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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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2
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Ringenbach S, Yoza R, Jones PA, Du M, Klugh KL, Peterson LW, Colabroy KL. Discovery and characterization of l-DOPA 2,3-dioxygenase from Streptomyces hygroscopicus jingganensis. Arch Biochem Biophys 2024; 755:109967. [PMID: 38556098 DOI: 10.1016/j.abb.2024.109967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
The largest natural reservoir of untapped carbon can be found in the cell-wall strengthening, plant woody-tissue polymer, lignin - a polymer of catechols or 1,2-dihydroxybenzene monomers. The catecholic carbon of lignin could be valorized into feedstocks and natural products by way of catabolic and biosynthetic transformations, including the oxygen-dependent cleavage reaction of extradiol dioxygenase (EDX) enzymes. The EDX l-DOPA 2,3-dioxygenase was first discovered as part of a biosynthetic gene cluster to the natural product antibiotic, lincomycin, and also contributes to the biosyntheses of anthramycin, sibiromycin, tomaymycin, porothramycin and hormaomycin. Using these l-DOPA 2,3-dioxygenases as a starting point, we searched sequence space in order to identify new sources of dioxygenase driven natural product diversity. A "vicinal-oxygen-chelate (VOC) family protein" from Streptomyces hygroscopicus jingganensis was identified using bioinformatic methods and biochemically investigated for dioxygenase activity against a suite of natural and synthetic catechols. Steady-state oxygen consumption assays were used to screen and identify substrates, and a steady-state kinetic model of oxygen consumption was developed to evaluate activity of the S. hygroscopicus jingganensis VOC-family-protein with respect to activity of l-DOPA 2,3-dioxygenases from Streptomyces lincolnensis and Streptomyces sclerotialus. Lastly, these data were integrated with steady-state kinetic methods to observe the formation of the EDX cleavage product with UV-visible spectroscopy. The genomic context and enzymatic activity of the S. hygroscopicus jingganensis VOC family protein are consistent with a l-DOPA 2,3-dioxygenase contained within a cryptic biosynthetic pathway.
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Affiliation(s)
- Sara Ringenbach
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Riri Yoza
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Paige A Jones
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, TN, 38112, USA
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew St, Allentown, PA, 18104, USA.
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3
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Li M, Cao L, Liu D, Su T, Cheng W, Li G, Ma T. Efficient bio-remediation of multiple aromatic hydrocarbons using different types of thermotolerant, ring-cleaving dioxygenases derived from Aeribacillus pallidus HB-1. BIORESOURCE TECHNOLOGY 2024; 398:130472. [PMID: 38387841 DOI: 10.1016/j.biortech.2024.130472] [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: 11/06/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
As toxic contaminants, aromatic compounds are widespread in most environmental matrices, and bioenzymatic catalysis plays a critical role in the degradation of xenobiotics. Here, a thermophillic aromatic hydrocarbon degrader Aeribacillus pallidus HB-1 was found. Bioinformatic analysis of the HB-1 genome revealed two ring-cleaving extradiol dioxygenases (EDOs), among which, EDO-0418 was assigned to a new subfamily of type I.1 EDOs and exhibited a broad substrate specificity, particularly towards biarylic substrate. Both EDOs exhibited optimal activities at elevated temperatures (55 and 65 °C, respectively) and showed remarkable thermostability, pH stability, metal ion resistance and tolerance to chemical reagents. Most importantly, simulated wastewater bioreactor experiments demonstrated efficient and uniform degradation performance of mixed aromatic substrates under harsh environments by the two enzymes combined for potential industrial applications. The unveiling of two thermostable dioxygenases with broad substrate specificities and stress tolerance provides a novel approach for highly efficient environmental bioremediation using composite enzyme systems.
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Affiliation(s)
- Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lu Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Dakun Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tianqi Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wei Cheng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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4
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Ehinger FJ, Niehs SP, Dose B, Dell M, Krabbe J, Pidot SJ, Stinear TP, Scherlach K, Ross C, Lackner G, Hertweck C. Analysis of Rhizonin Biosynthesis Reveals Origin of Pharmacophoric Furylalanine Moieties in Diverse Cyclopeptides. Angew Chem Int Ed Engl 2023; 62:e202308540. [PMID: 37650335 DOI: 10.1002/anie.202308540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023]
Abstract
Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3-furylalanine (Fua) residues, which also occur in pharmaceutically relevant cyclopeptides of the endolide and bingchamide families. The biosynthesis and incorporation of Fua by non-ribosomal peptide synthetases (NRPS), however, has remained elusive. By genome sequencing and gene inactivation we elucidated the gene cluster responsible for rhizonin biosynthesis. A suite of isotope labeling experiments identified tyrosine and l-DOPA as Fua precursors and provided the first mechanistic insight. Bioinformatics, mutational analysis and heterologous reconstitution identified dioxygenase RhzB as necessary and sufficient for Fua formation. RhzB is a novel type of heme-dependent aromatic oxygenases (HDAO) that enabled the discovery of the bingchamide biosynthesis gene cluster through genome mining.
