1
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The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. Nat Ecol Evol 2022; 6:1132-1144. [PMID: 35773344 DOI: 10.1038/s41559-022-01795-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/11/2022] [Indexed: 01/04/2023]
Abstract
The coral reef microbiome is central to reef health and resilience. Competitive interactions between opportunistic coral pathogens and other commensal microbes affect the health of coral. Despite great advances over the years in sequencing-based microbial profiling of healthy and diseased coral, the molecular mechanism underlying colonization competition has been much less explored. In this study, by examining the culturable bacteria inhabiting the gastric cavity of healthy Galaxea fascicularis, a scleractinian coral, we found that temperate phages played a major role in mediating colonization competition in the coral microbiota. Specifically, the non-toxigenic Vibrio sp. inhabiting the healthy coral had a much higher colonization capacity than the coral pathogen Vibrio coralliilyticus, yet this advantage was diminished by the latter killing the former. Pathogen-encoded LodAB, which produces hydrogen peroxide, triggers the lytic cycle of prophage in the non-toxicogenic Vibrio sp. Importantly, V. coralliilyticus could outcompete other coral symbiotic bacteria (for example, Endozoicomonas sp.) through LodAB-dependent prophage induction. Overall, we reveal that LodAB can be used by pathogens as an important weapon to gain a competitive advantage over lysogenic competitors when colonizing corals.
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2
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Oozeki T, Nakai T, Kozakai K, Okamoto K, Kuroda S, Kobayashi K, Tanizawa K, Okajima T. Functional and structural characterization of a flavoprotein monooxygenase essential for biogenesis of tryptophylquinone cofactor. Nat Commun 2021; 12:933. [PMID: 33568660 PMCID: PMC7876137 DOI: 10.1038/s41467-021-21200-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/14/2021] [Indexed: 01/07/2023] Open
Abstract
Bioconversion of peptidyl amino acids into enzyme cofactors is an important post-translational modification. Here, we report a flavoprotein, essential for biosynthesis of a protein-derived quinone cofactor, cysteine tryptophylquinone, contained in a widely distributed bacterial enzyme, quinohemoprotein amine dehydrogenase. The purified flavoprotein catalyzes the single-turnover dihydroxylation of the tryptophylquinone-precursor, tryptophan, in the protein substrate containing triple intra-peptidyl crosslinks that are pre-formed by a radical S-adenosylmethionine enzyme within the ternary complex of these proteins. Crystal structure of the peptidyl tryptophan dihydroxylase reveals a large pocket that may dock the protein substrate with the bound flavin adenine dinucleotide situated close to the precursor tryptophan. Based on the enzyme-protein substrate docking model, we propose a chemical reaction mechanism of peptidyl tryptophan dihydroxylation catalyzed by the flavoprotein monooxygenase. The diversity of the tryptophylquinone-generating systems suggests convergent evolution of the peptidyl tryptophan-derived cofactors in different proteins.
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Affiliation(s)
- Toshinori Oozeki
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Tadashi Nakai
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan ,grid.417545.60000 0001 0665 883XFaculty of Life Sciences, Hiroshima Institute of Technology, Hiroshima, Japan
| | - Kazuki Kozakai
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Kazuki Okamoto
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Shun’ichi Kuroda
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Kazuo Kobayashi
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Katsuyuki Tanizawa
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Toshihide Okajima
- grid.136593.b0000 0004 0373 3971Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
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3
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Draft Genome Sequence of Shewanella sp. Strain ISO12, a Candidate Probiotic Isolated from the Intestine of Fundulus heteroclitus. Microbiol Resour Announc 2020; 9:9/22/e00399-20. [PMID: 32467277 PMCID: PMC7256264 DOI: 10.1128/mra.00399-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The genome of Shewanella sp. strain ISO12, which was isolated from the intestine of wild-caught Fundulus heteroclitus, was sequenced and is reported here. Bioinformatic analysis revealed genes encoding the bacteriocin marinocine and those potentially associated with probiotic activity. The genome sequence will assist in further identifying probiotic and other antibacterial processes. The genome of Shewanella sp. strain ISO12, which was isolated from the intestine of wild-caught Fundulus heteroclitus, was sequenced and is reported here. Bioinformatic analysis revealed genes encoding the bacteriocin marinocine and those potentially associated with probiotic activity. The genome sequence will assist in further identifying probiotic and other antibacterial processes.
