed of 180 rpm, Mg2+ concentration of 2.0 mM and Fe2+ concentration of 1.0 mM. Draft genome sequencing and functional gene annotations identified three operons (i.e., pobRA, pcaRHGBD and pcaRIJ) and several free genes possibly participating in PHBA degradation. The key genes pobA, ubiA, fadA, ligK and ubiG involved in the regulation of protocatechuate and ubiquinone (UQ) metabolisms were successfully amplified in strain KLS-1 at mRNA level. Our data suggested that PHBA could be degraded by strain KLS-1 via the protocatechuate ortho-/meta-cleavage pathway and UQ biosynthesis pathway. This study has provided a new PHBA-degrading bacterium for potential bioremediation of PHBA pollution.
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Affiliation(s)
- Yi-Xi Li
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Wei Lin
- College of Life Science, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Yong-He Han
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China.
| | - Yao-Qiang Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Tao Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Hong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Yong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Shan-Shan Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
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Rafalowski A, Hassan BA, Lou K, Nguyen MC, Taylor EA. How Single Amino Acid Substitutions Can Disrupt a Protein Hetero-Dimer Interface: Computational and Experimental Studies of the LigAB Dioxygenase from Sphingobium sp. Strain SYK-6. Int J Mol Sci 2023; 24:ijms24076319. [PMID: 37047291 PMCID: PMC10094722 DOI: 10.3390/ijms24076319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Protocatechuate 4,5-dioxygenase (LigAB) is a heterodimeric enzyme that catalyzes the dioxygenation of multiple lignin derived aromatic compounds. The active site of LigAB is at the heterodimeric interface, with specificity conferred by the alpha subunit and catalytic residues contributed by the beta subunit. Previous research has indicated that the phenylalanine at the 103 position of the alpha subunit (F103α) controls selectivity for the C5 position of the aromatic substrates, and mutations of this residue can enhance the rate of catalysis for substrates with larger functional groups at this position. While several of the mutations to this position (Valine, V; Threonine, T; Leucine, L; and Histidine, H) were catalytically active, other mutations (Alanine, A; and Serine, S) were found to have reduced dimer interface affinity, leading to challenges in copurifing the catalytically active enzyme complex under high salt conditions. In this study, we aimed to experimentally and computationally interrogate residues at the dimer interface to discern the importance of position 103α for maintaining the integrity of the heterodimer. Molecular dynamic simulations and electrophoretic mobility assays revealed a preference for nonpolar/aromatic amino acids in this position, suggesting that while substitutions to polar amino acids may produce a dioxygenase with a useful substrate utilization profile, those considerations may be off-set by potential destabilization of the catalytically active oligomer. Understanding the dimerization of LigAB provides insight into the multimeric proteins within the largely uncharacterized superfamily and characteristics to consider when engineering proteins that can degrade lignin efficiently. These results shed light on the challenges associated with engineering proteins for broader substrate specificity.
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6
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Shapterhasmi T, Palani N, Velusamy M, Bhuvanesh NS, Sundaravel K, Easwaramoorthi S. Iron(III) Complexes of Pyrrolidine and Piperidine Appended Tridentate 3N Donor Ligands as Models for Catechol Dioxygenase Enzymes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Brennerova MV, Zavala-Meneses SG, Josefiova J, Branny P, Buriankova K, Vetrovsky T, Junca H. A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons. ENVIRONMENTAL RESEARCH 2022; 204:111954. [PMID: 34474030 DOI: 10.1016/j.envres.2021.111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.
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Affiliation(s)
- Maria V Brennerova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic.