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Affiliation(s)
- Friedrich J Ehinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Claudia Ross
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Gerald Lackner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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5
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Rios-Miguel AB, Smith GJ, Cremers G, van Alen T, Jetten MS, Op den Camp HJ, Welte CU. Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates. WATER RESEARCH X 2022; 16:100152. [PMID: 36042984 PMCID: PMC9420511 DOI: 10.1016/j.wroa.2022.100152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.
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Key Words
- 4-AP, 4-aminophenol
- APAP, N-acetyl-p-aminophenol or paracetamol
- Amidase evolution
- Deaminase
- Dioxygenase
- GAC, granular activated carbon
- HGT, horizontal gene transfer
- HQ, hydroquinone
- HRT, hydraulic retention time
- MAG, metagenome-assembled genome
- MBR, membrane bioreactor
- Metagenomics
- Mobile genetic elements
- Pfast, Pseudomonas sp. isolate growing fast on APAP as sole carbon source
- Pseudomonas
- Pslow, Pseudomonas sp. isolate growing slow on APAP as sole carbon source
- SRT, solid retention time
- TPM, transcripts per million
- WWTP, wastewater treatment plant
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Affiliation(s)
- Ana B. Rios-Miguel
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Garrett J. Smith
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Huub J.M. Op den Camp
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
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6
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Wang YS, Zheng W, Jiang N, Jin YX, Meng ZK, Sun MX, Zong YL, Xu T, Zhu J, Tan RX. Alteration of the Catalytic Reaction Trajectory of a Vicinal Oxygen Chelate Enzyme by Directed Evolution. Angew Chem Int Ed Engl 2022; 61:e202201321. [DOI: 10.1002/anie.202201321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yi Shuang Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Wan Zheng
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Nan Jiang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Yun Xia Jin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Zi Kang Meng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Meng Xin Sun
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yu Liang Zong
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Tong Xu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules School of Life Sciences Nanjing University Nanjing 210023 China
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7
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Wang YS, Zheng W, Jiang N, Jin YX, Meng ZK, Sun MX, Zong YL, Xu T, Zhu J, Tan RX. Alteration of the Catalytic Reaction Trajectory of a Vicinal Oxygen Chelate Enzyme by Directed Evolution. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi Shuang Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Wan Zheng
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Nan Jiang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Yun Xia Jin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Zi Kang Meng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Meng Xin Sun
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yu Liang Zong
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Tong Xu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules School of Life Sciences Nanjing University Nanjing 210023 China
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8
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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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9
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Chang CW, Lin YH, Tsai CH, Kulandaivel S, Yeh YC. Sequential detection of dopamine and L-DOPA by a 2,3-dopa-dioxygenase from Streptomyces sclerotialus. Anal Chim Acta 2022; 1202:339641. [DOI: 10.1016/j.aca.2022.339641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
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10
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Zhang X, Huang Z, Wang D, Zhang Y, Eser BE, Gu Z, Dai R, Gao R, Guo Z. A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126860. [PMID: 34399224 DOI: 10.1016/j.jhazmat.2021.126860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/22/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Extradiol dioxygenases (EDOs) catalyze the meta cleavage of catechol into 2-hydroxymuconaldehyde, a critical step in the degradation of aromatic compounds in the environment. In the present work, a novel thermophilic extradiol dioxygenase from Thermomonospora curvata DSM43183 was cloned, expressed, and characterized by phylogenetic and biochemical analyses. This enzyme exhibited excellent thermo-tolerance, displaying optimal activity at 50 °C, remaining >40% activity at 70 °C. Structural modeling and molecular docking demonstrated that both active center and pocket-construction loops locate at the C-terminal domain. Site-specific mutants D285A, H205V, F301V based on a rational design were obtained to widen the entrance of substrates; resulting in significantly improved catalytic performance for all the 3 mutants. Compared to the wild-type, the mutant D285A showed remarkably improved activities with respect to the 3,4-dihydroxyphenylacetic acid, catechol, and 3-chlorocatechol, by 17.7, 6.9, and 3.7-fold, respectively. The results thus verified the effectiveness of modeling guided design; and confirmed that the C-terminal loop structure indeed plays a decisive role in determining catalytic ring-opening efficiency and substrate specificity of the enzyme. This study provided a novel thermostable dioxygenase with a broad substrate promiscuity for detoxifying environmental pollutants and provided a new thinking for further enzyme engineering of EDOs.