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4
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Fisher B, Snodgrass HM, Jones KA, Andorfer MC, Lewis JC. Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS CENTRAL SCIENCE 2019; 5:1844-1856. [PMID: 31807686 PMCID: PMC6891866 DOI: 10.1021/acscentsci.9b00835] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 05/19/2023]
Abstract
Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.
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Affiliation(s)
- Brian
F. Fisher
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krysten A. Jones
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- E-mail:
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5
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Mamounis KJ, Avalos D, Yukl ET, Davidson VL. Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase. J Biol Chem 2019; 294:17463-17470. [PMID: 31615898 DOI: 10.1074/jbc.ra119.011255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/10/2019] [Indexed: 11/06/2022] Open
Abstract
PlGoxA from Pseudoalteromonas luteoviolacea is a glycine oxidase that utilizes a protein-derived cysteine tryptophylquinone (CTQ) cofactor. A notable feature of its catalytic mechanism is that it forms a stable product-reduced CTQ adduct that is not hydrolyzed in the absence of O2 Asp-678 resides near the quinone moiety of PlGoxA, and an Asp is structurally conserved in this position in all tryptophylquinone enzymes. In those other enzymes, mutation of that Asp results in no or negligible CTQ formation. In this study, mutation of Asp-678 in PlGoxA did not abolish CTQ formation. This allowed, for the first time, studying the role of this residue in catalysis. D678A and D678N substitutions yielded enzyme variants with CTQ, which did not react with glycine, although glycine was present in the crystal structures in the active site. D678E PlGoxA was active but exhibited a much slower k cat This mutation altered the kinetic mechanism of the reductive half-reaction such that one could observe a previously undetected reactive intermediate, an initial substrate-oxidized CTQ adduct, which converted to the product-reduced CTQ adduct. These results indicate that Asp-678 is involved in the initial deprotonation of the amino group of glycine, enabling nucleophilic attack of CTQ, as well as the deprotonation of the substrate-oxidized CTQ adduct, which is coupled to CTQ reduction. The structures also suggest that Asp-678 is acting as a proton relay that directs these protons to a water channel that connects the active sites on the subunits of this homotetrameric enzyme.
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Affiliation(s)
- Kyle J Mamounis
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32827
| | - Dante Avalos
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Erik T Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32827
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6
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Characterization of PlGoxB, a flavoprotein required for cysteine tryptophylquinone biosynthesis in glycine oxidase from Pseudoalteromonas luteoviolacea. Arch Biochem Biophys 2019; 674:108110. [PMID: 31541619 DOI: 10.1016/j.abb.2019.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/23/2022]
Abstract
LodA-like proteins are oxidases with a protein-derived cysteine tryptophylquinone (CTQ) prosthetic group. In Pseudoalteromonas luteoviolacea glycine oxidase (PlGoxA), CTQ biosynthesis requires post-translational modifications catalyzed by a modifying enzyme encoded by PlgoxB. The PlGoxB protein was expressed and shown to possess a flavin cofactor. PlGoxB was unstable in solution as it readily lost the flavin and precipitated. PlGoxB precipitation was significantly reduced by incubation with either excess FAD or an equal concentration of prePlGoxA, the precursor protein that is its substrate. In contrast, the mature CTQ-bearing PlGoxA had no stabilizing effect. A homology model of PlGoxB was generated using the structure of Alkylhalidase CmIS. The FAD-binding site of PlGoxB in the model was nearly identical to that of the template structure. The bound FAD in PlGoxB had significant solvent exposure, consistent with the observed tendency to lose FAD. This also suggested that interaction of prePlGoxA with PlGoxB at the exposed FAD-binding site could prevent the observed loss of FAD and subsequent precipitation of PlGoxB. A docking model of the putative PlGoxB-prePlGoxA complex was consistent with these hypotheses. The experimental results and computational analysis implicate structural features of PlGoxB that contribute to its stability and function.