| | - Sofía G Zavala-Meneses
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic; Charles University, Faculty of Science, Vinicna 5, 12844, Prague, Czech Republic
| | - Jirina Josefiova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Pavel Branny
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Karolina Buriankova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Tomas Vetrovsky
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008, Chia, Colombia
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Cho H, Lee H, Hong K, Chung H, Song I, Lee JS, Kim S. Bioinformatic Expansion of Borosins Uncovers Trans-Acting Peptide Backbone N-Methyltransferases in Bacteria. Biochemistry 2022; 61:183-194. [DOI: 10.1021/acs.biochem.1c00764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hyunjin Cho
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kyungtae Hong
- Bio-Med Program, KIST-School UST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Hannah Chung
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Inseok Song
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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Kasei A, Watanabe H, Ishiduka N, Noda K, Murata M, Sakuta M. Comparative Analysis of the Extradiol Ring-Cleavage Dioxygenase LigB from Arabidopsis and 3,4-Dihydroxyphenylalanine Dioxygenase from Betalain-Producing Plants. PLANT & CELL PHYSIOLOGY 2021; 62:732-740. [PMID: 33638982 DOI: 10.1093/pcp/pcab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Diverse arrays of naturally occurring compounds in plants are synthesized by specialized metabolic enzymes, many of which are distributed taxonomically. Although anthocyanin pigments are widely distributed and ubiquitous, betalains have replaced anthocyanins in most families in Caryophyllales. Anthocyanins and betalains never occur together in the same plant. The formation of betalamic acid, catalyzed by 3,4-dihydroxyphenylalanine (DOPA) 4,5-extradiol dioxygenase (DOD), is a key step in betalain biosynthesis. DODs in betalain-producing plants are coded by LigB genes, homologs of which have been identified in a wide range of higher plant orders, as well as in certain fungi and bacteria. Two classes of LigB homologs have been reported: those found in anthocyanin-producing species and those found in betalain-producing species, which contain DOD. To gain insight into the evolution of specialized metabolic enzymes involved in betalain biosynthesis, we performed a comparative biochemical analysis of Arabidopsis LigB, an extradiol ring-cleavage dioxygenase in anthocyanin-producing Arabidopsis and Phytolacca DOD1 of betalain-producing Phytolacca americana. We show that Arabidopsis LigB catalyzes 2,3-extradiol cleavage of DOPA to synthesize muscaflavin, whereas Phytolacca DOD1 converts DOPA to betalamic acid via 4,5-extradiol cleavage. Arabidopsis LigB also converts caffeic acid, a ubiquitous phenolic compound in higher plants, to iso-arabidopic acid in vitro via 2,3-extradiol cleavage of the aromatic ring. Amino-acid substitution in Arabidopsis LigB and Phytolacca DOD1 led to variable extradiol ring-cleavage function, supporting the suggestion that catalytic promiscuity serves as a starting point for the divergence of new enzymatic activities.
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Affiliation(s)
- Akane Kasei
- Department of Biological Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Hanako Watanabe
- Department of Biological Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Natsumi Ishiduka
- Department of Biological Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Kyoko Noda
- Department of Nutrition and Food Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Masatsune Murata
- Department of Nutrition and Food Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610 Japan
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10
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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11
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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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12
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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13
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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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14
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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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15
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Chauhan PS. Role of various bacterial enzymes in complete depolymerization of lignin: A review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101498] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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17
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Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach. mSystems 2019; 4:4/6/e00316-19. [PMID: 31771973 PMCID: PMC6880040 DOI: 10.1128/msystems.00316-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The release of synthetic chemical pollutants in the environment is posing serious health risks. Enzymes, including oxygenases, play a crucial role in xenobiotic degradation. In the present study, we employed a functional metagenomics approach to overcome the limitation of cultivability of microbes under standard laboratory conditions in order to isolate novel dioxygenases capable of degrading recalcitrant pollutants. Fosmid clones possessing dioxygenase activity were further sequenced, and their genes were identified using bioinformatics tools. Two positive fosmid clones, SD3 and RW1, suggested the presence of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC-SD3) and catechol 2,3-dioxygenase (C23O-RW1), respectively. Recombinant versions of these enzymes were purified to examine their pollutant-degrading abilities. The crystal structure of BphC-SD3 was determined at 2.6-Å resolution, revealing a two-domain architecture, i.e., N-terminal and C-terminal domains, with the sequential arrangement of βαβββ in each domain, characteristic of Fe-dependent class II type I extradiol dioxygenases. The structure also reveals the presence of conserved amino acids lining the catalytic pocket and Fe3+ metal ion in the large funnel-shaped active site in the C-terminal domain. Further studies suggest that Fe3+ bound in the BphC-SD3 active site probably imparts aerobic stability. We further demonstrate the potential application of BphC-SD3 in biosensing of catecholic compounds. The halotolerant and oxygen-resistant properties of these enzymes reported in this study make them potential candidates for bioremediation and biosensing applications.IMPORTANCE The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is currently not practical due to their aerobically unstable nature. The significance of our research lies in the discovery of aerobically stable and halotolerant catechol dioxygenases that are efficient in degrading the targeted environmental pollutants and, hence, could be used as cost-effective alternatives for the treatment of hypersaline industrial effluents. Moreover, the structural determination of novel catechol dioxygenases would greatly enhance our knowledge of the function of these enzymes and facilitate directed evolution to further enhance or engineer desired properties.