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Affiliation(s)
- Xiaowen Zhang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China; Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Dan Wang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Yan Zhang
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Rongrong Dai
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China.
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
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11
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Goldberg AM, Robinson MK, Starr ES, Marasco RN, Alana AC, Cochrane CS, Klugh KL, Strzeminski DJ, Du M, Colabroy KL, Peterson LW. L-DOPA Dioxygenase Activity on 6-Substituted Dopamine Analogues. Biochemistry 2021; 60:2492-2507. [PMID: 34324302 DOI: 10.1021/acs.biochem.1c00310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioxygenase enzymes are essential protein catalysts for the breakdown of catecholic rings, structural components of plant woody tissue. This powerful chemistry is used in nature to make antibiotics and other bioactive materials or degrade plant material, but we have a limited understanding of the breadth and depth of substrate space for these potent catalysts. Here we report steady-state and pre-steady-state kinetic analysis of dopamine derivatives substituted at the 6-position as substrates of L-DOPA dioxygenase, and an analysis of that activity as a function of the electron-withdrawing nature of the substituent. Steady-state and pre-steady-state kinetic data demonstrate the dopamines are impaired in binding and catalysis with respect to the cosubstrate molecular oxygen, which likely afforded spectroscopic observation of an early reaction intermediate, the semiquinone of dopamine. The reaction pathway of dopamine in the pre-steady state is consistent with a nonproductive mode of binding of oxygen at the active site. Despite these limitations, L-DOPA dioxygenase is capable of binding all of the dopamine derivatives and catalyzing multiple turnovers of ring cleavage for dopamine, 6-bromodopamine, 6-carboxydopamine, and 6-cyanodopamine. 6-Nitrodopamine was a single-turnover substrate. The variety of substrates accepted by the enzyme is consistent with an interplay of factors, including the capacity of the active site to bind large, negatively charged groups at the 6-position and the overall oxidizability of each catecholamine, and is indicative of the utility of extradiol cleavage in semisynthetic and bioremediation applications.
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Affiliation(s)
- Alexander M Goldberg
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Miranda K Robinson
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Erykah S Starr
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Ryan N Marasco
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Alexa C Alana
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - C Skyler Cochrane
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - David J Strzeminski
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
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12
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Wang Y, Davis I, Shin I, Xu H, Liu A. Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase. J Am Chem Soc 2021; 143:4680-4693. [PMID: 33734681 DOI: 10.1021/jacs.1c00175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The heme-dependent l-tyrosine hydroxylases (TyrHs) in natural product biosynthesis constitute a new enzyme family in contrast to the nonheme iron enzymes for DOPA production. A representative TyrH exhibits dual reactivity of C-H and C-F bond cleavage when challenged with 3-fluoro-l-tyrosine (3-F-Tyr) as a substrate. However, little is known about how the enzyme mediates two distinct reactions. Herein, a new TyrH from the thermophilic bacterium Streptomyces sclerotialus (SsTyrH) was functionally and structurally characterized. A de novo crystal structure of the enzyme-substrate complex at 1.89-Å resolution provides the first comprehensive structural study of this hydroxylase. The binding conformation of l-tyrosine indicates that C-H bond hydroxylation is initiated by electron transfer. Mutagenesis studies confirmed that an active site histidine, His88, participates in catalysis. We also obtained a 1.68-Å resolution crystal structure in complex with the monofluorinated substrate, 3-F-Tyr, which shows one binding conformation but two orientations of the fluorine atom with a ratio of 7:3, revealing that the primary factor of product distribution is the substrate orientation. During in crystallo reaction, a ferric-hydroperoxo intermediate (compound 0, Fe3+-OOH) was observed with 3-F-Tyr as a substrate based on characteristic spectroscopic features. We determined the crystal structure of this compound 0-type intermediate and refined it to 1.58-Å resolution. Collectively, this study provided the first molecular details of the heme-dependent TyrH and determined the primary factor that dictates the partitioning between the dual reactivities of C-H and C-F bond activation.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Hui Xu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, Texas 78249, United States
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13
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Colabroy KL, Horwitz AD, Basciano VR, Fu Y, Travitz KM, Robinson MK, Shimanski BA, Hoffmann TW. A New Way of Belonging: Active-Site Investigation of L-DOPA Dioxygenase, a VOC Family Enzyme from Lincomycin Biosynthesis. Biochemistry 2019; 58:4794-4798. [DOI: 10.1021/acs.biochem.9b00456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keri L. Colabroy
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Alyssa D. Horwitz
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Victoria R. Basciano
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Yizhi Fu
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Kelly M. Travitz
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Miranda K. Robinson
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Brittany A. Shimanski
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Thomas W. Hoffmann
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
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