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7
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Asano Y, Yasukawa K. Identification and development of amino acid oxidases. Curr Opin Chem Biol 2019; 49:76-83. [DOI: 10.1016/j.cbpa.2018.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 12/23/2022]
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8
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Yu Z, Yang Y, Wang Y, Yin J, Qiu J. Reactive oxygen species-scavenging system is involved in l-amino acid oxidase accumulation in Pseudoalteromonas sp. B3. 3 Biotech 2017; 7:326. [PMID: 28955623 DOI: 10.1007/s13205-017-0976-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/12/2017] [Indexed: 11/26/2022] Open
Abstract
To date, the mechanisms underlying the flavoprotein l-amino acid oxidase (LAAO) accumulation in cells remain unclear. In this study, using LAAO-producer Pseudoalteromonas spp. as model organisms, we found that the cell biomass is negatively associated with LAAO accumulation, whereas the LAAO accumulation is positively associated with the reactive oxygen species (ROS)-scavenging capability. The expression levels of ROS-scavenging-associated genes were up-regulated with LAAO accumulation in Pseudoalteromonas cells, which is presumably due to the requirement for the removal of LAAO-induced ROS. Exogenous H2O2 exposure experiment supported that the ROS-scavenging system is associated with LAAO accumulation in Pseudoalteromonas. All these observations indicate that ROS-scavenging capacity determines LAAO accumulation in bacterial cells. Our results shed a light on understanding the mechanism underlying controlling and adapting to LAAO accumulation in Pseudoalteromonas. Besides, our findings are critical to the improvement of heterologous expression of active LAAO in the future.
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Affiliation(s)
- Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Yanyan Yang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Yangsheng Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Juanping Qiu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
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9
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Williamson HR, Sehanobish E, Shiller AM, Sanchez-Amat A, Davidson VL. Roles of Copper and a Conserved Aspartic Acid in the Autocatalytic Hydroxylation of a Specific Tryptophan Residue during Cysteine Tryptophylquinone Biogenesis. Biochemistry 2017; 56:997-1004. [PMID: 28140566 DOI: 10.1021/acs.biochem.6b01137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first posttranslational modification step in the biosynthesis of the tryptophan-derived quinone cofactors is the autocatalytic hydroxylation of a specific Trp residue at position C-7 on the indole side chain. Subsequent modifications are catalyzed by modifying enzymes, but the mechanism by which this first step occurs is unknown. LodA possesses a cysteine tryptophylquinone (CTQ) cofactor. Metal analysis as well as spectroscopic and kinetic studies of the mature and precursor forms of a D512A LodA variant provides evidence that copper is required for the initial hydroxylation of the precursor protein and that if alternative metals are bound, the modification does not occur and the precursor is unstable. It is shown that the mature native LodA also contains loosely bound copper, which affects the visible absorbance spectrum and quenches the fluorescence spectrum that is attributed to the mature CTQ cofactor. When copper is removed, the fluorescence appears, and when it is added back to the protein, the fluorescence is quenched, indicating that copper reversibly binds in the proximity of CTQ. Removal of copper does not diminish the enzymatic activity of LodA. This distinguishes LodA from enzymes with protein-derived tyrosylquinone cofactors in which copper is present near the cofactor and is absolutely required for activity. Mechanisms are proposed for the role of copper in the hydroxylation of the unactivated Trp side chain. These results demonstrate that the reason that the highly conserved Asp512 is critical for LodA, and possibly all tryptophylquinone enzymes, is not because it is required for catalysis but because it is necessary for CTQ biosynthesis, more specifically to facilitate the initial copper-dependent hydroxylation of a specific Trp residue.