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18
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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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19
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Nerdinger S, Kuatsjah E, Hurst TE, Schlapp-Hackl I, Kahlenberg V, Wurst K, Eltis LD, Snieckus V. Bacterial Catabolism of Biphenyls: Synthesis and Evaluation of Analogues. Chembiochem 2018; 19:1771-1778. [PMID: 29905982 DOI: 10.1002/cbic.201800231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 12/31/2022]
Abstract
A series of alkylated 2,3-dihydroxybiphenyls has been prepared on the gram scale by using an effective Directed ortho Metalation-Suzuki-Miyaura cross-coupling strategy. These compounds have been used to investigate the substrate specificity of the meta-cleavage dioxygenase BphC, a key enzyme in the microbial catabolism of biphenyl. Isolation and characterization of the meta-cleavage products will allow further study of related processes, including the catabolism of lignin-derived biphenyls.
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Affiliation(s)
- Sven Nerdinger
- Global Commercial Operations, Sandoz GmbH, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Eugene Kuatsjah
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Timothy E Hurst
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
| | - Inge Schlapp-Hackl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Center for Chemistry and Biomedicine, Innrain 80-82, 6020, Innsbruck, Austria
| | - Volker Kahlenberg
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Lindsay D Eltis
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Snieckus
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
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20
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Liu S, Guo C, Lin W, Wu F, Lu G, Lu J, Dang Z. Comparative transcriptomic evidence for Tween80-enhanced biodegradation of phenanthrene by Sphingomonas sp. GY2B. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1161-1171. [PMID: 28787790 DOI: 10.1016/j.scitotenv.2017.07.245] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
Previous study of the effects of surfactants on the biodegradation of phenanthrene focused on investigating alterations of the cell characteristics of Sphingomonas sp. GY2B. However, genes regulation associated with biodegradation and biological processes in response to the presence of surfactants, remains unclear. In this study, comparative transcriptome analysis was conducted to observe the gene expression of GY2B during phenanthrene biodegradation in the presence and absence of Tween80. A diverse set of genes was regulated by Tween80, leading to increased biodegradation of phenanthrene by GY2B: (i) Tween80 increased expression of genes related to H+ transport in the plasma membrane to provide a driving force (i.e., ATP) for accelerating transmembrane transport of phenanthrene with increasing Tween80 concentrations, thereby enhancing the uptake and degradation of phenanthrene by GY2B; (ii) Tween80 (1 and 8 CMC) promoted intracellular biodegradation of phenanthrene by stimulating expression of genes encoding dioxygenases and monooxygenase, increasing expression of genes involved in intracellular metabolic processes (e.g., TCA cycle); and (iii) Tween80 likely increased GY2B vitality and growth by inducing expression of genes associated with ABC transporters and protein transport, regulating genes involved in other biological processes (e.g., transcription, translation).
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Affiliation(s)
- Shasha Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, PR China.
| | - Weijia Lin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Fengji Wu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, PR China
| | - Jing Lu
- School of Chemical Engineering and Environment, North University of China, Taiyuan 030051, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, PR China
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21
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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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22
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Lakshman TR, Chatterjee S, Chakraborty B, Paine TK. Substrate-dependent aromatic ring fission of catechol and 2-aminophenol with O2 catalyzed by a nonheme iron complex of a tripodal N4 ligand. Dalton Trans 2016; 45:8835-44. [PMID: 27148606 DOI: 10.1039/c5dt04541j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic reactivity of an iron(ii) complex [(TPA)Fe(II)(CH3CN)2](2+) (1) (TPA = tris(2-pyridylmethyl)amine) towards oxygenative aromatic C-C bond cleavage of catechol and 2-aminophenol is presented. Complex 1 exhibits catalytic and regioselective C-C bond cleavage of 3,5-di-tert-butylcatechol (H2DBC) to form intradiol products, whereas it catalyzes extradiol-type C-C bond cleavage of 2-amino-4,6-di-tert-butylphenol (H2AP). The catalytic reactions are found to be pH-dependent and the complex exhibits maximum turnovers at pH 5 in acetonitrile-phthalate buffer. An iron(iii)-catecholate complex [(TPA)Fe(III)(DBC)](+) (2) is formed in the ring cleavage of catechol. In the extradiol-type cleavage of H2AP, an iron(iii)-2-iminobenzosemiquinonate complex [(TPA)Fe(III)(ISQ)](2+) (3) (ISQ = 4,6-di-tert-butyl-2-iminobenzosemiquinonate radical anion) is observed in the reaction pathway. This work shows the importance of the nature of 'redox non-innocent' substrates in governing the mode of ring fission reactivity.
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Affiliation(s)
- Triloke Ranjan Lakshman
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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23
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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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Qi Y, Lu J, Lai W. Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study. J Phys Chem B 2016; 120:4579-90. [PMID: 27119315 DOI: 10.1021/acs.jpcb.6b03006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.
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Affiliation(s)
- Yue Qi
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Jiarui Lu
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
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25
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Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases. Appl Environ Microbiol 2016; 82:2467-2478. [PMID: 26896130 DOI: 10.1128/aem.03811-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/19/2016] [Indexed: 12/26/2022] Open
Abstract
A metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic DNA. The library, consisting of 6.5 Gb of metagenomic DNA, was screened for extradiol dioxygenase (Edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. Fifty-eight independent clones encoding extradiol dioxygenase activity were identified. Forty-one different Edo-encoding genes were identified. The population of Edo genes was not dominated by a particular gene or by highly similar genes; rather, the genes had an even distribution and high diversity. Phylogenetic analyses revealed that most of the genes could not be ascribed to previously defined subfamilies of Edos. Rather, the Edo genes led to the definition of 10 new subfamilies of type I Edos. Phylogenetic analysis of type II enzymes defined 7 families, 2 of which harbored the type II Edos that were found in this work. Particularly striking was the diversity found in family I.3 Edos; 15 out of the 17 sequences assigned to this family belonged to 7 newly defined subfamilies. A strong bias was found that depended on the substrate used for the screening: catechol mainly led to the detection of Edos belonging to the I.2 family, while 2,3-dihydroxybiphenyl led to the detection of most other Edos. Members of the I.2 family showed a clear substrate preference for monocyclic substrates, while those from the I.3 family showed a broader substrate range and high activity toward 2,3-dihydroxybiphenyl. This metagenomic analysis has substantially increased our knowledge of the existing biodiversity of Edos.
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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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Barry KP, Cohn EF, Ngu A, Taylor EA. Improving alternate lignin catabolite utilization of LigAB from Sphingobium sp. strain SYK-6 through site directed mutagenesis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Kovaleva EG, Rogers MS, Lipscomb JD. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Biochemistry 2015; 54:5329-39. [PMID: 26267790 DOI: 10.1021/acs.biochem.5b00709] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species.
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Affiliation(s)
- Elena G Kovaleva
- Institute of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Barry KP, Ngu A, Cohn EF, Cote JM, Burroughs AM, Gerbino JP, Taylor EA. Exploring allosteric activation of LigAB from Sphingobium sp. strain SYK-6 through kinetics, mutagenesis and computational studies. Arch Biochem Biophys 2015; 567:35-45. [PMID: 25562402 DOI: 10.1016/j.abb.2014.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022]
Abstract
The protocatechuate 4,5-dioxygenase (LigAB) from Sphingobium sp. strain SYK-6 is the defining member of the Type II extradiol dioxygenase superfamily (a.k.a. PCA Dioxygenase Superfamily or PCADSF) and plays a key aromatic ring-opening role in the metabolism of several lignin derived aromatic compounds. In our search for alternate substrates and inhibitors of LigAB, we discovered allosteric rate enhancement in the presence of non-substrate protocatechuate-like aldehydes such as vanillin. LigAB has the broadest substrate utilization profile of all protocatechuate (PCA) 4,5-dioxygenase described in the literature, however, the rate enhancement is only observed with PCA, with vanillin increasing kcat for LigAB by 36%. Computational docking has identified a potential site of allosteric binding near the entrance to the active site. Examination of a multiple sequence alignment reveals that many of the residues contributing to this newly identified allosteric pocket are highly conserved within the LigB family of the PCADSF. Point mutants of Phe103α and Ala18β, two residues located in the putative allosteric pocket, display altered rate enhancement as compared to LigAB-WT, providing support for the computationally identified allosteric binding site. Further investigation of this binding site may provide insight into the mechanism of this never before observed allosteric activation in extradiol dioxygenases.
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Affiliation(s)
| | - Abraham Ngu
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Erin Frances Cohn
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Joy Marie Cote
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Erika Anne Taylor
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA.