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Affiliation(s)
- Heather R Williamson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Alan M Shiller
- Division of Marine Science, The University of Southern Mississippi, Stennis Space Center , Mississippi 39529, United States
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia , Murcia 30100, Spain
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
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10
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Sehanobish E, Williamson HR, Davidson VL. Roles of Conserved Residues of the Glycine Oxidase GoxA in Controlling Activity, Cooperativity, Subunit Composition, and Cysteine Tryptophylquinone Biosynthesis. J Biol Chem 2016; 291:23199-23207. [PMID: 27637328 DOI: 10.1074/jbc.m116.741835] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/06/2022] Open
Abstract
GoxA is a glycine oxidase that possesses a cysteine tryptophylquinone (CTQ) cofactor that is formed by posttranslational modifications that are catalyzed by a modifying enzyme GoxB. It is the second known tryptophylquinone enzyme to function as an oxidase, the other being the lysine ϵ-oxidase, LodA. All other enzymes containing CTQ or tryptophan tryptophylquinone (TTQ) cofactors are dehydrogenases. Kinetic analysis of GoxA revealed allosteric cooperativity for its glycine substrate, but not O2 This is the first CTQ- or TTQ-dependent enzyme to exhibit cooperativity. Here, we show that cooperativity and homodimer stabilization are strongly dependent on the presence of Phe-237. Conversion of this residue, which is a Tyr in LodA, to Tyr or Ala eliminates the cooperativity and destabilizes the dimer. These mutations also significantly affect the kcat and Km values for the substrates. On the basis of structural and modeling studies, a mechanism by which Phe-237 exerts this influence is presented. Two active site residues, Asp-547 and His-466, were also examined and shown by site-directed mutagenesis to be critical for CTQ biogenesis. This result is compared with the results of similar studies of mutagenesis of structurally conserved residues of other tryptophylquinone enzymes. These results provide insight into the roles of specific active-site residues in catalysis and CTQ biogenesis, as well as describing an interesting mechanism by which a single residue can dictate whether or not an enzyme exhibits cooperative allosteric behavior toward a substrate.
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Affiliation(s)
- Esha Sehanobish
- From the Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32827
| | - Heather R Williamson
- From the Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32827
| | - Victor L Davidson
- From the Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32827
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11
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Sehanobish E, Campillo-Brocal JC, Williamson HR, Sanchez-Amat A, Davidson VL. Interaction of GoxA with Its Modifying Enzyme and Its Subunit Assembly Are Dependent on the Extent of Cysteine Tryptophylquinone Biosynthesis. Biochemistry 2016; 55:2305-8. [PMID: 27064961 DOI: 10.1021/acs.biochem.6b00274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GoxA is a glycine oxidase bearing a protein-derived cysteine tryptophylquinone (CTQ) cofactor that is formed by posttranslational modifications catalyzed by a flavoprotein, GoxB. Two forms of GoxA were isolated: an active form with mature CTQ and an inactive precursor protein that lacked CTQ. The active GoxA was present as a homodimer with no detectable affinity for GoxB, whereas the precursor was isolated as a monomer in a tight complex with one GoxB. Thus, the interaction of GoxA with GoxB and subunit assembly of mature GoxA are each dependent on the extent of CTQ biosynthesis.
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Affiliation(s)
- Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | | | - Heather R Williamson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia , Murcia 30100, Spain
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
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12
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Campillo-Brocal JC, Lucas-Elío P, Sanchez-Amat A. Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria. Mar Drugs 2015; 13:7403-18. [PMID: 26694422 PMCID: PMC4699246 DOI: 10.3390/md13127073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022] Open
Abstract
Amino acid oxidases (AAOs) catalyze the oxidative deamination of amino acids releasing ammonium and hydrogen peroxide. Several kinds of these enzymes have been reported. Depending on the amino acid isomer used as a substrate, it is possible to differentiate between l-amino acid oxidases and d-amino acid oxidases. Both use FAD as cofactor and oxidize the amino acid in the alpha position releasing the corresponding keto acid. Recently, a novel class of AAOs has been described that does not contain FAD as cofactor, but a quinone generated by post-translational modification of residues in the same protein. These proteins are named as LodA-like proteins, after the first member of this group described, LodA, a lysine epsilon oxidase synthesized by the marine bacterium Marinomonas mediterranea. In this review, a phylogenetic analysis of all the enzymes described with AAO activity has been performed. It is shown that it is possible to recognize different groups of these enzymes and those containing the quinone cofactor are clearly differentiated. In marine bacteria, particularly in the genus Pseudoalteromonas, most of the proteins described as antimicrobial because of their capacity to generate hydrogen peroxide belong to the group of LodA-like proteins.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
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13
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Matsui D, Asano Y. Heterologous production of l-lysine ε-oxidase by directed evolution using a fusion reporter method. Biosci Biotechnol Biochem 2015; 79:1473-80. [DOI: 10.1080/09168451.2015.1034654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
For the heterologous production of l-lysine ε-oxidase (LodA), we constructed a new plasmid carrying LodA gene fused in-frame with an antibiotic (phleomycine) resistant gene. The new plasmid was randomly mutated and the mutated plasmids were transformed into Escherichia coli BL21 (DE3) harboring lodB, which encodes a protein (LodB) acting in posttranslational modification of LodA, and active mutants were selected by phleomycin resistance and oxidase activities. One soluble LodA variant isolated by this method contained six silent mutations and one missense mutation. At these mutation points, the codon adaptations at Lys92, Ala550, and Thr646, and the amino acid substitution at His286 to Arg contributed to the production of its functional form. The active form of LodA variant was induced by post-modification of LodB in the heterologous coexpression, and the activity increased with additional NaCl and heat treatment. This is the first report of heterologous production of LodA by random mutagenesis.