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Duarte M, Jauregui R, Vilchez-Vargas R, Junca H, Pieper DH. AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau118. [PMID: 25468931 PMCID: PMC4250580 DOI: 10.1093/database/bau118] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL:http://aromadeg.siona.helmholtz-hzi.de
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Affiliation(s)
- Márcia Duarte
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Ramiro Vilchez-Vargas
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Howard Junca
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI-Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany, Research Group Microbial Ecology, Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen. Carrera 5 No. 66A-35, Bogotá, Colombia and Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada-UMNG, Campus Cajicá, Bogotá DC, Colombia
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31
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Du X, Jing A, Hu X. A novel feature extraction scheme for prediction of protein-protein interaction sites. MOLECULAR BIOSYSTEMS 2014; 11:475-85. [PMID: 25413666 DOI: 10.1039/c4mb00625a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identifying protein-protein interaction (PPI) sites plays an important and challenging role in some topics of biology. Although many methods have been proposed, this problem is still far away to be solved. Here, a feature selection approach with an 11-sliding window and random forest algorithm is proposed, which is called DX-RF. This method has achieved an accuracy of 88.79%, recall of 82.09%, and precision of 85.76% with top-ranked 34 features on the Hetero test dataset and has 91.6% accuracy, 89.2% precision, 83.54% recall with top-ranked 25 features set on the Homo test dataset. Compared to other methods, the results indicate that the DX-RF method has a strong ability to select relevance features to get a higher performance. Moreover, in order to further understand protein interactions, feature analysis in this study is also performed.
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Affiliation(s)
- Xiuquan Du
- Key Laboratory of Intelligent Computing & Signal Processing, Ministry of Education, Anhui University, Anhui, China.
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32
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Balamurugan M, Vadivelu P, Palaniandavar M. Iron(iii) complexes of tripodal tetradentate 4N ligands as functional models for catechol dioxygenases: the electronic vs. steric effect on extradiol cleavage. Dalton Trans 2014; 43:14653-68. [DOI: 10.1039/c3dt52145a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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34
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Sugimoto K, Senda M, Kasai D, Fukuda M, Masai E, Senda T. Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6. PLoS One 2014; 9:e92249. [PMID: 24657997 PMCID: PMC3962378 DOI: 10.1371/journal.pone.0092249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/20/2014] [Indexed: 11/18/2022] Open
Abstract
DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.
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Affiliation(s)
- Keisuke Sugimoto
- Department of Materials Chemistry, Asahikawa National College of Technology, Asahikawa, Hokkaido, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
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35
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Fielding AJ, Lipscomb JD, Que L. A two-electron-shell game: intermediates of the extradiol-cleaving catechol dioxygenases. J Biol Inorg Chem 2014; 19:491-504. [PMID: 24615282 DOI: 10.1007/s00775-014-1122-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/13/2014] [Indexed: 11/29/2022]
Abstract
Extradiol-cleaving catechol dioxygenases function by binding both the organic substrate and O2 at a divalent metal center in the active site. They have proven to be a particularly versatile group of enzymes with which to study the O2 activation process. Here, recent studies of homoprotocatechuate 2,3-dioxygenase are summarized, showing how nature can utilize the enzyme structure and the properties of the metal and the substrate to select among many possible chemical paths to achieve both specificity and efficiency. Possible intermediates in the mechanism have been trapped by swapping active-site metals, introducing active-site amino acid substituted variants, and using substrates with different electron-donating capacities. Although each of these intermediates could form part of a viable reaction pathway, kinetic measurements significantly limit the likely candidates. Structural, kinetic, spectroscopic, and computational analyses of the various intermediates shed light on how catalytic efficiency can be achieved.
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Affiliation(s)
- Andrew J Fielding
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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36
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Sheykhi H, Safaei E. A proline-based aminophenol ligand: synthesis, iron complexation, magnetic, electronic and redox investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:915-920. [PMID: 24161856 DOI: 10.1016/j.saa.2013.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/25/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
A new proline-based aminophenol ligand was synthesized by a convenient procedure. The ligand was characterized by (1)H NMR, (13)C NMR and IR spectroscopies, elemental analysis and optical activity measurements. Mononuclear iron(III) complex (FeL(Pro)) of this ligand was synthesized and characterized by IR, UV-vis, ESI-MS, magnetic susceptibility studies and cyclic voltammetry techniques. The equilibrium formation constant of FeL(Pro) and the pure UV-vis spectral profile of the complex was determined by multivariate hard modeling method. The molecular structure of FeL(Pro) determined by ESI-MS consist of two aminophenolate ligands. The variation of magnetic susceptibility with temperature indicates paramagnetic iron(III) in the monomeric complex. FeL(Pro) complex undergo metal-centered reduction, and ligand-centered oxidation.
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Affiliation(s)
- Hamid Sheykhi
- Institute for Advanced Studies in Basic Sciences (IASBS), 45195 Zanjan, Iran
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37
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Sheykhi H, Safaei E. Cysteine and Methionine Derivatives of Aminophenol Ligands: Synthesis, Iron Complexation, Magnetic, Electronic and Redox Investigation. J CHIN CHEM SOC-TAIP 2014. [DOI: 10.1002/jccs.201300374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Sankaralingam M, Saravanan N, Anitha N, Suresh E, Palaniandavar M. Biomimetic iron(iii) complexes of facially and meridionally coordinating tridentate 3N ligands: tuning of regioselective extradiol dioxygenase activity in organized assemblies. Dalton Trans 2014; 43:6828-41. [DOI: 10.1039/c3dt52350k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Barry KP, Taylor EA. Characterizing the promiscuity of LigAB, a lignin catabolite degrading extradiol dioxygenase from Sphingomonas paucimobilis SYK-6. Biochemistry 2013; 52:6724-36. [PMID: 23977959 DOI: 10.1021/bi400665t] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LigAB from Sphingomonas paucimobilis SYK-6 is the only structurally characterized dioxygenase of the largely uncharacterized superfamily of Type II extradiol dioxygenases (EDO). This enzyme catalyzes the oxidative ring-opening of protocatechuate (3,4-dihydroxybenzoic acid or PCA) in a pathway allowing the degradation of lignin derived aromatic compounds (LDACs). LigAB has also been shown to utilize two other LDACs from the same metabolic pathway as substrates, gallate, and 3-O-methyl gallate; however, kcat/KM had not been reported for any of these compounds. In order to assess the catalytic efficiency and get insights into the observed promiscuity of this enzyme, steady-state kinetic analyses were performed for LigAB with these and a library of related compounds. The dioxygenation of PCA by LigAB was highly efficient, with a kcat of 51 s(-1) and a kcat/KM of 4.26 × 10(6) M(-1)s(-1). LigAB demonstrated the ability to use a variety of catecholic molecules as substrates beyond the previously identified gallate and 3-O-methyl gallate, including 3,4-dihydroxybenzamide, homoprotocatechuate, catechol, and 3,4-dihydroxybenzonitrile. Interestingly, 3,4-dihydroxybenzamide (DHBAm) behaves in a manner similar to that of the preferred benzoic acid substrates, with a kcat/Km value only ∼4-fold lower than that for gallate and ∼10-fold higher than that for 3-O-methyl gallate. All of these most active substrates demonstrate mechanistic inactivation of LigAB. Additionally, DHBAm exhibits potent product inhibition that leads to an inactive enzyme, being more highly deactivating at lower substrate concentration, a phenomena that, to our knowledge, has not been reported for another dioxygenase substrate/product pair. These results provide valuable catalytic insight into the reactions catalyzed by LigAB and make it the first Type II EDO that is fully characterized both structurally and kinetically.
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Affiliation(s)
- Kevin P Barry
- Department of Chemistry, Wesleyan University , 52 Lawn Avenue, Middletown, Connecticut 06459, United States
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40
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Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity. Appl Microbiol Biotechnol 2013; 98:1165-74. [DOI: 10.1007/s00253-013-4961-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 01/09/2023]
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41
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Chatterjee S, Sheet D, Paine TK. Catalytic and regiospecific extradiol cleavage of catechol by a biomimetic iron complex. Chem Commun (Camb) 2013; 49:10251-3. [DOI: 10.1039/c3cc44124e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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42
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Li DF, Zhang JY, Hou YJ, Liu L, Hu Y, Liu SJ, Wang DC, Liu W. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:32-43. [PMID: 23275161 DOI: 10.1107/s0907444912042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/08/2012] [Indexed: 11/10/2022]
Abstract
Dioxygen activation by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Here, crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported. The Fe-ligand binding schemes observed in these structures revealed some common geometrical characteristics that are shared by the published structures of extradiol dioxygenases, suggesting that enzymes that catalyse the oxidation of noncatecholic compounds are very likely to utilize a similar strategy for dioxygen activation and the fission of aromatic rings as the canonical mechanism. The Fe-ligation arrangement, however, is strikingly enantiomeric to that of all other 2-His-1-carboxylate enzymes apart from protocatechuate 4,5-dioxygenase. This structural variance leads to the generation of an uncommon O(-)-Fe(2+)-O(-) species prior to O(2) binding, which probably forms the structural basis on which APD distinguishes its specific substrate and inhibitor, which share an analogous molecular structure.