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Affiliation(s)
- Daisuke Matsui
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan
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14
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Sehanobish E, Chacón-Verdú MD, Sanchez-Amat A, Davidson VL. Roles of active site residues in LodA, a cysteine tryptophylquinone dependent ε-lysine oxidase. Arch Biochem Biophys 2015; 579:26-32. [PMID: 26048732 DOI: 10.1016/j.abb.2015.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/13/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
Site-directed mutagenesis identified residues in the substrate channel of LodA that play multiple roles in regulating Km values of substrates, kcat and the extent of biosynthesis of the protein-derived cysteine tryptophylquinone (CTQ) cofactor. Mutations of Cys448 increase Km values for lysine and O2, with the larger effect on Klysine. Tyr211 resides within a mobile loop and is seen in the crystal structure of LodA to form a hydrogen bond with Lys530 that appears to stabilize its position in the channel. Y211F LodA had reduced levels of CTQ but near normal levels of kcat. K530A and K530R variants exhibited diminished levels of CTQ but significantly increased kcat. The Y211F, K530A and K530R mutations each caused large increases in the Km values for lysine and O2. These effects of the mutations of Tyr211 and Lys530 suggest that when these residues are hydrogen-bonded they may form a gate that controls entry and exit of substrates and products from the active site. Y211A and Y211E variants had the highest level of CTQ but exhibited no activity. These results highlight the different evolutionary factors that must be considered for enzymes which possess protein-derived cofactors, in which the catalytic cofactor must be generated by posttranslational modifications.
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Affiliation(s)
- Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | | | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Murcia 30100, Spain
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States.
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15
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Campillo-Brocal JC, Chacón-Verdú MD, Lucas-Elío P, Sánchez-Amat A. Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity. BMC Genomics 2015; 16:231. [PMID: 25886995 PMCID: PMC4417212 DOI: 10.1186/s12864-015-1455-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/09/2015] [Indexed: 11/16/2022] Open
Abstract
Background L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. The marine bacterium Marinomonas mediterranea synthesizes LodA, the first known LAO that contains a quinone cofactor. LodA is encoded in an operon that contains a second gene coding for LodB, a protein required for the post-translational modification generating the cofactor. Recently, GoxA, a quinoprotein with sequence similarity to LodA but with a different enzymatic activity (glycine oxidase instead of lysine-ε-oxidase) has been described. The aim of this work has been to study the distribution of genes similar to lodA and/or goxA in sequenced microbial genomes and to get insight into the evolution of this novel family of proteins through phylogenetic analysis. Results Genes encoding LodA-like proteins have been detected in several bacterial classes. However, they are absent in Archaea and detected only in a small group of fungi of the class Agaromycetes. The vast majority of the genes detected are in a genome region with a nearby lodB-like gene suggesting a specific interaction between both partner proteins. Sequence alignment of the LodA-like proteins allowed the detection of several conserved residues. All of them showed a Cys and a Trp that aligned with the residues that are forming part of the cysteine tryptophilquinone (CTQ) cofactor in LodA. Phylogenetic analysis revealed that LodA-like proteins can be clustered in different groups. Interestingly, LodA and GoxA are in different groups, indicating that those groups are related to the enzymatic activity of the proteins detected. Conclusions Genome mining has revealed for the first time the broad distribution of LodA-like proteins containing a CTQ cofactor in many different microbial groups. This study provides a platform to explore the potentially novel enzymatic activities of the proteins detected, the mechanisms of post-translational modifications involved in their synthesis, as well as their biological relevance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1455-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - María Dolores Chacón-Verdú
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain.