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Affiliation(s)
- De Feng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
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Li DF, Zhang JY, Hou Y, Liu L, Liu SJ, Liu W. Crystallization and preliminary crystallographic analysis of 2-aminophenol 1,6-dioxygenase complexed with substrate and with an inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1337-40. [PMID: 23143244 PMCID: PMC3515376 DOI: 10.1107/s1744309112038705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/10/2012] [Indexed: 11/10/2022]
Abstract
Dioxygen activation implemented by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Extradiol dioxygenase is the archetypal member of this superfamily and catalyzes the oxygenolytic ring opening of catechol analogues. Here, the crystallization and preliminary X-ray analysis of 2-aminophenol 1,6-dioxygenase, an enzyme representing a minor subset of extradiol dioxygenases that catalyze the fission of 2-aminophenol rather than catecholic compounds, is reported. Crystals of the holoenzyme with FeII and of complexes with the substrate 2-aminophenol and the suicide inhibitor 4-nitrocatechol were grown using the cocrystallization method under the same conditions as used for the crystallization of the apoenzyme. The crystals belonged to space group C2 and diffracted to 2.3-2.7 Å resolution; the crystal that diffracted to the highest resolution had unit-cell parameters a=270.24, b=48.39, c=108.55 Å, β=109.57°. All X-ray data sets collected from diffraction-quality crystals were suitable for structure determination.
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Affiliation(s)
- De-Feng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jia-Yue Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yanjie Hou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Lei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Wei Liu
- Institute of Immunology, The Third Military Medical University, Chongqing 400038, People’s Republic of China
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Kovaleva EG, Lipscomb JD. Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Biochemistry 2012; 51:8755-63. [PMID: 23066739 DOI: 10.1021/bi301115c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homoprotocatechuate 2,3-dioxygenase (FeHPCD) utilizes an active site Fe(II) to activate O(2) in a reaction cycle that ultimately results in aromatic ring cleavage. Here, the roles of the conserved active site residue Tyr257 are investigated by solving the X-ray crystal structures of the Tyr257-to-Phe variant (Y257F) in complex with the substrate homoprotocatechuate (HPCA) and the alternative substrate 4-nitrocatechol (4NC). These are compared with structures of the analogous wild type enzyme complexes. In addition, the oxy intermediate of the reaction cycle of Y257F-4NC + O(2) is formed in crystallo and structurally characterized. It is shown that both substrates adopt a previously unrecognized, slightly nonplanar, strained conformation affecting the geometries of all aromatic ring carbons when bound in the FeHPCD active site. This global deviation from planarity is not observed for the Y257F variant. In the Y257F-4NC-oxy complex, the O(2) is bound side-on to the Fe(II), while the 4NC is chelated in two adjacent sites. The ring of the 4NC in this complex is planar, in contrast to the equivalent FeHPCD intermediate, which exhibits substantial local distortion of the substrate hydroxyl moiety (C2-O(-)) that is hydrogen bonded to Tyr257. We propose that Tyr257 induces the global and local distortions of the substrate ring in two different ways. First, van der Waals conflict between the Tyr257-OH substituent and the substrate C2 carbon is relieved by adopting the globally strained structure. Second, Tyr257 stabilizes the localized out-of-plane position of the C2-O(-) by forming a stronger hydrogen bond as the distortion increases. Both types of distortions favor transfer of one electron out of the substrate to form a reactive semiquinone radical. Then, the localized distortion at substrate C2 promotes formation of the key alkylperoxo intermediate of the cycle resulting from oxygen attack on the activated substrate at C2, which becomes sp(3) hybridized. The inability of Y257F to promote the distorted substrate structure may explain the observed 100-fold decrease in the rates of the O(2) activation and insertion steps of the reaction.