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Chacón-Verdú MD, Campillo-Brocal JC, Lucas-Elío P, Davidson VL, Sánchez-Amat A. Characterization of recombinant biosynthetic precursors of the cysteine tryptophylquinone cofactors of l-lysine-epsilon-oxidase and glycine oxidase from Marinomonas mediterranea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1123-31. [PMID: 25542375 DOI: 10.1016/j.bbapap.2014.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 01/31/2023]
Abstract
The lysine-ε-oxidase, LodA, and glycine oxidase, GoxA, from Marinomonas mediteranea each possesses a cysteine tryptophylquinone (CTQ) cofactor. This cofactor is derived from posttranslational modifications which are covalent crosslinking of tryptophan and cysteine residues and incorporation of two oxygen atoms into the indole ring of Trp. In this manuscript, it is shown that the recombinant synthesis of LodA and GoxA containing a fully synthesized CTQ cofactor requires coexpression of a partner flavoprotein, LodB for LodA and GoxB for GoxA, which are not interchangeable. An inactive precursor of LodA or GoxA which contained a monohydroxylated Trp residue and no crosslink to the Cys was isolated from the soluble fraction when they were expressed alone. The structure of LodA revealed an Asp residue close to the cofactor which is conserved in quinohemoprotein amine dehydrogenase (QHNDH), containing CTQ, and methylamine dehydrogenase (MADH) containing tryptophan tryptophylquinone (TTQ) as cofactor. To study the role of this residue in the synthesis of the LodA precursor, Asp-512 was mutated to Ala. When the mutant protein was coexpressed with LodB an inactive protein was isolated which was soluble and contained no modifications at all, suggesting a role for this Asp in the initial LodB-independent hydroxylation of Trp. A similar role had been proposed for this conserved Asp residue in MADH. It is noteworthy that the formation of TTQ in MADH from the precursor also requires an accessory enzyme for its biosynthesis but it is a diheme enzyme MauG and not a flavoprotein. The results presented reveal novel mechanisms of post-translational modification involved in the generation of protein-derived cofactors. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- María Dolores Chacón-Verdú
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA.
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain.
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Advances in Detection Methods of l-Amino Acid Oxidase Activity. Appl Biochem Biotechnol 2014; 174:13-27. [DOI: 10.1007/s12010-014-1005-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
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Sehanobish E, Shin S, Sanchez-Amat A, Davidson VL. Steady-state kinetic mechanism of LodA, a novel cysteine tryptophylquinone-dependent oxidase. FEBS Lett 2014; 588:752-6. [PMID: 24462691 DOI: 10.1016/j.febslet.2014.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 11/19/2022]
Abstract
LodA is a novel lysine-ε-oxidase which possesses a cysteine tryptophylquinone cofactor. It is the first tryptophylquinone enzyme known to function as an oxidase. A steady-state kinetic analysis shows that LodA obeys a ping-pong kinetic mechanism with values of kcat of 0.22±0.04 s(-1), Klysine of 3.2±0.5 μM and KO2 of 37.2±6.1 μM. The kcat exhibited a pH optimum at 7.5 while kcat/Klysine peaked at 7.0 and remained constant to pH 8.5. Alternative electron acceptors could not effectively substitute for O2 in the reaction. A mechanism for the reductive half reaction of LodA is proposed that is consistent with the ping-pong kinetics.
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Affiliation(s)
- Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | - Sooim Shin
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia, Murcia 30100, Spain
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, United States.
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