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Affiliation(s)
- Elena G Kovaleva
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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Mbughuni MM, Meier KK, Münck E, Lipscomb JD. Substrate-mediated oxygen activation by homoprotocatechuate 2,3-dioxygenase: intermediates formed by a tyrosine 257 variant. Biochemistry 2012; 51:8743-54. [PMID: 23066705 DOI: 10.1021/bi301114x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homoprotocatechuate (HPCA; 3,4-dihydroxyphenylacetate or 4-carboxymethyl catechol) and O(2) bind in adjacent ligand sites of the active site Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD). We have proposed that electron transfer from the chelated aromatic substrate through the Fe(II) to O(2) gives both substrates radical character. This would promote reaction between the substrates to form an alkylperoxo intermediate as the first step in aromatic ring cleavage. Several active site amino acids are thought to promote these reactions through acid/base chemistry, hydrogen bonding, and electrostatic interactions. Here the role of Tyr257 is explored by using the Tyr257Phe (Y257F) variant, which decreases k(cat) by about 75%. The crystal structure of the FeHPCD-HPCA complex has shown that Tyr257 hydrogen bonds to the deprotonated C2-hydroxyl of HPCA. Stopped-flow studies show that at least two reaction intermediates, termed Y257F(Int1)(HPCA) and Y257F(Int2)(HPCA), accumulate during the Y257F-HPCA + O(2) reaction prior to formation of the ring-cleaved product. Y257F(Int1)(HPCA) is colorless and is formed as O(2) binds reversibly to the HPCA−enzyme complex. Y257F(Int2)(HPCA) forms spontaneously from Y257F(Int1)(HPCA) and displays a chromophore at 425 nm (ε(425) = 10 500 M(−1) cm(−1)). Mössbauer spectra of the intermediates trapped by rapid freeze quench show that both intermediates contain Fe(II). The lack of a chromophore characteristic of a quinone or semiquinone form of HPCA, the presence of Fe(II), and the low O(2) affinity suggest that Y257F(Int1)(HPCA) is an HPCA-Fe(II)-O(2) complex with little electron delocalization onto the O(2). In contrast, the intense spectrum of Y257F(Int2)(HPCA) suggests the intermediate is most likely an HPCA quinone-Fe(II)-(hydro)peroxo species. Steady-state and transient kinetic analyses show that steps of the catalytic cycle are slowed by as much as 100-fold by the mutation. These effects can be rationalized by a failure of Y257F to facilitate the observed distortion of the bound HPCA that is proposed to promote transfer of one electron to O(2).
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Affiliation(s)
- Michael M Mbughuni
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Visvaganesan K, Ramachitra S, Palaniandavar M. Functional models for enzyme–substrate adducts of catechol dioxygenase enzymes: The Lewis basicity of facially coordinating tridentate phenolate ligands tunes the rate of dioxygenation and product selectivity. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Bugg TDH, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 2011; 28:1883-96. [PMID: 21918777 DOI: 10.1039/c1np00042j] [Citation(s) in RCA: 457] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.
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PALANIANDAVAR MALLAYAN, VISVAGANESAN KUSALENDIRAN. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of N-alkyl substitution on regioselectivity and reaction rate. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0110-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kolvenbach BA, Lenz M, Benndorf D, Rapp E, Fousek J, Vlcek C, Schäffer A, Gabriel FLP, Kohler HPE, Corvini PFX. Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3. AMB Express 2011; 1:8. [PMID: 21906340 PMCID: PMC3222310 DOI: 10.1186/2191-0855-1-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/27/2011] [Indexed: 11/11/2022] Open
Abstract
Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1 mg of the purified enzyme with unsubstituted hydroquinone was 6.1 μmol per minute, the apparent Km 2.2 μM. ICP-MS analysis revealed an iron content of 1.4 moles per mole enzyme. The enzyme lost activity upon exposure to oxygen, but could be reactivated by Fe(II) in presence of ascorbate. SDS-PAGE analysis of the purified enzyme yielded two bands of an apparent size of 38 kDa and 19 kDa, respectively. Data from MALDI-TOF analyses of peptides of the respective bands matched with the deduced amino acid sequences of two neighboring open reading frames found in genomic DNA of Sphingomonas sp strain TTNP3. The deduced amino acid sequences showed 62% and 47% identity to the large and small subunit of hydroquinone dioxygenase from Pseudomonas fluorescens strain ACB, respectively. This heterotetrameric enzyme is the first of its kind found in a strain of the genus Sphingomonas sensu latu.
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Safaei E, Sheykhi H, Wojtczak A, Jagličić Z, Kozakiewicz A. Synthesis and characterization of an iron(III) complex of glycine derivative of bis(phenol)amine ligand in relevance to catechol dioxygenase active site. Polyhedron 2011. [DOI: 10.1016/j.poly.2011.01.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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